diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 1fc00370..e1fd1cc8 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -27,6 +27,7 @@ jobs: sudo apt-get -o Acquire::Retries=3 update sudo apt-get -o Acquire::Retries=3 install libxcb-xinerama0 sudo apt-get -o Acquire::Retries=3 install libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xfixes0 + sudo apt-get -o Acquire::Retries=3 install libxcb-shape0 sudo apt-get -o Acquire::Retries=3 install libpulse-mainloop-glib0 # sudo apt-get install libgfortran4 # echo "QT_DEBUG_PLUGINS=1" >> $GITHUB_ENV @@ -89,11 +90,7 @@ jobs: run: poetry run python ${{ env.SCRIPTS_PATH }}/FreezeApp.py - name: Create offline and online app installers from freezed app bundle - run: poetry run python ${{ env.SCRIPTS_PATH }}/MakeInstaller.py ${{ secrets.BINARY_SIGN_WIN }} ${{ secrets.CERT_ZIP_PASS }} - - - name: Sign the installer - if: False # temporarily disabled until EC signing is automated - run: poetry run python ${{ env.SCRIPTS_PATH }}/Signatures.py ${{ secrets.BINARY_SIGN_WIN }} ${{ secrets.CERT_ZIP_PASS }} + run: poetry run python ${{ env.SCRIPTS_PATH }}/MakeInstaller.py - name: Set up screen recording dependencies (macOS) if: runner.os == 'macOS' @@ -125,10 +122,22 @@ jobs: run: poetry run python ${{ env.SCRIPTS_PATH }}/RunApp.py --testmode - name: Rename test videos - run: poetry run python ${{ env.SCRIPTS_PATH }}/CreateTestVideos.py ${{ env.BRANCH_NAME }} + run: > + poetry run python ${{ env.SCRIPTS_PATH }}/RenameTestVideos.py + ${{ env.BRANCH_NAME }} + + - name: Sign app installer + if: github.event_name == 'push' && env.BRANCH_NAME == 'master' + run: > + poetry run python ${{ env.SCRIPTS_PATH }}/SignAppInstaller.py + ${{ env.BRANCH_NAME }} + ${{ secrets.MACOS_CERTIFICATE_ENCODED }} ${{ secrets.MACOS_CERTIFICATE_PASSWORD }} + ${{ secrets.APPSTORE_NOTARIZATION_USERNAME }} ${{ secrets.APPSTORE_NOTARIZATION_PASSWORD }} - - name: Create zip archive of offline app installer - run: poetry run python ${{ env.SCRIPTS_PATH }}/ZipArtifacts.py ${{ env.BRANCH_NAME }} + - name: Create zip archive of offline app installer for distribution + run: > + poetry run python ${{ env.SCRIPTS_PATH }}/ZipAppInstaller.py + ${{ env.BRANCH_NAME }} - name: Upload zipped offline app installer to GitHub releases (non-master branch) if: github.event_name == 'push' && env.BRANCH_NAME != 'master' @@ -139,7 +148,7 @@ jobs: allowUpdates: true replacesArtifacts: true token: ${{ secrets.GITHUB_TOKEN }} - artifacts: "${{ env.DISTRIBUTION_PATH }}/${{ env.APP_NAME }}_*.zip,${{ env.DISTRIBUTION_PATH }}/tutorial_*.mp4" + artifacts: "${{ env.DISTRIBUTION_PATH }}/*.zip,${{ env.DISTRIBUTION_PATH }}/*.mp4" tag: ${{ env.BRANCH_NAME }} name: ${{ env.BRANCH_NAME }} bodyFile: "RELEASE.md" @@ -153,11 +162,14 @@ jobs: allowUpdates: true replacesArtifacts: true token: ${{ secrets.GITHUB_TOKEN }} - artifacts: "${{ env.DISTRIBUTION_PATH }}/${{ env.APP_NAME }}_*.zip" + artifacts: "${{ env.DISTRIBUTION_PATH }}/*.zip" tag: ${{ env.RELEASE_TAG }} name: ${{ env.RELEASE_TITLE }} bodyFile: "RELEASE.md" - name: Upload online app installer to repository via FTP if: github.event_name == 'push' - run: poetry run python ${{ env.SCRIPTS_PATH }}/UploadToFtp.py ${{ env.BRANCH_NAME }} ${{ secrets.APP_REPO_FTP_PASSWORD }} + run: > + poetry run python ${{ env.SCRIPTS_PATH }}/UploadToFtp.py + ${{ env.BRANCH_NAME }} + ${{ secrets.APP_REPO_FTP_PASSWORD }} diff --git a/CHANGELOG.md b/CHANGELOG.md index 7e91eacb..92d1b416 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,24 @@ +# Version 0.8.4-beta (28 Jul 2022) + +### New Features + +- Simulating and fitting polarised data using the [CrysPy](https://github.com/ikibalin/cryspy) calculation engine. +- Reading CIF files with experimental data and instrumental parameters. + +### Changes + +- Default example with experimental phase has been modified. +- Added example projects with polarised data. +- Windows installer is now 64-bit. + +### Bug Fixes + +- CrysFML simulation now shows Bragg peaks. +- Inclusion of the space group setting in calculations. +- The `Project save` button is now disabled for read-only example projects. +- The `Reset state` functionality now resets calculator choice. +- Overall performance has been improved. + # Version 0.8.3-beta (27 Jan 2022) ### Features diff --git a/README.md b/README.md index f6bb3e95..717064da 100644 --- a/README.md +++ b/README.md @@ -2,26 +2,26 @@ -**easyDiffraction** is a scientific software for modelling and analysis of diffraction data. Currently, **easyDiffraction** covers classical 1D unpolarized neutron powder diffraction data collected using constant wavelength (CW) or time-of-flight (TOF) diffractometers. +**EasyDiffraction** is a scientific software for modelling and analysis of diffraction data. Currently, **EasyDiffraction** covers classical 1D unpolarized neutron powder diffraction data collected using constant wavelength (CW) or time-of-flight (TOF) diffractometers. ![easyDiffraction Screenshot](./resources/images/ed_analysis_dark.png) -## What is easydiffraction for? +## What is EasyDiffraction for? -**easyDiffraction** allows simulation of diffraction patterns based on a structural model and refinement of its parameters. For refinement, the program uses a number of fitting engines (minimizers) such as [lmfit](https://lmfit.github.io/lmfit-py), [bumps](https://github.com/bumps/bumps) and [DFO-LS](https://github.com/numericalalgorithmsgroup/dfols). +**EasyDiffraction** allows simulation of diffraction patterns based on a structural model and refinement of its parameters. For refinement, the program uses a number of fitting engines (minimizers) such as [lmfit](https://lmfit.github.io/lmfit-py), [bumps](https://github.com/bumps/bumps) and [DFO-LS](https://github.com/numericalalgorithmsgroup/dfols). -**easyDiffraction** is similar to crystallographic programs like FullProf, Jana, GSAS, ShelX, etc. Unlike these programs **easyDiffraction** is based on _external_ crystallographic libraries (calculation engines) such as [CrysPy](https://github.com/ikibalin/cryspy), [CrysFML](https://code.ill.fr/scientific-software/crysfml) and [GSAS-II](https://subversion.xray.aps.anl.gov/trac/pyGSAS). This allows **easyDiffraction** to cover different functionality aspects within a single, intuitive and user-friendly graphical interface. These libraries are included with the installation so there is no need to compile/install them separately. +**EasyDiffraction** is similar to crystallographic programs like FullProf, Jana, GSAS, ShelX, etc. Unlike these programs **EasyDiffraction** is based on _external_ crystallographic libraries (calculation engines) such as [CrysPy](https://github.com/ikibalin/cryspy), [CrysFML](https://code.ill.fr/scientific-software/crysfml) and [GSAS-II](https://subversion.xray.aps.anl.gov/trac/pyGSAS) (experimental). This allows **EasyDiffraction** to cover different functionality aspects within a single, intuitive and user-friendly graphical interface. These libraries are included with the installation so there is no need to compile/install them separately. ## Main features -**easyDiffraction** is an open source project under the [BSD-3-Clause License](LICENSE.md). +**EasyDiffraction** is an open source project under the [BSD-3-Clause License](LICENSE.md). -**easyDiffraction** application is cross-platform, with support for Windows, macOS and Linux (Ubuntu). Its intuitive tabbed interface allows for a clear and defined data modelling and analysis workflow. There are also built-in step-by-step user guides and tutorials for new users. +**EasyDiffraction** application is cross-platform, with support for Windows, macOS and Linux (Ubuntu). Its intuitive tabbed interface allows for a clear and defined data modelling and analysis workflow. There are also built-in step-by-step user guides and tutorials for new users. -Current main features of **easydiffraction**: +Current main features of **Easydiffraction**: - Support for both constant-wavelength and time-of-flight 1D unpolarized neutron powder diffraction data. -- Simulations of diffraction pattern using [CrysPy](https://github.com/ikibalin/cryspy), [CrysFML](https://code.ill.fr/scientific-software/crysfml) and [GSAS-II](https://subversion.xray.aps.anl.gov/trac/pyGSAS) calculation engines. +- Simulations of diffraction pattern using [CrysPy](https://github.com/ikibalin/cryspy), [CrysFML](https://code.ill.fr/scientific-software/crysfml) and [GSAS-II](https://subversion.xray.aps.anl.gov/trac/pyGSAS) (experimental) calculation engines. - Structure refinement (yet unstable) using aforementioned engines. - Multiple minimization engines: [lmfit](https://lmfit.github.io/lmfit-py), [bumps](https://github.com/bumps/bumps) and [DFO-LS](https://github.com/numericalalgorithmsgroup/dfols). - Parameter constraints during refinement. @@ -32,7 +32,7 @@ Current main features of **easydiffraction**: - Interactive HTML and standard PDF report generation. - Undo/redo for both parameter changes and fitting. -Planned improvements / new functionality for **easydiffraction**: +Planned improvements / new functionality for **EasyDiffraction**: - Improved refinement. - Time-of-flight support using [CrysFML](https://code.ill.fr/scientific-software/crysfml) and [GSAS-II](https://subversion.xray.aps.anl.gov/trac/pyGSAS). @@ -49,25 +49,25 @@ Planned improvements / new functionality for **easydiffraction**: ### Downloading -The official **easyDiffraction** installer for Windows, macOS and Linux (Ubuntu) can be found [here](https://github.com/easyScience/easyDiffractionApp/releases): +The official **EasyDiffraction** installer for Windows, macOS and Linux (Ubuntu) can be found [here](https://github.com/easyScience/easyDiffractionApp/releases): ### Installing -Run **easyDiffraction** installer and follow the instructions. +Run **EasyDiffraction** installer and follow the instructions. ### Uninstalling -Run **MaintenanceTool** from the **easydiffraction** installation directory, select _Remove all components_ and follow the instructions. +Run **MaintenanceTool** from the **EasyDiffraction** installation directory, select _Remove all components_ and follow the instructions. ## Common Issues -- On `macOS`, if you see the message _easyDiffractionSetup.app can't be opened because it is from an unidentified developer_, do the following: -In the **Finder**, locate the **easydiffraction** installer application, then _control-click_ the installer icon, then choose _Open_ from the shortcut menu and finally click _Open_. +- On `macOS`, if you see the message _EasyDiffractionSetup.app can't be opened because it is from an unidentified developer_, do the following: +In the **Finder**, locate the **EasyDiffraction** installer application, then _control-click_ the installer icon, then choose _Open_ from the shortcut menu and finally click _Open_. - On `Linux` based system there can be the following error on startup: _Failed to create OpenGL context for format QSurfaceFormat_. This is due to a system OpenGL driver problem. Please re-install your graphics card drivers. ## Contributing -We absolutely welcome contributions. **easyDiffraction** is maintained by the [European Spallation Source ERIC (ESS)](https://europeanspallationsource.se/) and on a volunteer basis and thus we need to foster a community that can support user questions and develop new features to make this software a useful tool for all users while encouraging every member of the community to share their ideas. +We absolutely welcome contributions. **EasyDiffraction** is maintained by the [European Spallation Source ERIC (ESS)](https://europeanspallationsource.se/) and on a volunteer basis and thus we need to foster a community that can support user questions and develop new features to make this software a useful tool for all users while encouraging every member of the community to share their ideas. ## Get in touch diff --git a/RELEASE.md b/RELEASE.md index 416fdb99..2186c5e4 100644 --- a/RELEASE.md +++ b/RELEASE.md @@ -1,3 +1,18 @@ +### New Features + +- Simulating and fitting polarised data using the [CrysPy](https://github.com/ikibalin/cryspy) calculation engine. +- Reading CIF files with experimental data and instrumental parameters. + ### Changes -- The Python-based backend framework has been updated from version 3.7 to 3.8. +- Default example with experimental phase has been modified. +- Added example projects with polarised data. +- Windows installer is now 64-bit. + +### Bug Fixes + +- CrysFML simulation now shows Bragg peaks. +- Inclusion of the space group setting in calculations. +- The `Project save` button is now disabled for read-only example projects. +- The `Reset state` functionality now resets calculator choice. +- Overall performance has been improved. diff --git a/easyDiffractionApp/Gui/Components/AnalysisDataChartBokeh.qml b/easyDiffractionApp/Gui/Components/AnalysisDataChartBokeh.qml index 310f687f..0fd05678 100644 --- a/easyDiffractionApp/Gui/Components/AnalysisDataChartBokeh.qml +++ b/easyDiffractionApp/Gui/Components/AnalysisDataChartBokeh.qml @@ -18,9 +18,12 @@ EaCharts.BaseBokeh { phaseData: ExGlobals.Constants.proxy.plotting1d.bokehPhasesDataObj plotRanges: ExGlobals.Constants.proxy.plotting1d.analysisPlotRangesObj + isSpinPolarized: ExGlobals.Constants.proxy.experiment.isSpinPolarized + setSpinComponent: ExGlobals.Constants.proxy.experiment.setSpinComponent + spinComponent: ExGlobals.Constants.proxy.experiment.spinComponent xAxisTitle: { - if (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCW') { + if ((ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCW') || (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCWpol')) { return "2θ (deg)" } else if (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DTOF') { return "TOF (μs)" diff --git a/easyDiffractionApp/Gui/Components/ApplicationWindow.qml b/easyDiffractionApp/Gui/Components/ApplicationWindow.qml index a66f9437..c977a97d 100644 --- a/easyDiffractionApp/Gui/Components/ApplicationWindow.qml +++ b/easyDiffractionApp/Gui/Components/ApplicationWindow.qml @@ -34,7 +34,8 @@ EaComponents.ApplicationWindow { EaElements.ToolButton { enabled: ExGlobals.Constants.proxy.project.stateHasChanged && - ExGlobals.Constants.proxy.project.currentProjectPath !== '--- EXAMPLE ---' + ExGlobals.Constants.proxy.project.projectCreated && + !ExGlobals.Constants.proxy.project.readOnly highlighted: true fontIcon: "save" ToolTip.text: qsTr("Save current state of the project") diff --git a/easyDiffractionApp/Gui/Components/ExperimentDataChartBokeh.qml b/easyDiffractionApp/Gui/Components/ExperimentDataChartBokeh.qml index 95393b42..ebc22319 100644 --- a/easyDiffractionApp/Gui/Components/ExperimentDataChartBokeh.qml +++ b/easyDiffractionApp/Gui/Components/ExperimentDataChartBokeh.qml @@ -13,8 +13,12 @@ EaCharts.BaseBokeh { plotRanges: ExGlobals.Constants.proxy.plotting1d.experimentPlotRangesObj + isSpinPolarized: ExGlobals.Constants.proxy.experiment.isSpinPolarized + setSpinComponent: ExGlobals.Constants.proxy.experiment.setSpinComponent + spinComponent: ExGlobals.Constants.proxy.experiment.spinComponent + xAxisTitle: { - if (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCW') { + if ((ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCW') || (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCWpol')) { return "2θ (deg)" } else if (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DTOF') { return "TOF (μs)" diff --git a/easyDiffractionApp/Gui/Components/ProjectExamples.qml b/easyDiffractionApp/Gui/Components/ProjectExamples.qml index 8380444f..509be92f 100644 --- a/easyDiffractionApp/Gui/Components/ProjectExamples.qml +++ b/easyDiffractionApp/Gui/Components/ProjectExamples.qml @@ -17,6 +17,7 @@ import Gui.Globals 1.0 as ExGlobals EaComponents.TableView { id: tableView + maxRowCountShow: 9 defaultInfoText: qsTr("No Examples Available") // Table model @@ -57,7 +58,7 @@ EaComponents.TableView { text: model.name } - EaComponents.TableViewLabel { + EaComponents.TableViewLabelControl { id: descriptionColumn width: EaStyle.Sizes.fontPixelSize * 24 @@ -66,6 +67,7 @@ EaComponents.TableView { headerText: "Description" text: model.description + ToolTip.text: model.description } EaComponents.TableViewButton { diff --git a/easyDiffractionApp/Gui/Components/SampleAdps.qml b/easyDiffractionApp/Gui/Components/SampleAdps.qml index c4113f79..ff929db3 100644 --- a/easyDiffractionApp/Gui/Components/SampleAdps.qml +++ b/easyDiffractionApp/Gui/Components/SampleAdps.qml @@ -15,6 +15,17 @@ import easyApp.Gui.Logic 1.0 as EaLogic import Gui.Globals 1.0 as ExGlobals EaComponents.TableView { + property int numColumnWidth: EaStyle.Sizes.fontPixelSize * 2.5 + property int labelColumnWidth: EaStyle.Sizes.fontPixelSize * 2.5 + property int typeColumnWidth: EaStyle.Sizes.fontPixelSize * 4.0 + property int numFixedColumn: 3 + property int numFlexColumn: 7 + property int flexColumnWidth: (width - + numColumnWidth - + labelColumnWidth - + typeColumnWidth - + EaStyle.Sizes.tableColumnSpacing * (numFixedColumn + numFlexColumn - 1)) / + numFlexColumn // Table model @@ -49,22 +60,21 @@ EaComponents.TableView { property string modelAdpType: model.adpType EaComponents.TableViewLabel { - width: EaStyle.Sizes.fontPixelSize * 2.5 + width: numColumnWidth headerText: "No." text: model.index + 1 } EaComponents.TableViewLabel { - id: adpAtomLabel horizontalAlignment: Text.AlignLeft - width: EaStyle.Sizes.fontPixelSize * 3.8 + width: labelColumnWidth headerText: "Label" text: model.label } EaComponents.TableViewComboBox { enabled: false - width: adpAtomLabel.width * 1.2 + width: typeColumnWidth headerText: "Type" model: ["Uiso", "Uani", "Biso", "Bani"] //currentIndex: model.indexOf(modelAdpType) @@ -72,49 +82,49 @@ EaComponents.TableView { } EaComponents.TableViewTextInput { - width: adpAtomLabel.width + width: flexColumnWidth headerText: "Iso" text: EaLogic.Utils.toFixed(model.adpIso) onEditingFinished: editParameterValue(model.adpIsoId, text) } EaComponents.TableViewTextInput { - width: adpAtomLabel.width + width: flexColumnWidth headerText: "Ani11" text: EaLogic.Utils.toFixed(model.adpAni11) onEditingFinished: editParameterValue(model.adpAniId11, text) } EaComponents.TableViewTextInput { - width: adpAtomLabel.width + width: flexColumnWidth headerText: "Ani22" text: EaLogic.Utils.toFixed(model.adpAni22) onEditingFinished: editParameterValue(model.adpAniId22, text) } EaComponents.TableViewTextInput { - width: adpAtomLabel.width + width: flexColumnWidth headerText: "Ani33" text: EaLogic.Utils.toFixed(model.adpAni33) onEditingFinished: editParameterValue(model.adpAniId33, text) } EaComponents.TableViewTextInput { - width: adpAtomLabel.width + width: flexColumnWidth headerText: "Ani12" text: EaLogic.Utils.toFixed(model.adpAni12) onEditingFinished: editParameterValue(model.adpAniId12, text) } EaComponents.TableViewTextInput { - width: adpAtomLabel.width + width: flexColumnWidth headerText: "Ani13" text: EaLogic.Utils.toFixed(model.adpAni13) onEditingFinished: editParameterValue(model.adpAniId13, text) } EaComponents.TableViewTextInput { - width: adpAtomLabel.width + width: flexColumnWidth headerText: "Ani23" text: EaLogic.Utils.toFixed(model.adpAni23) onEditingFinished: editParameterValue(model.adpAniId23, text) diff --git a/easyDiffractionApp/Gui/Components/SampleAtoms.qml b/easyDiffractionApp/Gui/Components/SampleAtoms.qml index 894f8394..785dd3ba 100644 --- a/easyDiffractionApp/Gui/Components/SampleAtoms.qml +++ b/easyDiffractionApp/Gui/Components/SampleAtoms.qml @@ -31,7 +31,6 @@ EaComponents.TableView { XmlRole { name: "label"; query: "label/value/string()" } XmlRole { name: "type"; query: "specie/value/string()" } - //XmlRole { name: "color"; query: "color/string()" } XmlRole { name: "x"; query: "fract_x/value/number()" } XmlRole { name: "y"; query: "fract_y/value/number()" } XmlRole { name: "z"; query: "fract_z/value/number()" } @@ -65,14 +64,6 @@ EaComponents.TableView { onEditingFinished: editDescriptorValue(model.labelId, text) } - /* - EaComponents.TableViewComboBox { - width: atomLabel.width - currentIndex: model.indexOf(modelType) - headerText: "Atom" - model: ["Mn", "Fe", "Co", "Ni", "Cu", "Si", "O"] - } - */ EaComponents.TableViewTextInput { width: atomLabel.width horizontalAlignment: Text.AlignLeft @@ -258,9 +249,19 @@ EaComponents.TableView { 'Ts' : '#000000', 'Og' : '#000000' } + // Simple case, e.g. Co if (colors.hasOwnProperty(symbol)) { return colors[symbol] } + // First 2 symbols, if valency is given for 2 characters element, e.g. Mn3+ + if (colors.hasOwnProperty(symbol.substring(0, 2))) { + return colors[symbol.substring(0, 2)] + } + // First symbol, if valency is given for 1 characters element, e.g. O2- + if (colors.hasOwnProperty(symbol.substring(0, 1))) { + return colors[symbol.substring(0, 1)] + } + // Transparent color if no elements found return 'transparent' } diff --git a/easyDiffractionApp/Gui/Components/SampleMsps.qml b/easyDiffractionApp/Gui/Components/SampleMsps.qml new file mode 100644 index 00000000..2c85e5e5 --- /dev/null +++ b/easyDiffractionApp/Gui/Components/SampleMsps.qml @@ -0,0 +1,149 @@ +// SPDX-FileCopyrightText: 2022 easyDiffraction contributors +// SPDX-License-Identifier: BSD-3-Clause +// © 2021-2022 Contributors to the easyDiffraction project + +import QtQuick 2.13 +import QtQuick.Controls 2.13 +import QtQuick.XmlListModel 2.13 + +import easyApp.Gui.Globals 1.0 as EaGlobals +import easyApp.Gui.Style 1.0 as EaStyle +import easyApp.Gui.Elements 1.0 as EaElements +import easyApp.Gui.Components 1.0 as EaComponents +import easyApp.Gui.Logic 1.0 as EaLogic + +import Gui.Globals 1.0 as ExGlobals + +EaComponents.TableView { + property int numColumnWidth: EaStyle.Sizes.fontPixelSize * 2.5 + property int labelColumnWidth: EaStyle.Sizes.fontPixelSize * 2.5 + property int typeColumnWidth: EaStyle.Sizes.fontPixelSize * 4.5 + property int numFixedColumn: 3 + property int numFlexColumn: 6 + property int flexColumnWidth: (width - + numColumnWidth - + labelColumnWidth - + typeColumnWidth - + EaStyle.Sizes.tableColumnSpacing * (numFixedColumn + numFlexColumn - 1)) / + numFlexColumn + + // Table model + + model: XmlListModel { + property int phaseIndex: ExGlobals.Constants.proxy.phase.currentPhaseIndex + 1 + + xml: ExGlobals.Constants.proxy.phase.phasesAsXml + query: `/root/item[${phaseIndex}]/atoms/data/item` + + XmlRole { name: "label"; query: "label/value/string()" } + XmlRole { name: "mspType"; query: "msp/msp_type/value/string()" } + XmlRole { name: "mspIso"; query: "msp/msp_class/chi/value/number()" } + XmlRole { name: "mspAni11"; query: "msp/msp_class/chi_11/value/number()" } + XmlRole { name: "mspAni22"; query: "msp/msp_class/chi_22/value/number()" } + XmlRole { name: "mspAni33"; query: "msp/msp_class/chi_33/value/number()" } + XmlRole { name: "mspAni12"; query: "msp/msp_class/chi_12/value/number()" } + XmlRole { name: "mspAni13"; query: "msp/msp_class/chi_13/value/number()" } + XmlRole { name: "mspAni23"; query: "msp/msp_class/chi_23/value/number()" } + + XmlRole { name: "mspIsoId"; query: "msp/msp_class/chi/key[4]/string()" } + XmlRole { name: "mspAniId11"; query: "msp/msp_class/chi_11/key[4]/string()" } + XmlRole { name: "mspAniId22"; query: "msp/msp_class/chi_22/key[4]/string()" } + XmlRole { name: "mspAniId33"; query: "msp/msp_class/chi_33/key[4]/string()" } + XmlRole { name: "mspAniId12"; query: "msp/msp_class/chi_12/key[4]/string()" } + XmlRole { name: "mspAniId13"; query: "msp/msp_class/chi_13/key[4]/string()" } + XmlRole { name: "mspAniId23"; query: "msp/msp_class/chi_23/key[4]/string()" } + } + + // Table rows + + delegate: EaComponents.TableViewDelegate { + property string modelMspType: model.mspType + + EaComponents.TableViewLabel { + width: numColumnWidth + headerText: "No." + text: model.index + 1 + } + + EaComponents.TableViewLabel { + horizontalAlignment: Text.AlignLeft + width: labelColumnWidth + headerText: "Label" + text: model.label + } + + EaComponents.TableViewComboBox { + enabled: false + width: typeColumnWidth + headerText: "Type" + model: ["None", "Cani", "Ciso"] + //currentIndex: model.indexOf(modelMspType) + Component.onCompleted: { + currentIndex = model.indexOf(modelMspType) + if (currentIndex === -1) { + currentIndex = 0 + } + } + } + + /* + EaComponents.TableViewTextInput { + width: flexColumnWidth + headerText: "Iso"//"\u03C7Iso" + text: EaLogic.Utils.toFixed(model.mspIso) + onEditingFinished: editParameterValue(model.mspIsoId, text) + } + */ + + EaComponents.TableViewTextInput { + width: flexColumnWidth + headerText: "\u03C711" + text: EaLogic.Utils.toFixed(model.mspAni11) + onEditingFinished: editParameterValue(model.mspAniId11, text) + } + + EaComponents.TableViewTextInput { + width: flexColumnWidth + headerText: "\u03C722" + text: EaLogic.Utils.toFixed(model.mspAni22) + onEditingFinished: editParameterValue(model.mspAniId22, text) + } + + EaComponents.TableViewTextInput { + width: flexColumnWidth + headerText: "\u03C733" + text: EaLogic.Utils.toFixed(model.mspAni33) + onEditingFinished: editParameterValue(model.mspAniId33, text) + } + + EaComponents.TableViewTextInput { + width: flexColumnWidth + headerText: "\u03C712" + text: EaLogic.Utils.toFixed(model.mspAni12) + onEditingFinished: editParameterValue(model.mspAniId12, text) + } + + EaComponents.TableViewTextInput { + width: flexColumnWidth + headerText: "\u03C713" + text: EaLogic.Utils.toFixed(model.mspAni13) + onEditingFinished: editParameterValue(model.mspAniId13, text) + } + + EaComponents.TableViewTextInput { + width: flexColumnWidth + headerText: "\u03C723" + text: EaLogic.Utils.toFixed(model.mspAni23) + onEditingFinished: editParameterValue(model.mspAniId23, text) + } + + } + + // Logic + + function editParameterValue(id, value) { + ExGlobals.Constants.proxy.parameters.editParameter(id, parseFloat(value)) + } + +} + diff --git a/easyDiffractionApp/Gui/Components/SamplePhasesExplorer.qml b/easyDiffractionApp/Gui/Components/SamplePhasesExplorer.qml index fe9e763b..e5552813 100644 --- a/easyDiffractionApp/Gui/Components/SamplePhasesExplorer.qml +++ b/easyDiffractionApp/Gui/Components/SamplePhasesExplorer.qml @@ -49,7 +49,7 @@ EaComponents.TableView { EaComponents.TableViewLabel { headerText: "Color" //backgroundColor: model.color ? model.color : "transparent" - backgroundColor: EaStyle.Colors.chartForegroundsExtra[model.index] + backgroundColor: EaStyle.Colors.chartForegroundsExtra[model.index] ? EaStyle.Colors.chartForegroundsExtra[model.index] : "transparent" } EaComponents.TableViewButton { diff --git a/easyDiffractionApp/Gui/Components/UserGuides.qml b/easyDiffractionApp/Gui/Components/UserGuides.qml index ad15229c..6cc3c0ed 100644 --- a/easyDiffractionApp/Gui/Components/UserGuides.qml +++ b/easyDiffractionApp/Gui/Components/UserGuides.qml @@ -65,9 +65,15 @@ Item { } EaComponents.GuideWindow { + property var loadExampleProjectButton: ExGlobals.Variables.loadExampleProjectButton container: projectPageGuidesContainer - parent: ExGlobals.Variables.loadExampleProjectButton text: qsTr("Or click this button to load one of the examples.") + //parent: ExGlobals.Variables.loadExampleProjectButton // This generates a QML warning because the loadExampleProjectButton is still not defined when this window is created + onLoadExampleProjectButtonChanged: { + if (typeof loadExampleProjectButton !== "undefined") { + parent = loadExampleProjectButton + } + } } EaComponents.GuideWindow { diff --git a/easyDiffractionApp/Gui/Components/UserTutorialsController.qml b/easyDiffractionApp/Gui/Components/UserTutorialsController.qml index bea80798..bbee75b4 100644 --- a/easyDiffractionApp/Gui/Components/UserTutorialsController.qml +++ b/easyDiffractionApp/Gui/Components/UserTutorialsController.qml @@ -246,7 +246,7 @@ EaElements.RemoteController { //rc.keyClick(Qt.Key_Right) //rc.keyClick(Qt.Key_Right) rc.deleteCharacters(6) - rc.typeText("7.00") + rc.typeText("6.00") rc.keyClick(Qt.Key_Enter) // DOESN'T WORK ON CI XVFB ? rc.showPointer() diff --git a/easyDiffractionApp/Gui/Components/qmldir b/easyDiffractionApp/Gui/Components/qmldir index c1a8d2d5..78360d25 100644 --- a/easyDiffractionApp/Gui/Components/qmldir +++ b/easyDiffractionApp/Gui/Components/qmldir @@ -24,6 +24,7 @@ SampleSymmetry 1.0 SampleSymmetry.qml SampleCell 1.0 SampleCell.qml SampleAtoms 1.0 SampleAtoms.qml SampleAdps 1.0 SampleAdps.qml +SampleMsps 1.0 SampleMsps.qml ExperimentDataExplorer 1.0 ExperimentDataExplorer.qml ExperimentAssociatedPhases 1.0 ExperimentAssociatedPhases.qml diff --git a/easyDiffractionApp/Gui/Globals/Constants.qml b/easyDiffractionApp/Gui/Globals/Constants.qml index 57bdcef8..1309b326 100644 --- a/easyDiffractionApp/Gui/Globals/Constants.qml +++ b/easyDiffractionApp/Gui/Globals/Constants.qml @@ -13,9 +13,11 @@ QtObject { readonly property var proxy: typeof _pyQmlProxyObj !== "undefined" && _pyQmlProxyObj !== null ? _pyQmlProxyObj : new ExLogic.PyQmlProxy.PyQmlProxy() readonly property bool remote: typeof EaGlobals.Variables.projectConfig.ci.app.info !== 'undefined' - readonly property string appName: EaGlobals.Variables.projectConfig.release.app_name.toLowerCase() - readonly property string appPrefixName: "easy" + readonly property string appName: EaGlobals.Variables.projectConfig.release.app_name + readonly property string appPrefixName: "Easy" readonly property string appSuffixName: appName.replace(appPrefixName, "") + readonly property string appPrefixNameLogo: appPrefixName.toLowerCase() + readonly property string appSuffixNameLogo: appSuffixName.toLowerCase() readonly property string appLogo: logo('App.svg') readonly property string appUrl: EaGlobals.Variables.projectConfig.tool.poetry.homepage diff --git a/easyDiffractionApp/Gui/Logic/PyQmlProxy.js b/easyDiffractionApp/Gui/Logic/PyQmlProxy.js index 469ed998..860eb580 100644 --- a/easyDiffractionApp/Gui/Logic/PyQmlProxy.js +++ b/easyDiffractionApp/Gui/Logic/PyQmlProxy.js @@ -103,7 +103,7 @@ class Plotting1d { class BackgroundProxy { get asXml() { return "1018315189.3620210.12" } - addPoint() {} + addDefaultPoint() {} removePoint() {} setDefaultPoints() {} } @@ -136,9 +136,9 @@ class PyQmlProxy { get currentPhaseAsExtendedCif() { return "data_PbSO4\n\n_cell_length_a 8.48\n_cell_length_b 5.398\n_cell_length_c 6.958\n_cell_angle_alpha 90.0\n_cell_angle_beta 90.0\n_cell_angle_gamma 90.0\n_space_group_name_H-M_alt 'P n m a'\n\nloop_\n _atom_site_label\n _atom_site_type_symbol\n _atom_site_occupancy\n _atom_site_fract_x\n _atom_site_fract_y\n _atom_site_fract_z\n _atom_site_adp_type\n _atom_site_U_iso_or_equiv\n Pb Pb 1.0 0.1882 0.25 0.167 Uiso 0.01\n S S 1.0 0.063 0.25 0.686 Uiso 0.01\n O1 O 1.0 -0.095 0.25 0.6 Uiso 0.01\n O2 O 1.0 0.181 0.25 0.543 Uiso 0.01\n O3 O 1.0 0.085 0.026 0.806 Uiso 0.01\n\nloop_\n _symmetry_equiv_pos_as_xyz\n x, y, z\n -x+1/2, -y, z+1/2\n x+1/2, -y+1/2, -z+1/2\n -x, y+1/2, -z\n -x, -y, -z\n x-1/2, y, -z-1/2\n -x-1/2, y-1/2, z-1/2\n x, -y-1/2, z\n" } get simulationParametersAsObj() { return {"x_min":0.0,"x_max":180.0,"x_step":0.1} } - get patternParametersAsObj() { return {"@class":"Pattern1D","@id":"235306787479125642831052951811720128629","@module":"easyDiffractionLib.Elements.Experiments.Pattern","@version":"0.0.1","backgrounds":{"@class":"BackgroundContainer","@id":"139473442961863835657737519744271292581","@module":"easyDiffractionLib.Elements.Backgrounds.Background","@version":"0.0.1","data":[{"@class":"PointBackground","@id":"16987436134835037543583378081580455245","@module":"easyDiffractionLib.Elements.Backgrounds.Point","@version":"0.0.1","data":[{"@class":"BackgroundPoint","@id":"48120881597964880327487710994758951847","@module":"easyDiffractionLib.Elements.Backgrounds.Point","@version":"0.0.1","name":"0,0_deg","x":{"@class":"Descriptor","@id":"288090348448534868221730803213038029022","@module":"easyCore.Objects.Base","@version":"0.0.1","description":"","display_name":"x","enabled":true,"name":"x","units":"dimensionless","url":"","value":0},"y":{"@class":"Parameter","@id":"137037127745954677857293726260361766007","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"intensity","units":"dimensionless","value":200}},{"@class":"BackgroundPoint","@id":"19712983927671480265632707115800277823","@module":"easyDiffractionLib.Elements.Backgrounds.Point","@version":"0.0.1","name":"140,0_deg","x":{"@class":"Descriptor","@id":"190452147068224568495345721159542846071","@module":"easyCore.Objects.Base","@version":"0.0.1","description":"","display_name":"x","enabled":true,"name":"x","units":"dimensionless","url":"","value":140},"y":{"@class":"Parameter","@id":"9848774947907778112153717389371819117","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"intensity","units":"dimensionless","value":200}}],"linked_experiment":"NEED_TO_CHANGE"}]},"scale":{"@class":"Parameter","@id":"257586745724955043863419443187177591221","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"scale","units":"dimensionless","value":1},"zero_shift":{"@class":"Parameter","@id":"18356802038126633443019469022087609013","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"zero_shift","units":"degree","value":0}} } - get instrumentParametersAsObj() { return {"@class":"Pars1D","@id":"231637247225317532808673822399324226265","@module":"easyDiffractionLib.Elements.Experiments.Experiment","@version":"0.0.1","resolution_u":{"@class":"Parameter","@id":"216416169571596710924454185657227957884","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"resolution_u","units":"dimensionless","value":0.14},"resolution_v":{"@class":"Parameter","@id":"229518756686753763681436602723598562742","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"resolution_v","units":"dimensionless","value":-0.42},"resolution_w":{"@class":"Parameter","@id":"145771429849507483099716492453028221196","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"resolution_w","units":"dimensionless","value":0.38},"resolution_x":{"@class":"Parameter","@id":"306405939773089505104389768906946166134","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"resolution_x","units":"dimensionless","value":0},"resolution_y":{"@class":"Parameter","@id":"269181530393529631791687470824092236788","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"resolution_y","units":"dimensionless","value":0},"wavelength":{"@class":"Parameter","@id":"254770323993335101529924844209104083188","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"wavelength","units":"angstrom","value":1.912}} } - get instrumentParametersAsXml() { return 'easyDiffractionLib.Elements.Experiments.InstrumentPars1D0.0.1easyCore.Objects.BaseParameter0.0.1u_resolution0.40.0-infinfTruedimensionless312322313537709477997004899613590636884TrueeasyCore.Objects.BaseParameter0.0.1v_resolution-0.50.0-infinfTruedimensionless220595112252802717438017278456713837342TrueeasyCore.Objects.BaseParameter0.0.1w_resolution0.90.0-infinfTruedimensionless309956937743928332407241175311265873557TrueeasyCore.Objects.BaseParameter0.0.1x_resolution0.00.0-infinfTruedimensionless234578176552449284759584024822421612517TrueeasyCore.Objects.BaseParameter0.0.1wavelength1.540560.0-infinfTrueangstrom169780687797892758527734945250252699192True227239201627625589021374889924472937495' } + get patternParametersAsObj() { return {"@class":"Pattern1D","@id":"235306787479125642831052951811720128629","@module":"easyDiffractionLib.elements.Experiments.Pattern","@version":"0.0.1","backgrounds":{"@class":"BackgroundContainer","@id":"139473442961863835657737519744271292581","@module":"easyDiffractionLib.elements.Backgrounds.Background","@version":"0.0.1","data":[{"@class":"PointBackground","@id":"16987436134835037543583378081580455245","@module":"easyDiffractionLib.elements.Backgrounds.Point","@version":"0.0.1","data":[{"@class":"BackgroundPoint","@id":"48120881597964880327487710994758951847","@module":"easyDiffractionLib.elements.Backgrounds.Point","@version":"0.0.1","name":"0,0_deg","x":{"@class":"Descriptor","@id":"288090348448534868221730803213038029022","@module":"easyCore.Objects.Base","@version":"0.0.1","description":"","display_name":"x","enabled":true,"name":"x","units":"dimensionless","url":"","value":0},"y":{"@class":"Parameter","@id":"137037127745954677857293726260361766007","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"intensity","units":"dimensionless","value":200}},{"@class":"BackgroundPoint","@id":"19712983927671480265632707115800277823","@module":"easyDiffractionLib.elements.Backgrounds.Point","@version":"0.0.1","name":"140,0_deg","x":{"@class":"Descriptor","@id":"190452147068224568495345721159542846071","@module":"easyCore.Objects.Base","@version":"0.0.1","description":"","display_name":"x","enabled":true,"name":"x","units":"dimensionless","url":"","value":140},"y":{"@class":"Parameter","@id":"9848774947907778112153717389371819117","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"intensity","units":"dimensionless","value":200}}],"linked_experiment":"NEED_TO_CHANGE"}]},"scale":{"@class":"Parameter","@id":"257586745724955043863419443187177591221","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"scale","units":"dimensionless","value":1},"zero_shift":{"@class":"Parameter","@id":"18356802038126633443019469022087609013","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"zero_shift","units":"degree","value":0}} } + get instrumentParametersAsObj() { return {"@class":"Pars1D","@id":"231637247225317532808673822399324226265","@module":"easyDiffractionLib.elements.Experiments.Experiment","@version":"0.0.1","resolution_u":{"@class":"Parameter","@id":"216416169571596710924454185657227957884","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"resolution_u","units":"dimensionless","value":0.14},"resolution_v":{"@class":"Parameter","@id":"229518756686753763681436602723598562742","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"resolution_v","units":"dimensionless","value":-0.42},"resolution_w":{"@class":"Parameter","@id":"145771429849507483099716492453028221196","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"resolution_w","units":"dimensionless","value":0.38},"resolution_x":{"@class":"Parameter","@id":"306405939773089505104389768906946166134","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"resolution_x","units":"dimensionless","value":0},"resolution_y":{"@class":"Parameter","@id":"269181530393529631791687470824092236788","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"resolution_y","units":"dimensionless","value":0},"wavelength":{"@class":"Parameter","@id":"254770323993335101529924844209104083188","@module":"easyCore.Objects.Base","@version":"0.0.1","enabled":true,"error":"","fixed":true,"max":null,"min":null,"name":"wavelength","units":"angstrom","value":1.912}} } + get instrumentParametersAsXml() { return 'easyDiffractionLib.elements.Experiments.InstrumentPars1D0.0.1easyCore.Objects.BaseParameter0.0.1u_resolution0.40.0-infinfTruedimensionless312322313537709477997004899613590636884TrueeasyCore.Objects.BaseParameter0.0.1v_resolution-0.50.0-infinfTruedimensionless220595112252802717438017278456713837342TrueeasyCore.Objects.BaseParameter0.0.1w_resolution0.90.0-infinfTruedimensionless309956937743928332407241175311265873557TrueeasyCore.Objects.BaseParameter0.0.1x_resolution0.00.0-infinfTruedimensionless234578176552449284759584024822421612517TrueeasyCore.Objects.BaseParameter0.0.1wavelength1.540560.0-infinfTrueangstrom169780687797892758527734945250252699192True227239201627625589021374889924472937495' } get experimentDataAsObj() { return [{"name": "D1A@ILL"}]} get experimentDataAsXml() { return 'D1A@ILL'} diff --git a/easyDiffractionApp/Gui/Pages/Analysis/SideBarAdvanced.qml b/easyDiffractionApp/Gui/Pages/Analysis/SideBarAdvanced.qml index a28b37ec..494fabf0 100644 --- a/easyDiffractionApp/Gui/Pages/Analysis/SideBarAdvanced.qml +++ b/easyDiffractionApp/Gui/Pages/Analysis/SideBarAdvanced.qml @@ -133,7 +133,7 @@ EaComponents.SideBarColumn { EaElements.GroupBox { title: qsTr("Fitting constraints") enabled: ExGlobals.Constants.proxy.experiment.experimentLoaded - last: true + last: !ExGlobals.Constants.proxy.experiment.isSpinPolarized ExComponents.AnalysisConstraints {} @@ -330,4 +330,20 @@ EaComponents.SideBarColumn { } } + + EaElements.GroupBox { + title: qsTr("Fitting componenets") + last: true + visible: ExGlobals.Constants.proxy.experiment.isSpinPolarized + enabled: ExGlobals.Constants.proxy.experiment.experimentLoaded || + ExGlobals.Constants.proxy.experiment.experimentSkipped + + Loader { + source: { + return 'SideBarGroups/Refinement.qml' + } + } + + Component.onCompleted: ExGlobals.Variables.associatedPhasesGroup = this + } } diff --git a/easyDiffractionApp/Gui/Pages/Analysis/SideBarBasic.qml b/easyDiffractionApp/Gui/Pages/Analysis/SideBarBasic.qml index 188d4e69..5634a28c 100644 --- a/easyDiffractionApp/Gui/Pages/Analysis/SideBarBasic.qml +++ b/easyDiffractionApp/Gui/Pages/Analysis/SideBarBasic.qml @@ -78,6 +78,7 @@ EaComponents.SideBarColumn { { value: ".atoms.", text: formatFilterText("gem", "atom", "Atoms") }, { value: ".fract_", text: formatFilterText("gem", "map-marker-alt", "Coordinates") }, { value: ".adp.", text: formatFilterText("gem", "arrows-alt", "ADPs") }, + { value: ".msp.", text: formatFilterText("gem", "arrows-alt", "MSPs") }, { value: ".resolution_", text: formatFilterText("microscope", "grip-lines-vertical", "Resolution") }, //"delicious"//"grip-lines"//"flipboard" { value: ".background.", text: formatFilterText("microscope", "wave-square", "Background") } //"water" ] diff --git a/easyDiffractionApp/Gui/Pages/Analysis/SideBarGroups/Refinement.qml b/easyDiffractionApp/Gui/Pages/Analysis/SideBarGroups/Refinement.qml new file mode 100644 index 00000000..57e9f85e --- /dev/null +++ b/easyDiffractionApp/Gui/Pages/Analysis/SideBarGroups/Refinement.qml @@ -0,0 +1,56 @@ +// SPDX-FileCopyrightText: 2022 easyDiffraction contributors +// SPDX-License-Identifier: BSD-3-Clause +// © 2021-2022 Contributors to the easyDiffraction project + +import QtQuick 2.13 +import QtQuick.Controls 2.13 + +import easyApp.Gui.Style 1.0 as EaStyle +import easyApp.Gui.Elements 1.0 as EaElements +import easyApp.Gui.Logic 1.0 as EaLogic + +import Gui.Globals 1.0 as ExGlobals + +Row { + spacing: 2 * EaStyle.Sizes.fontPixelSize + + EaElements.CheckBox { + topPadding: 0 + + text: "\u2191 + \u2193" + ToolTip.text: qsTr("Sum: spin-up \uff0b spin-down component") + + checked: ExGlobals.Constants.proxy.experiment.refineSum + onCheckedChanged: ExGlobals.Constants.proxy.experiment.refineSum = checked + } + + EaElements.CheckBox { + topPadding: 0 + + text: "\u2191 \u2212 \u2193" + ToolTip.text: qsTr("Difference: spin-up \uff0d spin-down component") + + checked: ExGlobals.Constants.proxy.experiment.refineDiff + onCheckedChanged: ExGlobals.Constants.proxy.experiment.refineDiff = checked + } + + EaElements.CheckBox { + topPadding: 0 + + text: "\u2191" + ToolTip.text: qsTr("Spin-up component") + + checked: ExGlobals.Constants.proxy.experiment.refineUp + onCheckedChanged: ExGlobals.Constants.proxy.experiment.refineUp = checked + } + + EaElements.CheckBox { + topPadding: 0 + + text: "\u2193" + ToolTip.text: qsTr("Spin-down component") + + checked: ExGlobals.Constants.proxy.experiment.refineDown + onCheckedChanged: ExGlobals.Constants.proxy.experiment.refineDown = checked + } +} diff --git a/easyDiffractionApp/Gui/Pages/Analysis/SideBarGroups/qmldir b/easyDiffractionApp/Gui/Pages/Analysis/SideBarGroups/qmldir new file mode 100644 index 00000000..d78a5787 --- /dev/null +++ b/easyDiffractionApp/Gui/Pages/Analysis/SideBarGroups/qmldir @@ -0,0 +1,3 @@ +module SideBarGroups + +Refinement 1.0 Refinement.qml diff --git a/easyDiffractionApp/Gui/Pages/Experiment/SideBarBasic.qml b/easyDiffractionApp/Gui/Pages/Experiment/SideBarBasic.qml index 65af2945..18bf1588 100644 --- a/easyDiffractionApp/Gui/Pages/Experiment/SideBarBasic.qml +++ b/easyDiffractionApp/Gui/Pages/Experiment/SideBarBasic.qml @@ -54,7 +54,7 @@ EaComponents.SideBarColumn { } EaElements.GroupBox { - title: qsTr("Instrument and experiment type") + title: qsTr("Experiment type") // qsTr("Instrument and experiment type") enabled: ExGlobals.Constants.proxy.experiment.experimentLoaded || ExGlobals.Constants.proxy.experiment.experimentSkipped @@ -116,7 +116,7 @@ EaComponents.SideBarColumn { EaElements.ComboBox { enabled: !ExGlobals.Constants.proxy.experiment.experimentLoaded - width: (EaStyle.Sizes.sideBarContentWidth - EaStyle.Sizes.fontPixelSize * 2 ) / 3 + width: (EaStyle.Sizes.sideBarContentWidth - EaStyle.Sizes.fontPixelSize) / 2 model: ["Neutron"] } } @@ -131,7 +131,7 @@ EaComponents.SideBarColumn { property string experimentType: ExGlobals.Constants.proxy.sample.experimentType enabled: !ExGlobals.Constants.proxy.experiment.experimentLoaded - width: (EaStyle.Sizes.sideBarContentWidth - EaStyle.Sizes.fontPixelSize * 2 ) / 3 + width: (EaStyle.Sizes.sideBarContentWidth - EaStyle.Sizes.fontPixelSize) / 2 textRole: "text" valueRole: "value" @@ -154,6 +154,11 @@ EaComponents.SideBarColumn { } } } + } + + Row { + visible: true + spacing: EaStyle.Sizes.fontPixelSize Column { EaElements.Label { @@ -163,10 +168,43 @@ EaComponents.SideBarColumn { EaElements.ComboBox { enabled: !ExGlobals.Constants.proxy.experiment.experimentLoaded - width: (EaStyle.Sizes.sideBarContentWidth - EaStyle.Sizes.fontPixelSize * 2 ) / 3 + width: (EaStyle.Sizes.sideBarContentWidth - EaStyle.Sizes.fontPixelSize) / 2 model: ["Powder"] } } + + Column { + EaElements.Label { + enabled: false + text: qsTr("Polarization") + } + + EaElements.ComboBox { + property bool experimentType: ExGlobals.Constants.proxy.experiment.isSpinPolarized + enabled: !ExGlobals.Constants.proxy.experiment.experimentLoaded + width: (EaStyle.Sizes.sideBarContentWidth - EaStyle.Sizes.fontPixelSize) / 2 + + textRole: "text" + valueRole: "value" + + model: [ + { value: false, text: qsTr("Unpolarized") }, + { value: true, text: qsTr("Polarized") } + ] + + onExperimentTypeChanged: { + if (experimentType === false) { + currentIndex = 0 + } else if (experimentType === true) { + currentIndex = 1 + } + } + + onActivated: { + ExGlobals.Constants.proxy.experiment.setSpinPolarization(currentValue) + } + } + } } } } @@ -181,7 +219,7 @@ EaComponents.SideBarColumn { Loader { source: { - if (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCW') { + if ((ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCW') || (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCWpol')) { return 'SideBarGroups/RangesPdCw1d.qml' } else if (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DTOF') { return 'SideBarGroups/RangesPdTof1d.qml' @@ -197,7 +235,7 @@ EaComponents.SideBarColumn { Loader { source: { - if (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCW') { + if ((ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCW') || (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCWpol')) { return 'SideBarGroups/InstrumentSetupPdCw1d.qml' } else if (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DTOF') { return 'SideBarGroups/InstrumentSetupPdTof1d.qml' @@ -206,6 +244,19 @@ EaComponents.SideBarColumn { } } + EaElements.GroupBox { + title: qsTr("Diffraction radiation") + visible: ExGlobals.Constants.proxy.experiment.isSpinPolarized + enabled: ExGlobals.Constants.proxy.experiment.experimentLoaded || + ExGlobals.Constants.proxy.experiment.experimentSkipped + + Loader { + source: { + return 'SideBarGroups/DiffractionRadiation.qml' + } + } + } + EaElements.GroupBox { title: qsTr("Peak profile") enabled: ExGlobals.Constants.proxy.experiment.experimentLoaded || @@ -213,7 +264,7 @@ EaComponents.SideBarColumn { Loader { source: { - if (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCW') { + if ((ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCW') || (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCWpol')) { return 'SideBarGroups/PeakProfilePdCw1d.qml' } else if (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DTOF') { return 'SideBarGroups/PeakProfilePdTof1d.qml' @@ -229,7 +280,7 @@ EaComponents.SideBarColumn { Loader { source: { - if (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCW') { + if ((ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCW') || (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DCWpol')) { return 'SideBarGroups/BackgroundPdCw1d.qml' } else if (ExGlobals.Constants.proxy.sample.experimentType === 'powder1DTOF') { return 'SideBarGroups/BackgroundPdTof1d.qml' @@ -251,12 +302,12 @@ EaComponents.SideBarColumn { // Load experimental data file dialog - Dialogs1.FileDialog{ + Dialogs1.FileDialog { id: loadExperimentDataFileDialog - nameFilters: [ qsTr("Data files") + " (*.xye *.xys *.xy)" ] + nameFilters: [ qsTr("CIF files (*.cif)"), qsTr("Data files (*.xye *.xys *.xy)") ] - onAccepted: ExGlobals.Constants.proxy.experiment.addExperimentDataFromXye(fileUrl) + onAccepted: ExGlobals.Constants.proxy.experiment.addExperimentData(fileUrl) } // Logic diff --git a/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/BackgroundPdCw1d.qml b/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/BackgroundPdCw1d.qml index 21ad0edd..a8ca55e7 100644 --- a/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/BackgroundPdCw1d.qml +++ b/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/BackgroundPdCw1d.qml @@ -103,7 +103,7 @@ Column { EaElements.SideBarButton { fontIcon: "plus-circle" text: qsTr("Append new point") - onClicked: ExGlobals.Constants.proxy.background.addPoint() + onClicked: ExGlobals.Constants.proxy.background.addDefaultPoint() } EaElements.SideBarButton { diff --git a/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/BackgroundPdTof1d.qml b/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/BackgroundPdTof1d.qml index 3134ae4c..ce22584a 100644 --- a/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/BackgroundPdTof1d.qml +++ b/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/BackgroundPdTof1d.qml @@ -103,7 +103,7 @@ Column { EaElements.SideBarButton { fontIcon: "plus-circle" text: qsTr("Append new point") - onClicked: ExGlobals.Constants.proxy.background.addPoint() + onClicked: ExGlobals.Constants.proxy.background.addDefaultPoint() } EaElements.SideBarButton { diff --git a/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/DiffractionRadiation.qml b/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/DiffractionRadiation.qml new file mode 100644 index 00000000..63688ef7 --- /dev/null +++ b/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/DiffractionRadiation.qml @@ -0,0 +1,69 @@ +// SPDX-FileCopyrightText: 2022 easyDiffraction contributors +// SPDX-License-Identifier: BSD-3-Clause +// © 2021-2022 Contributors to the easyDiffraction project + +import QtQuick 2.13 +import QtQuick.Controls 2.13 + +import easyApp.Gui.Style 1.0 as EaStyle +import easyApp.Gui.Elements 1.0 as EaElements +import easyApp.Gui.Logic 1.0 as EaLogic + +import Gui.Globals 1.0 as ExGlobals + + +Grid { + columns: 2 + columnSpacing: EaStyle.Sizes.fontPixelSize + + Column { + EaElements.Label { + enabled: false + text: qsTr("Polarization") + } + + EaElements.Parameter { + width: inputFieldWidth() + units: "%" + text: (ExGlobals.Constants.proxy.experiment.isSpinPolarized ? + EaLogic.Utils.toFixed(ExGlobals.Constants.proxy.parameters.patternParametersAsObj.beam.polarization.value * 100.0) : + qsTr("")) + onEditingFinished:{ + var value = Number(text)/100.0; + var value_string = value.toString(); + editParameterValue(ExGlobals.Constants.proxy.parameters.patternParametersAsObj.beam.polarization["@id"], value_string) + } + + } + } + + Column { + EaElements.Label { + enabled: false + text: qsTr("Polarizing efficiency") + } + + EaElements.Parameter { + width: inputFieldWidth() + units: "%" + text: (ExGlobals.Constants.proxy.experiment.isSpinPolarized ? + EaLogic.Utils.toFixed(ExGlobals.Constants.proxy.parameters.patternParametersAsObj.beam.efficiency.value * 100.0) : + qsTr("")) + onEditingFinished: { + var value = Number(text)/100.0; + var value_string = value.toString(); + editParameterValue(ExGlobals.Constants.proxy.parameters.patternParametersAsObj.beam.efficiency["@id"], value_string) + } + } + } + + // Logic + + function inputFieldWidth() { + return (EaStyle.Sizes.sideBarContentWidth - columnSpacing * (columns - 1)) / columns + } + + function editParameterValue(id, value) { + ExGlobals.Constants.proxy.parameters.editParameter(id, parseFloat(value)) + } +} diff --git a/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/InstrumentSetupPdCw1d.qml b/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/InstrumentSetupPdCw1d.qml index 1c45a51c..5d105493 100644 --- a/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/InstrumentSetupPdCw1d.qml +++ b/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/InstrumentSetupPdCw1d.qml @@ -13,7 +13,7 @@ import Gui.Globals 1.0 as ExGlobals Grid { - columns: 2 + columns: ExGlobals.Constants.proxy.experiment.isSpinPolarized ? 3 : 2 columnSpacing: EaStyle.Sizes.fontPixelSize Column { @@ -44,6 +44,22 @@ Grid { } } + Column { + visible: ExGlobals.Constants.proxy.experiment.isSpinPolarized + + EaElements.Label { + enabled: false + text: qsTr("Magnetic field") + } + + EaElements.Parameter { + width: inputFieldWidth() + units: "T" + text: EaLogic.Utils.toFixed(ExGlobals.Constants.proxy.parameters.patternParametersAsObj.field.value) + onEditingFinished: editParameterValue(ExGlobals.Constants.proxy.parameters.patternParametersAsObj.field["@id"], text) + } + } + // Logic function inputFieldWidth() { diff --git a/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/qmldir b/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/qmldir index a11aa4cd..e724307e 100644 --- a/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/qmldir +++ b/easyDiffractionApp/Gui/Pages/Experiment/SideBarGroups/qmldir @@ -9,3 +9,5 @@ RangesPdTof1d 1.0 RangesPdTof1d.qml InstrumentSetupPdTof1d 1.0 InstrumentSetupPdTof1d.qml PeakProfilePdTof1d 1.0 PeakProfilePdTof1d.qml BackgroundPdTof1d 1.0 BackgroundPdTof1d.qml + +DiffractionRadiation 1.0 DiffractionRadiation.qml diff --git a/easyDiffractionApp/Gui/Pages/Home/AboutDialog.qml b/easyDiffractionApp/Gui/Pages/Home/AboutDialog.qml index 95ea9ec7..93ffeb32 100644 --- a/easyDiffractionApp/Gui/Pages/Home/AboutDialog.qml +++ b/easyDiffractionApp/Gui/Pages/Home/AboutDialog.qml @@ -16,8 +16,8 @@ EaComponents.AboutDialog { appIconPath: ExGlobals.Constants.appLogo appUrl: ExGlobals.Constants.appUrl - appPrefixName: ExGlobals.Constants.appPrefixName - appSuffixName: ExGlobals.Constants.appSuffixName + appPrefixName: ExGlobals.Constants.appPrefixNameLogo + appSuffixName: ExGlobals.Constants.appSuffixNameLogo appVersion: ExGlobals.Constants.appVersion appDate: ExGlobals.Constants.appDate diff --git a/easyDiffractionApp/Gui/Pages/Home/MainContent.qml b/easyDiffractionApp/Gui/Pages/Home/MainContent.qml index 5bb12d3d..8857c16b 100644 --- a/easyDiffractionApp/Gui/Pages/Home/MainContent.qml +++ b/easyDiffractionApp/Gui/Pages/Home/MainContent.qml @@ -49,13 +49,13 @@ Item { font.family: parent.fontFamily font.pixelSize: parent.fontPixelSize font.weight: Font.Light - text: ExGlobals.Constants.appPrefixName + text: ExGlobals.Constants.appPrefixNameLogo } EaElements.Label { font.family: parent.fontFamily font.pixelSize: parent.fontPixelSize font.weight: Font.DemiBold - text: ExGlobals.Constants.appSuffixName + text: ExGlobals.Constants.appSuffixNameLogo } } diff --git a/easyDiffractionApp/Gui/Pages/Project/MainContentDescription.qml b/easyDiffractionApp/Gui/Pages/Project/MainContentDescription.qml index 4210c397..ae670190 100644 --- a/easyDiffractionApp/Gui/Pages/Project/MainContentDescription.qml +++ b/easyDiffractionApp/Gui/Pages/Project/MainContentDescription.qml @@ -47,12 +47,14 @@ Rectangle { } EaElements.Label { - visible: ExGlobals.Constants.proxy.project.currentProjectPath !== '--- EXAMPLE ---' + visible: ExGlobals.Constants.proxy.project.projectCreated && + !ExGlobals.Constants.proxy.project.readOnly font.bold: true text: qsTr("Location:") } EaElements.Label { - visible: ExGlobals.Constants.proxy.project.currentProjectPath !== '--- EXAMPLE ---' + visible: ExGlobals.Constants.proxy.project.projectCreated && + !ExGlobals.Constants.proxy.project.readOnly text: ExGlobals.Constants.proxy.project.currentProjectPath } diff --git a/easyDiffractionApp/Gui/Pages/Sample/SideBarBasic.qml b/easyDiffractionApp/Gui/Pages/Sample/SideBarBasic.qml index abce7748..c6372349 100644 --- a/easyDiffractionApp/Gui/Pages/Sample/SideBarBasic.qml +++ b/easyDiffractionApp/Gui/Pages/Sample/SideBarBasic.qml @@ -98,14 +98,19 @@ EaComponents.SideBarColumn { EaElements.GroupBox { title: qsTr("Atomic displacement parameters") - last: true enabled: ExGlobals.Constants.proxy.phase.samplesPresent - ExComponents.SampleAdps {} - Component.onCompleted: ExGlobals.Variables.adpsGroup = this } + EaElements.GroupBox { + title: qsTr("Magnetic susceptibility parameters") + last: true + enabled: ExGlobals.Constants.proxy.phase.samplesPresent && + (ExGlobals.Constants.proxy.experiment.isSpinPolarized || ExGlobals.Constants.proxy.phase.hasMsp) + ExComponents.SampleMsps{} + } + // Open phase CIF file dialog Dialogs1.FileDialog{ diff --git a/easyDiffractionApp/Gui/Pages/Summary/MainContentReport.qml b/easyDiffractionApp/Gui/Pages/Summary/MainContentReport.qml index 6cdcccf8..39f2c31b 100644 --- a/easyDiffractionApp/Gui/Pages/Summary/MainContentReport.qml +++ b/easyDiffractionApp/Gui/Pages/Summary/MainContentReport.qml @@ -386,7 +386,7 @@ Item { hasMeasured: ExGlobals.Variables.analysisChart.hasMeasuredData, hasCalculated: ExGlobals.Variables.analysisChart.hasCalculatedData, - hasPhase: ExGlobals.Constants.proxy.plotting1d.hasSinglePhaseData, + hasPhase: typeof ExGlobals.Constants.proxy.plotting1d.hasSinglePhaseData !== "undefined" ? ExGlobals.Constants.proxy.plotting1d.hasSinglePhaseData : false, hasDifference: ExGlobals.Variables.analysisChart.hasDifferenceData, hasBragg: ExGlobals.Variables.analysisChart.hasBraggData, hasBackground: ExGlobals.Variables.analysisChart.hasBackgroundData, @@ -525,13 +525,16 @@ Item { property string fittingInfo: { if (!isFitting) return '' - const redchi2 = ExGlobals.Constants.proxy.fitResults.redchi2.toFixed(2) - let list = [ - '

', - `Goodness-of-fit (reduced \u03c7\u00b2): ${redchi2}
`, - '

' - ] - return list.join('\n') + if (typeof ExGlobals.Constants.proxy.fitResults !== 'undefined') { + const redchi2 = ExGlobals.Constants.proxy.fitResults.redchi2.toFixed(2) + let list = [ + '

', + `Goodness-of-fit (reduced \u03c7\u00b2): ${redchi2}
`, + '

' + ] + return list.join('\n') + } + return '' } property string analysisSection: { diff --git a/easyDiffractionApp/Gui/Pages/Summary/SideBarBasic.qml b/easyDiffractionApp/Gui/Pages/Summary/SideBarBasic.qml index cb8ffa49..8f654edd 100644 --- a/easyDiffractionApp/Gui/Pages/Summary/SideBarBasic.qml +++ b/easyDiffractionApp/Gui/Pages/Summary/SideBarBasic.qml @@ -20,7 +20,8 @@ EaComponents.SideBarColumn { EaElements.GroupBox { title: qsTr("Export report") - enabled: ExGlobals.Constants.proxy.project.currentProjectPath !== '--- EXAMPLE ---' && ExGlobals.Constants.proxy.project.projectCreated + enabled: ExGlobals.Constants.proxy.project.projectCreated && + !ExGlobals.Constants.proxy.project.readOnly collapsible: false last: true @@ -97,7 +98,7 @@ EaComponents.SideBarColumn { horizontalAlignment: TextInput.AlignLeft placeholderText: qsTr("Enter report location here") - text: ExGlobals.Constants.proxy.project.currentProjectPath !== '--- EXAMPLE ---' && ExGlobals.Constants.proxy.project.projectCreated ? + text: ExGlobals.Constants.proxy.project.projectCreated ? EaLogic.Utils.urlToLocalFile(reportParentDirDialog.folder + '/' + reportNameField.text + '.' + reportFormatField.currentValue) : '' diff --git a/examples/PdTof1d/CeCuAl/experiments/data.xye b/easyDiffractionApp/Gui/Resources/Examples/CeCuAl3/experiments/data.xye similarity index 100% rename from examples/PdTof1d/CeCuAl/experiments/data.xye rename to easyDiffractionApp/Gui/Resources/Examples/CeCuAl3/experiments/data.xye diff --git a/easyDiffractionApp/Gui/Resources/Examples/CeCuAl3/project.cif b/easyDiffractionApp/Gui/Resources/Examples/CeCuAl3/project.cif index 33e56369..7c662197 100644 --- a/easyDiffractionApp/Gui/Resources/Examples/CeCuAl3/project.cif +++ b/easyDiffractionApp/Gui/Resources/Examples/CeCuAl3/project.cif @@ -1,5 +1,5 @@ _name CeCuAl3 -_short_description 'neutrons, powder, time-of-flight, 1D' -_samples 'CeCuAl3' -_experiments 'Polaris@ISIS' -_modified '25.08.2021 11:00' +_short_description 'neutrons, powder, time-of-flight, Polaris@ISIS' +_samples CeCuAl3 +_experiments Polaris@ISIS +_modified '01.06.2022 17:37' \ No newline at end of file diff --git a/easyDiffractionApp/Gui/Resources/Examples/CeCuAl3/project.json b/easyDiffractionApp/Gui/Resources/Examples/CeCuAl3/project.json index 963f52ed..acce3411 100644 --- a/easyDiffractionApp/Gui/Resources/Examples/CeCuAl3/project.json +++ b/easyDiffractionApp/Gui/Resources/Examples/CeCuAl3/project.json @@ -4,24 +4,24 @@ "@class": "Sample", "@version": "0.0.1", "phases": { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phases", - "@version": "0.1.0", + "@version": "0.0.1", "name": "Phases", "data": [ { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phase", - "@version": "0.1.0", + "@version": "0.0.1", "name": "CeCuAl3", "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", "@class": "SpaceGroup", "@version": "0.1.0", "_space_group_HM_name": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "value": "I 4 m m:1", "units": "dimensionless", @@ -29,37 +29,36 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_name_H-M_alt.html", "display_name": "_space_group_HM_name", "enabled": true, - "@id": "22283614506081831411829733859089043903" + "@id": "92511438978541827671077057099865312947" }, "setting": "", - "@id": "202328858743821488918676270218647840864" + "@id": "222565624025825627389897792174009768146" }, "cell": { "@module": "easyCrystallography.Components.Lattice", "@class": "PeriodicLattice", "@version": "0.1.0", "length_a": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_a", - "value": 4.256846216308228, - "error": 4.571275213711247e-05, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "84084500609697859758284753800223898880" + "value": 4.25678, + "@id": "234672620443661706452513332120214942559", + "enabled": true }, "length_b": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_b", - "value": 4.256846216308228, "error": 0.0, "min": 0, "max": Infinity, @@ -67,31 +66,31 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": false, - "@id": "202916313494198444346088699246354533621" + "value": 4.25678, + "@id": 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+98,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "61339392366435092842999400548356920466" + "value": 90.0, + "@id": "219381851216903354666585703465148778448", + "enabled": false }, "angle_beta": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_beta", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -115,15 +114,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "241835503349643953524408728449572700413" + "value": 90.0, + "@id": "161908189792929465044933349045501351867", + "enabled": false }, "angle_gamma": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_gamma", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -131,17 +130,18 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "270076570943896211489339580082372811061" + "value": 90.0, + "@id": "188615872074363214500782718002580593354", + "enabled": false }, "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", "@class": "SpaceGroup", "@version": "0.1.0", "_space_group_HM_name": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "units": "dimensionless", "description": "Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting.", @@ -149,27 +149,27 @@ "display_name": "_space_group_HM_name", "enabled": true, "value": "I 4 m m:1", - "@id": "22283614506081831411829733859089043903" + "@id": "92511438978541827671077057099865312947" }, "setting": "", - "@id": "202328858743821488918676270218647840864" + "@id": "222565624025825627389897792174009768146" }, - "@id": "213074574027192196905197519906180906938" + "@id": "251035681628978485508314653975561393149" }, "atoms": { - "@module": "easyCrystallography.Components.Site", + "@module": "easyDiffractionLib.components.site", "@class": "Atoms", - "@version": "0.1.0", + "@version": "0.0.1", "name": "atoms", "data": [ { - "@module": "easyCrystallography.Components.Site", + "@module": "easyDiffractionLib.components.site", "@class": "Site", - "@version": "0.1.0", + "@version": "0.0.1", "label": { - "@module": "easyCore.Objects.Base", + "@module": 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"value": 1.0, "error": 0.0, "min": -Infinity, "max": Infinity, @@ -207,14 +201,14 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_occupancy.html", "units": "dimensionless", "enabled": true, - "@id": "27188870912743367377569707667364172182" + "value": 1.0, + "@id": "231764246536146134314677314758436272290" }, "fract_x": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_x", - "value": 0.0, "error": 0.0, "min": -Infinity, "max": Infinity, @@ -223,14 +217,14 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", "units": "dimensionless", "enabled": true, - "@id": "223381594979245076124270149668552857310" + "value": 0.0, + "@id": "178914306171140941393515950131744189456" }, "fract_y": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_y", - "value": 0.0, "error": 0.0, "min": -Infinity, "max": Infinity, @@ -239,14 +233,14 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", "units": "dimensionless", "enabled": true, - "@id": "338462120552749839778256118278623646969" + "value": 0.0, + "@id": "232349785463598868707487593330594222256" }, "fract_z": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_z", - "value": 0.0, "error": 0.0, "min": -Infinity, "max": Infinity, @@ -255,35 +249,35 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", "units": "dimensionless", "enabled": true, - "@id": "210994338016507535604849985768828884741" + "value": 0.0, + "@id": "45126251521571194758570586498759200759" }, "adp": { "@module": "easyCrystallography.Components.AtomicDisplacement", 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0.0059035389393267135, "error": 0.0, "min": 0, "max": Infinity, @@ -292,22 +286,63 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_U_iso_or_equiv.html", "units": "angstrom ** 2", "enabled": true, - "@id": "241629281029795982688423333125217103660" + "value": 0.00589, + "@id": "63301181802112889337684604981487069959" + }, + "@id": "151997838997967557787783348619143158541" + }, + "@id": "160088922246936874376725746634797663085" + }, + "msp": { + "@module": "easyCrystallography.Components.Susceptibility", + "@class": "MagneticSusceptibility", + "@version": "0.1.0", + "msp_type": { + "@module": "easyCore.Objects.Variable", + "@class": "Descriptor", + "@version": "0.2.2", + "name": "msp_type", + "units": "dimensionless", + "description": "", + "url": "", + "display_name": "msp_type", + "enabled": true, + "value": "Ciso", + "@id": "225635331927658481921706415706297625893" + }, + "msp_class": { + "@module": "easyCrystallography.Components.Susceptibility", + 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"fract_y": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_y", - "value": 0.0, "error": 0.0, "min": -Infinity, "max": Infinity, @@ -377,14 +406,14 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", "units": "dimensionless", "enabled": true, - "@id": "123450603273532362896068574257201217933" + "value": 0.0, + "@id": "100613948173519338857854127772622012873" }, "fract_z": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_z", - "value": 0.6320644882300109, "error": 0.0, "min": -Infinity, "max": Infinity, @@ -393,35 +422,35 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", "units": "dimensionless", "enabled": true, - "@id": "217809807241176530190222178500128297141" + 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"@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "Uiso", - "value": 0.00840363945271072, "error": 0.0, "min": 0, "max": Infinity, @@ -430,22 +459,63 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_U_iso_or_equiv.html", "units": "angstrom ** 2", "enabled": true, - "@id": "292981191369933351231876499794854006627" + "value": 0.0083, + "@id": "119791457857327397796669448848933890427" + }, + "@id": "114776496822555746092191843715824084995" + }, + "@id": "290962525387072211794650455898785619022" + }, + "msp": { + "@module": "easyCrystallography.Components.Susceptibility", + "@class": "MagneticSusceptibility", + "@version": "0.1.0", + "msp_type": { + "@module": "easyCore.Objects.Variable", + "@class": "Descriptor", + "@version": "0.2.2", + "name": "msp_type", + "units": "dimensionless", + "description": "", + "url": "", + "display_name": "msp_type", + "enabled": true, + "value": "Ciso", + "@id": "215333248237936279177684692489264072614" + }, + "msp_class": { + "@module": "easyCrystallography.Components.Susceptibility", + "@class": "Ciso", + "@version": "0.1.0", + "chi": { + "@module": "easyCore.Objects.Variable", + "@class": "Parameter", + "@version": "0.2.2", + "name": "chi_11", + "error": 0.0, + "min": -Infinity, + "max": Infinity, + "fixed": true, + "description": "Isotropic magnetic susceptibility parameter, or equivalent isotropic magnetic susceptibility parameter, C(equiv), in inverted teslas, calculated from anisotropic susceptibility components.", + "units": "1 / tesla", + "enabled": true, + "value": 0.0, + "@id": "335411271019359369643229606596026331490" }, - "@id": "229494011967827305280207169672115261787" + "@id": "274187121935023309293277508488606096419" }, - "@id": "61219206661588631709381263219363960936" + "@id": "332446135800674868148971035150779639202" }, - "@id": "202965600855628729808915394479482690483" + "@id": 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a/easyDiffractionApp/Gui/Resources/Examples/Co2SiO4/project.cif +++ b/easyDiffractionApp/Gui/Resources/Examples/Co2SiO4/project.cif @@ -1,5 +1,5 @@ _name Co2SiO4 -_short_description 'diffraction, powder, 1D' +_short_description 'neutrons, powder, constant wavelength, D20@ILL' _samples 'Co2SiO4' _experiments 'D20@ILL' _modified '26.04.2021 17:46' diff --git a/easyDiffractionApp/Gui/Resources/Examples/Co2SiO4/project.json b/easyDiffractionApp/Gui/Resources/Examples/Co2SiO4/project.json index 614f45f2..5304a243 100644 --- a/easyDiffractionApp/Gui/Resources/Examples/Co2SiO4/project.json +++ b/easyDiffractionApp/Gui/Resources/Examples/Co2SiO4/project.json @@ -4,24 +4,24 @@ "@class": "Sample", "@version": "0.0.1", "phases": { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phases", - "@version": "0.1.0", + "@version": "0.0.1", "name": "Phases", "data": [ { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phase", - "@version": "0.1.0", + "@version": "0.0.1", "name": "Co2SiO4", "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", "@class": "SpaceGroup", "@version": "0.1.0", "_space_group_HM_name": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "value": "P n m a:abc", "units": "dimensionless", @@ -29,69 +29,68 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_name_H-M_alt.html", "display_name": "_space_group_HM_name", "enabled": true, - "@id": "51444312652190354656233507787992578177" + "@id": "323012755685461218837420479122562525750" }, "setting": "", - "@id": "99980507236167308741922907311467866043" + "@id": "225169929931500954922138241907236280838" }, "cell": { "@module": "easyCrystallography.Components.Lattice", "@class": "PeriodicLattice", "@version": "0.1.0", "length_a": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_a", - "value": 10.309140862048409, - "error": 0.00018220893837092144, + "error": 0.0001911652170368589, "min": 0, "max": Infinity, "fixed": false, "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "213551681157810189833132241890417492893" + "value": 10.309958682104202, + "@id": "77166956011965649788471922494852784835", + "enabled": true }, "length_b": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_b", - "value": 6.004275578119403, - "error": 0.00010553217677769064, + "error": 0.00011232396320325683, "min": 0, 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"25.08.2021 10:18" + "modified": "20.07.2022 08:20" }, "interface": "CrysPy", "minimizer": { diff --git a/easyDiffractionApp/Gui/Resources/Examples/Co2SiO4/samples/Co2SiO4.cif b/easyDiffractionApp/Gui/Resources/Examples/Co2SiO4/samples/Co2SiO4.cif index b66b84a5..c78b15a8 100644 --- a/easyDiffractionApp/Gui/Resources/Examples/Co2SiO4/samples/Co2SiO4.cif +++ b/easyDiffractionApp/Gui/Resources/Examples/Co2SiO4/samples/Co2SiO4.cif @@ -1,11 +1,10 @@ data_Co2SiO4 -_space_group_name_H-M_ref 'P n m a' -_space_group_IT_coordinate_system_code abc +_space_group_name_H-M_alt 'P n m a' -_cell_length_a 10.28 -_cell_length_b 6.03 -_cell_length_c 4.75 +_cell_length_a 10.3100 +_cell_length_b 6.0045 +_cell_length_c 4.7872 _cell_angle_alpha 90.0 _cell_angle_beta 90.0 _cell_angle_gamma 90.0 @@ -18,8 +17,8 @@ _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy _atom_site_adp_type -_atom_site_u_iso_or_equiv -Co1 Co 0.0 0.0 0.0 1.0 Uiso 0.004 +_atom_site_U_iso_or_equiv +Co1 Co 0.0 0.0 0.0 1.0 Uiso 0.004 Co2 Co 0.279 0.25 0.985 1.0 Uiso 0.007 Si Si 0.094 0.25 0.429 1.0 Uiso 0.005 O1 O 0.091 0.25 0.771 1.0 Uiso 0.008 diff --git a/easyDiffractionApp/Gui/Resources/Examples/Dy3Al5O12/project.cif b/easyDiffractionApp/Gui/Resources/Examples/Dy3Al5O12/project.cif index dcc1612f..94bca08e 100644 --- a/easyDiffractionApp/Gui/Resources/Examples/Dy3Al5O12/project.cif +++ b/easyDiffractionApp/Gui/Resources/Examples/Dy3Al5O12/project.cif @@ -1,5 +1,5 @@ _name Dy3Al5O12 -_short_description 'diffraction, powder, 1D' +_short_description 'neutrons, powder, constant wavelength, G41@LLB' _samples 'Dy3Al5O12' _experiments 'G41@LLB' _modified '26.04.2021 20:07' diff --git a/easyDiffractionApp/Gui/Resources/Examples/Dy3Al5O12/project.json b/easyDiffractionApp/Gui/Resources/Examples/Dy3Al5O12/project.json index 3712b314..f0b13e8b 100644 --- a/easyDiffractionApp/Gui/Resources/Examples/Dy3Al5O12/project.json +++ b/easyDiffractionApp/Gui/Resources/Examples/Dy3Al5O12/project.json @@ -4,24 +4,24 @@ "@class": "Sample", "@version": "0.0.1", "phases": { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phases", - "@version": "0.1.0", + "@version": "0.0.1", "name": "Phases", "data": [ { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phase", - "@version": "0.1.0", + "@version": "0.0.1", "name": "Dy3Al5O12", "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", "@class": "SpaceGroup", "@version": "0.1.0", "_space_group_HM_name": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "value": "I a -3 d:1", "units": "dimensionless", @@ -29,37 +29,36 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_name_H-M_alt.html", "display_name": "_space_group_HM_name", "enabled": true, - "@id": "237087496219934773319155177509872920662" + "@id": "29214101360585411911591445881576148800" }, "setting": "", - "@id": "249518765247200362220127170341694001815" + "@id": "286981274392192463488439017875314105906" }, "cell": { "@module": "easyCrystallography.Components.Lattice", "@class": "PeriodicLattice", "@version": "0.1.0", "length_a": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_a", - "value": 11.899241913110943, - "error": 0.0010174172271434562, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "76558582941150031190231170948465017590" + "value": 11.8993, + "@id": "205275846955820659600226090102179059750", + "enabled": true }, "length_b": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_b", - "value": 11.899241913110943, "error": 0.0, "min": 0, "max": Infinity, @@ -67,15 +66,15 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": false, - "@id": "141787708533770333742071047158385386255" + "value": 11.8993, + "@id": "120220800643955197686488654000435124176", + "enabled": false }, "length_c": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_c", - "value": 11.899241913110943, "error": 0.0, "min": 0, "max": Infinity, @@ -83,15 +82,15 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": false, - "@id": "90941996440095289148875349602423818763" + "value": 11.8993, + "@id": "193429044294434803972816913633079082278", + "enabled": false }, "angle_alpha": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_alpha", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -99,15 +98,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "280909348664559425527703280151230844595" + "value": 90.0, + "@id": "129931072237923508169515371158306016380", + "enabled": false }, "angle_beta": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - 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25.11 535.41 24.27 +81.8 604.92 24.92 559.32 24.65 +82.0 589.97 24.97 499.26 24.46 diff --git a/easyDiffractionApp/Gui/Resources/Examples/Ho2Ti2O7/project.cif b/easyDiffractionApp/Gui/Resources/Examples/Ho2Ti2O7/project.cif new file mode 100644 index 00000000..178299c3 --- /dev/null +++ b/easyDiffractionApp/Gui/Resources/Examples/Ho2Ti2O7/project.cif @@ -0,0 +1,5 @@ +_name Ho2Ti2O7 +_short_description 'neutrons, powder, constant wavelength, polarised, VIP@LLB' +_samples 'Ho2Ti2O7' +_experiments 'VIP@LLB-5K5T' +_modified '24.05.2022 09:52' diff --git a/easyDiffractionApp/Gui/Resources/Examples/Ho2Ti2O7/project.json b/easyDiffractionApp/Gui/Resources/Examples/Ho2Ti2O7/project.json new file mode 100644 index 00000000..fb088a2a --- /dev/null +++ b/easyDiffractionApp/Gui/Resources/Examples/Ho2Ti2O7/project.json @@ -0,0 +1,3571 @@ +{ + "sample": { + "@module": "easyDiffractionLib.sample", + "@class": "Sample", + "@version": "0.0.1", + "phases": { + "@module": 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+_cell_length_b 10.26593 +_cell_length_c 10.26593 +_cell_angle_alpha 90.0 +_cell_angle_beta 90.0 +_cell_angle_gamma 90.0 + +loop_ +_atom_site_label +_atom_site_type_symbol +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +_atom_site_occupancy +_atom_site_adp_type +_atom_site_U_iso_or_equiv +Ho Ho3+ 0.5 0.5 0.5 1.0 Uiso 0.0 +Ti Ti3+ 0.0 0.0 0.0 1.0 Uiso 0.0 +O1 O2- 0.32858 0.125 0.125 1.0 Uiso 0.0 +O2 O2- 0.375 0.375 0.375 1.0 Uiso 0.0 + +loop_ +_atom_site_susceptibility_label +_atom_site_susceptibility_chi_type +_atom_site_susceptibility_chi_11 +_atom_site_susceptibility_chi_22 +_atom_site_susceptibility_chi_33 +_atom_site_susceptibility_chi_12 +_atom_site_susceptibility_chi_13 +_atom_site_susceptibility_chi_23 +Ho Cani 3.826 3.826 3.826 3.738 3.738 3.738 + +loop_ +_atom_site_scat_label +_atom_site_scat_lande +_atom_site_scat_kappa +Ho 2.0 1.0 diff --git a/easyDiffractionApp/Gui/Resources/Examples/Na2Ca3Al2F14/project.cif b/easyDiffractionApp/Gui/Resources/Examples/Na2Ca3Al2F14/project.cif index 083ae018..b4931407 100644 --- a/easyDiffractionApp/Gui/Resources/Examples/Na2Ca3Al2F14/project.cif +++ b/easyDiffractionApp/Gui/Resources/Examples/Na2Ca3Al2F14/project.cif @@ -1,5 +1,5 @@ _name Na2Ca3Al2F14 -_short_description 'neutrons, powder, time-of-flight, 1D' -_samples 'Na2Ca3Al2F14' -_experiments 'Osiris@ISIS' -_modified '25.08.2021 14:05' +_short_description 'neutrons, powder, time-of-flight, Osiris@ISIS' +_samples Na2Ca3Al2F14 +_experiments Osiris@ISIS +_modified '25.08.2021 14:05' \ No newline at end of file diff --git a/easyDiffractionApp/Gui/Resources/Examples/Na2Ca3Al2F14/project.json b/easyDiffractionApp/Gui/Resources/Examples/Na2Ca3Al2F14/project.json index b727de85..4b72abf5 100644 --- a/easyDiffractionApp/Gui/Resources/Examples/Na2Ca3Al2F14/project.json +++ b/easyDiffractionApp/Gui/Resources/Examples/Na2Ca3Al2F14/project.json @@ -4,24 +4,24 @@ "@class": "Sample", "@version": "0.0.1", "phases": { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phases", - "@version": "0.1.0", + "@version": "0.0.1", "name": "Phases", "data": [ { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phase", - "@version": "0.1.0", + "@version": "0.0.1", "name": "Na2Ca3Al2F14", "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", "@class": "SpaceGroup", "@version": "0.1.0", "_space_group_HM_name": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "value": "I 21 3:1", "units": "dimensionless", @@ -29,37 +29,36 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_name_H-M_alt.html", "display_name": "_space_group_HM_name", "enabled": true, - "@id": "95963232699549765885194481117619249234" + "@id": "311273832785666460928873570792668941229" }, "setting": "", - "@id": "148974734727053953684020675847410967420" + "@id": "49227278386268860620315221578344518260" }, "cell": { "@module": "easyCrystallography.Components.Lattice", "@class": "PeriodicLattice", "@version": "0.1.0", "length_a": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_a", - "value": 10.251820338132141, - "error": 3.406138562717864e-05, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "9406231402425984623768387408717483366" + "value": 10.251820338132141, + "@id": "41228797693769696362407523616105143116", + "enabled": true }, "length_b": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_b", - "value": 10.251820338132141, "error": 0.0, "min": 0, "max": Infinity, @@ -67,15 +66,15 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": false, - "@id": "168467484142621677829416690537807387321" + "value": 10.251820338132141, + "@id": "37794723127754777355999250816696519437", + "enabled": false }, "length_c": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_c", - "value": 10.251820338132141, "error": 0.0, "min": 0, "max": Infinity, @@ -83,15 +82,15 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": false, - "@id": "100732989425168205615259822145492940832" + "value": 10.251820338132141, + "@id": "101038256814570159765841028351226119219", + "enabled": false }, "angle_alpha": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_alpha", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -99,15 +98,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "163790831735841542837999060024993151864" + "value": 90.0, + "@id": "187701156349594631947195256107043025437", + "enabled": false }, "angle_beta": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_beta", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -115,15 +114,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "91778655052563201261638432112044180010" + "value": 90.0, + "@id": "54290675182716979029081411790469556562", + "enabled": false }, "angle_gamma": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_gamma", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -131,17 +130,18 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "302488333107175015873334451352902250703" + "value": 90.0, + "@id": "307050862630844251066587007454078216320", + "enabled": false }, "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", "@class": "SpaceGroup", "@version": "0.1.0", "_space_group_HM_name": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "units": "dimensionless", "description": "Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting.", @@ -149,12 +149,12 @@ "display_name": "_space_group_HM_name", "enabled": true, "value": "I 21 3:1", - "@id": "95963232699549765885194481117619249234" + "@id": "311273832785666460928873570792668941229" }, "setting": "", - "@id": "148974734727053953684020675847410967420" + "@id": "49227278386268860620315221578344518260" 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"@id": "188453493857052917859235627998002318354" + "@id": "253541325252320996843722773200330455556" }, "occupancy": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "occupancy", - "value": 1.0, "error": 0.0, "min": -Infinity, "max": Infinity, @@ -207,14 +201,14 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_occupancy.html", "units": "dimensionless", "enabled": true, - "@id": "184181271049691780212001835683488143233" + "value": 1.0, + "@id": "197172235859885708825098915299858557557" }, "fract_x": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_x", - "value": 0.4675847593754685, "error": 0.0, "min": -Infinity, "max": Infinity, @@ -223,14 +217,14 @@ "url": 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"easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", @@ -1428,33 +1398,33 @@ "display_name": "x", "enabled": true, "value": 194036.0, - "@id": "19258416699345745817935375437013792786" + "@id": "132051700799581886351666861299460287777" }, "y": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 551.9459137907253, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "145013573923001692717012382842950045277" + "value": 551.9459137907253, + "@id": "104342304503448739135241599041482240716" }, "name": "194036,0_deg", - "@id": "273677484352121210296934134215485772443" + "@id": "304168699980879814254911833271219059540" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", @@ -1462,33 +1432,33 @@ "display_name": "x", "enabled": true, "value": 23154.0, - "@id": "262296892827364551691515956798895614108" + "@id": "85885633768345787525199481449541964042" }, "y": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 810.2000433902351, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "53600894667378297658397367214040258995" + "value": 810.2000433902351, + "@id": "50331429724301397092756703597112935786" }, "name": "23154,0_deg", - "@id": "189412016896787715692850513546258845181" + "@id": "53110989647804309364476963544704347287" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", @@ -1496,33 +1466,33 @@ "display_name": "x", "enabled": true, "value": 18320.0, - "@id": "274189004778932340485343447205980555686" + "@id": "107898262466617806059537621999625456690" }, "y": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 1376.048634632708, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "2237227066886337901013872314232302094" + "value": 1376.048634632708, + "@id": "94254777182714937101433280463001533290" }, "name": "18320,0_deg", - "@id": "129704182423767027075144544539323504044" + "@id": "43030222920322011296802035083022934432" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", @@ -1530,33 +1500,33 @@ "display_name": "x", "enabled": true, "value": 17112.0, - "@id": "8319937658719118529022995164140607128" + "@id": "333967934313530241834842983953916725701" }, "y": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 1525.919818024055, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "11186100753211355875332772208136434986" + "value": 1525.919818024055, + "@id": "100338212166998242171661150865852696586" }, "name": "17112,0_deg", - "@id": "221430666615411437237026032678343779496" + "@id": "71108518293334083861918492538099871649" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", @@ -1564,33 +1534,33 @@ "display_name": "x", "enabled": true, "value": 15660.0, - "@id": "5322434582275784558393979340278668939" + "@id": "78998150930008862902673395065806067272" }, "y": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 1575.0699943582474, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "92970022884036460695792573872281863066" + "value": 1575.0699943582474, + "@id": "8814535592110339915631872020203955268" }, "name": "15660,0_deg", - "@id": "32120942551516834518183775458263697761" + "@id": "73014033143060990818958976424187963974" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", @@ -1598,33 +1568,33 @@ "display_name": "x", "enabled": true, "value": 15385.0, - "@id": "191741073188651080418763665924735093793" + "@id": "178978408274079916162591934387119703232" }, "y": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 1869.806262401121, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "164902891842313208887461565381512914197" + "value": 1869.806262401121, + "@id": "230653936901968007759174991305887879711" }, "name": "15385,0_deg", - "@id": "34557595143795459082399512568001843320" + "@id": "285866609869193979983881269947458963601" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", @@ -1632,33 +1602,33 @@ "display_name": "x", "enabled": true, "value": 14951.0, - "@id": "201735722545509622719519338585513878191" + "@id": "246822236242620942476393918334989576888" }, "y": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 1603.594656042326, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "54005833829927322877602860040026401706" + "value": 1603.594656042326, + "@id": "9193245447209746359938726865063299910" }, "name": "14951,0_deg", - "@id": "109665638082250078377847237962999525212" + "@id": "302890606448211121312085024344948934373" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", @@ -1666,33 +1636,33 @@ "display_name": "x", "enabled": true, "value": 33600.0, - "@id": "179023599164288990674929768617230750463" + "@id": "17808168583035940850077603927352791694" }, "y": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 541.8254620156262, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "249554017304116928468840075773199241115" + "value": 541.8254620156262, + "@id": "284854460803271191533217192506838123359" }, "name": "33600,0_deg", - "@id": "93686168357842534785464841868819166880" + "@id": "134473837228186278360390925955178446088" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", @@ -1700,33 +1670,33 @@ "display_name": "x", "enabled": true, "value": 46000.0, - "@id": "92300292065238461352950359798643366665" + "@id": "292940064311009671001724335397772814825" }, "y": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 363.0133245765627, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "202213339743796706201646674435204994975" + "value": 363.0133245765627, + "@id": "162958713765441356855205037613872683905" }, "name": "46000,0_deg", - "@id": "243603774915118132219700846297722409656" + "@id": "17247356732174004393882047936049406606" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", @@ -1734,36 +1704,36 @@ "display_name": "x", "enabled": true, "value": 27000.0, - "@id": "213919004024610989213462344852649100435" + "@id": "54150078569043900426929384770965932237" }, "y": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 684.6716757924121, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "75865212683539940064148756502600282923" + "value": 684.6716757924121, + "@id": "194581295900387274263822856157106999679" }, "name": "27000,0_deg", - "@id": "199461017950908915525179511511032327541" + "@id": "68963622509153384356190637740651313139" } ], - "@id": "235482088132623133018984947681686750188", + "@id": "247430113901775778774806595768442511793", "linked_experiment": "current_exp" } ], - "@id": "140362285513685433172357944828672316932" + "@id": "336618857655082159908578929936842972768" }, - "@id": "279751021924317307628746022182622075865" + "@id": "107569213563381386587832436264316357667" }, "name": "easySample", - "@id": "64335324051102266841160194005536284735" + "@id": "182621821817253053386075827703882001571" }, "experiments": [ [ @@ -18298,9 +18268,10 @@ ] ], "experiment_skipped": false, + "read_only": true, "project_info": { "name": "Na2Ca3Al2F14", - "short_description": "neutrons, powder, time-of-flight, 1D", + "short_description": "neutrons, powder, time-of-flight, Osiris@ISIS", "samples": "Na2Ca3Al2F14", "experiments": "Osiris@ISIS", "modified": "25.08.2021 14:05" diff --git a/easyDiffractionApp/Gui/Resources/Examples/PbSO4/project.cif b/easyDiffractionApp/Gui/Resources/Examples/PbSO4/project.cif index 33db1821..f0325aa5 100644 --- a/easyDiffractionApp/Gui/Resources/Examples/PbSO4/project.cif +++ b/easyDiffractionApp/Gui/Resources/Examples/PbSO4/project.cif @@ -1,5 +1,5 @@ _name PbSO4 -_short_description 'neutrons, powder, constant wavelength, 1D' +_short_description 'neutrons, powder, constant wavelength, D1A@ILL' _samples 'PbSO4' _experiments 'D1A@ILL' -_modified '24.08.2021 13:37' +_modified '26.04.2021 12:46' diff --git a/easyDiffractionApp/Gui/Resources/Examples/PbSO4/project.json b/easyDiffractionApp/Gui/Resources/Examples/PbSO4/project.json index ec33b7a0..32bdb665 100644 --- a/easyDiffractionApp/Gui/Resources/Examples/PbSO4/project.json +++ b/easyDiffractionApp/Gui/Resources/Examples/PbSO4/project.json @@ -4,24 +4,24 @@ "@class": "Sample", "@version": "0.0.1", "phases": { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phases", - "@version": "0.1.0", + "@version": "0.0.1", "name": "Phases", "data": [ { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phase", - "@version": "0.1.0", + "@version": "0.0.1", "name": "PbSO4", "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", "@class": "SpaceGroup", "@version": "0.1.0", "_space_group_HM_name": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "value": "P n m a:abc", "units": "dimensionless", @@ -29,69 +29,68 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_name_H-M_alt.html", "display_name": "_space_group_HM_name", "enabled": true, - "@id": "214348249132987164499205812378350772359" + "@id": "190449306832608112257018576936052249392" }, "setting": "", - "@id": "326657860457201360536716486040739803906" + "@id": "289875906032027385427229624731989791491" }, "cell": { "@module": "easyCrystallography.Components.Lattice", "@class": "PeriodicLattice", "@version": "0.1.0", "length_a": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_a", - "value": 8.478139246723623, - "error": 9.46756278581907e-05, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "156516926709613279450313136011480677657" + "value": 8.4774, + "@id": "10971425981967737184650235645406766924", + "enabled": true }, "length_b": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_b", - "value": 5.396580598855251, - "error": 6.283040877129049e-05, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "327966790122473942618615485501724498360" + "value": 5.396, + "@id": "307679075055753684987562388239036674011", + "enabled": true }, "length_c": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_c", - "value": 6.9578169912254575, - "error": 8.707604811932274e-05, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "166901608120266313402299486998811229038" + "value": 6.957, + "@id": "43198596658802343767843434680670335454", + "enabled": true }, "angle_alpha": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_alpha", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -99,15 +98,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "216379293135119500044096254424943879495" + "value": 90.0, + "@id": "87081486690993477241190035210247325150", + "enabled": false }, "angle_beta": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_beta", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -115,15 +114,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "191653919808281686131496145363103765211" + "value": 90.0, + "@id": "293291295444280922208323006932792085825", + "enabled": false }, "angle_gamma": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_gamma", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -131,17 +130,18 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "309728146476323689382177170649528380229" + "value": 90.0, + "@id": "139049303085273651432772294294252660995", + "enabled": false }, "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", "@class": "SpaceGroup", "@version": "0.1.0", "_space_group_HM_name": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "units": "dimensionless", "description": "Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a 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a/easyDiffractionApp/Gui/Resources/Examples/Si3N4/project.cif +++ b/easyDiffractionApp/Gui/Resources/Examples/Si3N4/project.cif @@ -1,5 +1,5 @@ -_name Si3N4 -_short_description 'diffraction, powder, 1D' +_name 'Si3N4' +_short_description 'neutrons, powder, constant wavelength, multi-phase, 3T2@LLB' _samples 'Si3N4_alpha, Si3N4_beta' _experiments '3T2@LLB' -_modified '02.12.2021 10:15' +_modified '01.02.2022 10:16' diff --git a/easyDiffractionApp/Gui/Resources/Examples/Si3N4/project.json b/easyDiffractionApp/Gui/Resources/Examples/Si3N4/project.json index f5ffbbe4..7d65a204 100644 --- a/easyDiffractionApp/Gui/Resources/Examples/Si3N4/project.json +++ b/easyDiffractionApp/Gui/Resources/Examples/Si3N4/project.json @@ -4,15 +4,15 @@ "@class": "Sample", "@version": "0.0.1", "phases": { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phases", - "@version": "0.1.0", + "@version": "0.0.1", "name": "Phases", "data": [ { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phase", - "@version": "0.1.0", + "@version": "0.0.1", "name": "Si3N4_alpha", "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", @@ -21,7 +21,7 @@ "_space_group_HM_name": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "value": "P 3 1 c:r", "units": "dimensionless", @@ -29,10 +29,10 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_name_H-M_alt.html", "display_name": "_space_group_HM_name", "enabled": true, - "@id": "323241945591398306874692827938017348414" + "@id": "86303283277332365658229310607173746582" }, "setting": "", - "@id": "193046138044008511252559169148005569223" + "@id": "231959193280068587934112480710157782826" }, "cell": { "@module": "easyCrystallography.Components.Lattice", @@ -41,25 +41,24 @@ "length_a": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_a", - "value": 7.750937232235225, - "error": 7.813047787239839e-05, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "181991401382169934454776876765019937644" + "value": 7.75092882, + "@id": "296829975319484471340458433109455693563", + "enabled": true }, "length_b": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_b", - "value": 7.750937232235225, "error": 0.0, "min": 0, "max": Infinity, @@ -67,31 +66,31 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": false, - "@id": "257940179990375812233766193926225676842" + "value": 7.75092882, + "@id": "268411233507208252474429892848405077841", + "enabled": false }, "length_c": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_c", - "value": 5.6188624843154455, - "error": 6.571632875487679e-05, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "189377729326982989681979976614458164367" + "value": 5.61886556, + "@id": "207905530962558145358553910299546199405", + "enabled": true }, "angle_alpha": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_alpha", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -99,15 +98,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "129490205601582203133786442515140839093" + "value": 90.0, + "@id": "228430533379346032942186159257947728019", + "enabled": false }, "angle_beta": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_beta", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -115,15 +114,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "96058479203997940850338664668269508403" + "value": 90.0, + "@id": "91560787151282548333066320410523472702", + "enabled": false }, "angle_gamma": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_gamma", - "value": 120.0, "error": 0.0, "min": 0, "max": Infinity, @@ -131,8 +130,9 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "211244524058489656596228457777796015872" + "value": 120.0, + "@id": "146616716845168454195790472462586600855", + "enabled": false }, "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", @@ -141,7 +141,7 @@ "_space_group_HM_name": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "units": "dimensionless", "description": "Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting.", @@ -149,27 +149,27 @@ "display_name": "_space_group_HM_name", "enabled": true, "value": "P 3 1 c:r", - "@id": "323241945591398306874692827938017348414" + "@id": "86303283277332365658229310607173746582" }, "setting": "", - "@id": "193046138044008511252559169148005569223" + "@id": "231959193280068587934112480710157782826" }, - "@id": "285240588659650940043575158590322239931" + "@id": "155976119202582527829072713301365514991" }, "atoms": { - "@module": "easyCrystallography.Components.Site", + "@module": "easyDiffractionLib.components.site", "@class": "Atoms", - "@version": "0.1.0", + "@version": "0.0.1", "name": "atoms", "data": [ { - "@module": "easyCrystallography.Components.Site", + "@module": "easyDiffractionLib.components.site", "@class": "Site", - "@version": "0.1.0", + "@version": "0.0.1", "label": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "label", "units": "dimensionless", "description": "A unique identifier for a particular site in the crystal", @@ -177,85 +177,80 @@ "display_name": "label", "enabled": true, "value": "Si1", - "@id": "170995106079168173347706073583030598591" + "@id": "252349893550166803735678459796943282036" }, "specie": { "@module": "easyCrystallography.Components.Specie", "@class": "Specie", "@version": "0.1.0", - "specie": { - "@module": "easyCrystallography.Elements.periodic_table", - "@class": "Specie", - "element": "Si", - "oxidation_state": 0.0 - }, + "specie": "Si", "value": "Si", "units": "dimensionless", - "@id": "234508008732212473267666677214933190504" + "@id": "11812382042399330309843614236793936949" }, "occupancy": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "occupancy", - "value": 1.0, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "description": "The fraction of the atom type present at this site.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_occupancy.html", + "value": 1.0, "units": "dimensionless", - "enabled": true, - "@id": "185341575289014712862273893206838174538" + "@id": "28859164976850764726707217711360859854", + "enabled": true }, "fract_x": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_x", - "value": 0.0819, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "description": "Atom-site coordinate as fractions of the unit cell length.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", + "value": 0.0819, "units": "dimensionless", - "enabled": true, - "@id": "291762368800252591121433217167628932949" + "@id": "198396006713451371007965841510307750329", + "enabled": true }, "fract_y": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_y", - "value": 0.5118, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "description": "Atom-site coordinate as fractions of the unit cell length.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", + "value": 0.5118, "units": "dimensionless", - "enabled": true, - "@id": "320174685589061908372241494433418146960" + "@id": "154523197434132623578813101565243670751", + "enabled": true }, "fract_z": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_z", - "value": 0.65958, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "description": "Atom-site coordinate as fractions of the unit cell length.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", + "value": 0.65958, "units": "dimensionless", - "enabled": true, - "@id": "56493226233657170190197221031529925558" + "@id": "21929278650781288798970206598930600828", + "enabled": true }, "adp": { "@module": "easyCrystallography.Components.AtomicDisplacement", @@ -264,15 +259,15 @@ "adp_type": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "adp_type", "units": "dimensionless", - "description": "A standard code used to describe the type of atomic displacement parameters used for the site.", - "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_adp_type.html", + "description": "", + "url": "", "display_name": "adp_type", "enabled": true, "value": "Uiso", - "@id": "172993164894525169466453747509971684783" + "@id": "142315435170661291784100900126307511497" }, "adp_class": { "@module": "easyCrystallography.Components.AtomicDisplacement", @@ -281,33 +276,33 @@ "Uiso": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "Uiso", - "value": 0.0018430490936811675, - "error": 0.000378241223340326, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "The standard anisotropic atomic displacement components in angstroms squared which appear in the structure-factor term.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_U_iso_or_equiv.html", "units": "angstrom ** 2", - "enabled": true, - "@id": "93550894432416978203527030270631656274" + "value": 0.0018421, + "@id": "17393123368801072202484554015097240857", + "enabled": true }, - "@id": "205352601965746492012165534649173455318" + "@id": "24322348403683779888283149117420195814" }, - "@id": "123396978013611077015265835198678291083" + "@id": "85509183444002604028206669150297724325" }, - "@id": "266121421336683548397269686472031201735" + "@id": "187310347499425504790110682256281912221" }, { - "@module": "easyCrystallography.Components.Site", + "@module": "easyDiffractionLib.components.site", "@class": "Site", - "@version": "0.1.0", + "@version": "0.0.1", "label": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "label", "units": "dimensionless", "description": "A unique identifier for a particular site in the crystal", @@ -315,85 +310,80 @@ "display_name": "label", "enabled": true, "value": "Si2", - "@id": "264539404952456363461618827888951674881" + "@id": "222511211850661028710757635239924326187" }, "specie": { "@module": "easyCrystallography.Components.Specie", "@class": "Specie", "@version": "0.1.0", - "specie": { - "@module": "easyCrystallography.Elements.periodic_table", - "@class": "Specie", - "element": "Si", - "oxidation_state": 0.0 - }, + "specie": "Si", "value": "Si", "units": "dimensionless", - "@id": "22381459926619614776739261061585816569" + "@id": "175018261205757503281059862798186428078" }, "occupancy": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "occupancy", - "value": 1.0, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "description": "The fraction of the atom type present at this site.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_occupancy.html", + "value": 1.0, "units": "dimensionless", - "enabled": true, - "@id": "115875901419425049555728384163446195043" + "@id": "126931383050637456248122413463949022818", + "enabled": true }, "fract_x": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_x", - "value": 0.25323, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "description": "Atom-site coordinate as fractions of the unit cell length.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", + "value": 0.25323, "units": "dimensionless", - "enabled": true, - "@id": 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"url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", + "value": 0.4509, "units": "dimensionless", - "enabled": true, - "@id": "164103254660652809020426889413245563861" + "@id": "38100923552425385078516547489942717436", + "enabled": true }, "adp": { "@module": "easyCrystallography.Components.AtomicDisplacement", @@ -402,15 +392,15 @@ "adp_type": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "adp_type", "units": "dimensionless", - "description": "A standard code used to describe the type of atomic displacement parameters used for the site.", - "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_adp_type.html", + "description": "", + "url": "", "display_name": "adp_type", "enabled": true, "value": "Uiso", - "@id": "213177797075153259404784878100742452587" + "@id": "151171284128110554879142502312134722760" }, "adp_class": { "@module": 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}, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", @@ -1985,33 +1940,33 @@ "display_name": "x", "enabled": true, "value": 25.0, - "@id": "260468662874416964815457434953184628274" + "@id": "97924160944286647837195614005674337099" }, "y": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 130.00772000428603, - "error": 0.6711999531766398, + "error": 0.0, "min": -Infinity, "max": Infinity, - "fixed": false, + "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "199841728767757006077275701094305634918" + "value": 130.008, + "@id": "33496849611213535533412709390350005127" }, "name": 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"46022181937871319093130426075917174246" + "value": 131.549, + "@id": "191167785678367879588985614609017207262" }, "name": "45,0_deg", - "@id": "107256400794049927870434858137320673687" + "@id": "28616743581573971090165025255132653772" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", "url": "", "display_name": "x", "enabled": true, - "value": 85.0, - "@id": "181341336812532206605262913679208928930" + "value": 70.0, + "@id": "266637866989461288716222441043534158986" }, "y": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 138.5795423850155, - "error": 1.0366668698090238, + "error": 0.0, "min": -Infinity, "max": Infinity, - "fixed": false, + "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "68696587828725803217852329995528332796" + "value": 137.786, + "@id": "60174622118133062162655080987887099084" }, - "name": "85,0_deg", - "@id": "161938267720901227264623439406609114773" + "name": "70,0_deg", + "@id": "158576800769603786521700374384939892007" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", "url": "", "display_name": "x", "enabled": true, - "value": 105.0, - "@id": "88794353065263264278269552435700153515" + "value": 77.0, + "@id": "226336747979148471610963465260337802408" }, "y": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 148.390040420825, - "error": 0.9183922833024244, + "error": 0.0, "min": -Infinity, "max": Infinity, - "fixed": false, + "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "122686422969669763459883504727345615378" + "value": 134.0414, + "@id": "227867970102371069369901560050391003504" }, - "name": "105,0_deg", - "@id": "137385048138151395286416169195774749947" + "name": "77,0_deg", + "@id": "71432759886976177074067694755968394147" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", "url": "", "display_name": "x", "enabled": true, - "value": 6.0, - "@id": "25625451245914501661604770455486944193" + "value": 85.0, + "@id": "305388591962372926972703144323907879214" }, "y": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 165.41193272852385, - "error": 2.223977121168442, + "error": 0.0, "min": -Infinity, "max": Infinity, - "fixed": false, + "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "93879187548840318756941208594388517588" + "value": 138.579, + "@id": "81156089439462989588123974793153391027" }, - "name": "6,0_deg", - "@id": "155244133936981109619673835999147085559" + "name": "85,0_deg", + "@id": "20266302324085955319949786345019362671" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", "url": "", "display_name": "x", "enabled": true, - "value": 9.0, - "@id": "204913858836968533592550971619888988958" + "value": 105.0, + "@id": "146428127554859198899538962790999780442" }, "y": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 149.88372267370147, - "error": 1.7029631693435, + "error": 0.0, "min": -Infinity, "max": Infinity, - "fixed": false, + "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "181694054362901891369544556614813416648" + "value": 148.39, + "@id": "259658649512553935381956578791755647055" }, - "name": "9,0_deg", - "@id": "32263350899970974060464509609289271812" + "name": "105,0_deg", + "@id": "299430418819809054026745249160676039591" }, { - "@module": "easyDiffractionLib.Elements.Backgrounds.Point", + "@module": "easyDiffractionLib.elements.Backgrounds.Point", "@class": "BackgroundPoint", "@version": "0.0.1", "x": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "x", "units": "dimensionless", "description": "", "url": "", "display_name": "x", "enabled": true, - "value": 77.0, - "@id": "245399100573151250579306150924451376308" + "value": 125.0, + "@id": "83068256469657465369452422729309135533" }, "y": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "intensity", - "value": 134.04140942397038, - "error": 0.8104089592856186, + "error": 0.0, "min": -Infinity, "max": Infinity, - "fixed": false, + "fixed": true, "units": "dimensionless", "enabled": true, - "@id": "12477264049998098209013781861270511843" + "value": 157.505, + "@id": "295018045407048487482261769146429121680" }, - "name": "77,0_deg", - "@id": "62773492451063145027368301635666167433" + "name": "125,0_deg", + "@id": "270738673231623426042436281024702137165" } ], - "@id": "151238178686825126455281053647341476852", + "@id": "87230681367240879358362504412675971857", "linked_experiment": "current_exp" } ], - "@id": "59436888496241803269443684628306727418" + "@id": "67593751496468925824576400934378232582" }, - "@id": "91809965133523759693155732921215412530" + "@id": "164617770833469586882890467553663414791" }, "name": "easySample", - "@id": "195262697602864733544803148452188384260" + "@id": "132659903369418757236213243635775850216" }, "experiments": [ [ @@ -9432,12 +9387,13 @@ ] ], "experiment_skipped": false, + "read_only": true, "project_info": { "name": "Si3N4", - "short_description": "diffraction, powder, 1D", - "samples": "Si3N4_alpha, Si3N4_beta", + "short_description": "neutrons, powder, constant wavelength, multi-phase, 3T2@LLB", + "samples": "Si3N4_alpha", "experiments": "3T2@LLB", - "modified": "02.12.2021 10:16" + "modified": "02.06.2022 15:07" }, "interface": "CrysPy", "minimizer": { diff --git a/easyDiffractionApp/Gui/Resources/Examples/Si3N4/samples/Si3N4_alpha.cif b/easyDiffractionApp/Gui/Resources/Examples/Si3N4/samples/Si3N4_alpha.cif index db9d86cd..e776a4cd 100644 --- a/easyDiffractionApp/Gui/Resources/Examples/Si3N4/samples/Si3N4_alpha.cif +++ b/easyDiffractionApp/Gui/Resources/Examples/Si3N4/samples/Si3N4_alpha.cif @@ -1,26 +1,25 @@ data_Si3N4_alpha -_space_group_name_H-M_alt 'P 3 1 c' - -_cell_length_a 7.751856 -_cell_length_b 7.751856 -_cell_length_c 5.619506 -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 120.0 +_cell_length_a 7.75092882 +_cell_length_b 7.75092882 +_cell_length_c 5.61886556 +_cell_angle_alpha 90.0 +_cell_angle_beta 90.0 +_cell_angle_gamma 120.0 +_space_group_name_H-M_alt 'P 3 1 c' loop_ - _atom_site_label - _atom_site_type_symbol - _atom_site_occupancy - _atom_site_fract_x - _atom_site_fract_y - _atom_site_fract_z - _atom_site_adp_type - _atom_site_U_iso_or_equiv - Si1 Si 1.0 0.08185 0.51180 0.65958 Uiso 0.01 - Si2 Si 1.0 0.25323 0.16763 0.45090 Uiso 0.01 - N1 N 1.0 0.65512 0.61058 0.43269 Uiso 0.01 - N2 N 1.0 0.31514 0.31865 0.69801 Uiso 0.01 - N3 N 1.0 0.33333 0.66667 0.60394 Uiso 0.01 - N4 N 1.0 0.00000 0.00000 0.45292 Uiso 0.01 +_atom_site_label +_atom_site_type_symbol +_atom_site_occupancy +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +_atom_site_adp_type +_atom_site_U_iso_or_equiv +Si1 Si 1.0 0.0819 0.5118 0.65958 Uiso 0.0018421 +Si2 Si 1.0 0.25323 0.16763 0.4509 Uiso 0.003458 +N1 N 1.0 0.65512 0.61058 0.43269 Uiso 0.00484863 +N2 N 1.0 0.31514 0.31865 0.69801 Uiso 0.00501808 +N3 N 1.0 0.33333333 0.66666667 0.60394 Uiso 0.00490371 +N4 N 1.0 0.0 0.0 0.45292 Uiso 0.00487042 diff --git a/easyDiffractionApp/Gui/Resources/Examples/Si3N4/samples/Si3N4_beta.cif b/easyDiffractionApp/Gui/Resources/Examples/Si3N4/samples/Si3N4_beta.cif index 3d0be16d..8815502f 100644 --- a/easyDiffractionApp/Gui/Resources/Examples/Si3N4/samples/Si3N4_beta.cif +++ b/easyDiffractionApp/Gui/Resources/Examples/Si3N4/samples/Si3N4_beta.cif @@ -1,23 +1,22 @@ data_Si3N4_beta -_space_group_name_H-M_alt 'P 63/m' - -_cell_length_a 7.605376 -_cell_length_b 7.605376 -_cell_length_c 2.907065 -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 120.0 +_cell_length_a 7.60375657 +_cell_length_b 7.60375657 +_cell_length_c 2.9066949 +_cell_angle_alpha 90.0 +_cell_angle_beta 90.0 +_cell_angle_gamma 120.0 +_space_group_name_H-M_alt 'P 63/m' loop_ - _atom_site_label - _atom_site_type_symbol - _atom_site_occupancy - _atom_site_fract_x - _atom_site_fract_y - _atom_site_fract_z - _atom_site_adp_type - _atom_site_U_iso_or_equiv - Si Si 1.0 0.17522 0.76977 0.25000 Uiso 0.01 - N1 N 1.0 0.33131 0.03120 0.25000 Uiso 0.01 - N2 N 1.0 0.33333 0.66667 0.25000 Uiso 0.01 +_atom_site_label +_atom_site_type_symbol +_atom_site_occupancy +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +_atom_site_adp_type +_atom_site_U_iso_or_equiv +Si Si 1.0 0.17522 0.76977 0.25 Uiso 0.00301531 +N1 N 1.0 0.33131 0.0312 0.25 Uiso 0.00660646 +N2 N 1.0 0.33333333 0.66666667 0.25 Uiso 0.01067827 diff --git a/easyDiffractionApp/Logic/Background.py b/easyDiffractionApp/Logic/Background.py index 2fffda3b..2f8c18d5 100644 --- a/easyDiffractionApp/Logic/Background.py +++ b/easyDiffractionApp/Logic/Background.py @@ -6,7 +6,7 @@ from dicttoxml import dicttoxml from PySide2.QtCore import QObject, Signal -from easyDiffractionLib.Elements.Backgrounds.Point import PointBackground, BackgroundPoint +from easyDiffractionLib.elements.Backgrounds.Point import PointBackground, BackgroundPoint class BackgroundLogic(QObject): @@ -86,19 +86,33 @@ def initializeContainer(self, experiment_name: str = 'current_exp', container_ty ) self._background_as_obj = self._background_obj() - def addPoint(self): - print(f"+ addBackgroundPoint") + def addPoint(self, x: float, y: float, silently: bool = False): + print(f"+ add background point ({x}, {y})") if self._background_as_obj is None: # TODO THIS IS NOT HOW TO DO THINGS!!! self.initializeContainer() - x = 0.0 - y = 100.0 - if self._background_as_obj.x_sorted_points.size: - x = self._background_as_obj.x_sorted_points[-1] + 10.0 point = BackgroundPoint.from_pars(x=x, y=y) self._background_as_obj.append(point) + if not silently: + self.asObjChanged.emit(self._background_as_obj) + + def addPoints(self, xarray, yarray): + if self._background_as_obj is None: + self.initializeContainer() + for x, y in zip(xarray, yarray): + print(f"+ add background point ({x}, {y})") + point = BackgroundPoint.from_pars(x=x, y=y) + self._background_as_obj.append(point) self.asObjChanged.emit(self._background_as_obj) + def addDefaultPoint(self): + print(f"+ add default background point") + x = 0.0 + y = 100.0 + if self._background_as_obj is not None and self._background_as_obj.x_sorted_points.size: + x = self._background_as_obj.x_sorted_points[-1] + 10.0 + self.addPoint(x, y) + def removePoint(self, point_name: str): print(f"+ removeBackgroundPoint for point_name: {point_name}") point_names = self._background_as_obj.names diff --git a/easyDiffractionApp/Logic/DataStore.py b/easyDiffractionApp/Logic/DataStore.py index 2e461ab5..858e4117 100644 --- a/easyDiffractionApp/Logic/DataStore.py +++ b/easyDiffractionApp/Logic/DataStore.py @@ -74,7 +74,9 @@ class DataSet1D(MSONable): def __init__(self, name: str = 'Series', x: Union[np.ndarray, list] = None, y: Union[np.ndarray, list] = None, + yb: Union[np.ndarray, list] = None, e: Union[np.ndarray, list] = None, + eb: Union[np.ndarray, list] = None, data_type: str = 'simulation', x_label: str = 'x', y_label: str = 'y'): @@ -87,19 +89,22 @@ def __init__(self, name: str = 'Series', if x is None: x = np.array([]) if y is None: - y = np.array([]) + y = yb = np.array([]) if e is None: - e = np.zeros_like(x) + e = eb = np.zeros_like(x) self.name = name if not isinstance(x, np.ndarray): x = np.array(x) if not isinstance(y, np.ndarray): y = np.array(y) + yb = np.array(yb) self.x = x self.y = y + self.yb = yb self.e = e + self.eb = eb self.x_label = x_label self.y_label = y_label diff --git a/easyDiffractionApp/Logic/Experiment.py b/easyDiffractionApp/Logic/Experiment.py index 52fc15b9..ef942d81 100644 --- a/easyDiffractionApp/Logic/Experiment.py +++ b/easyDiffractionApp/Logic/Experiment.py @@ -5,6 +5,8 @@ # noqa: E501 from dicttoxml import dicttoxml +from gemmi import cif +import numpy as np import pathlib import json @@ -24,11 +26,11 @@ class ExperimentLogic(QObject): patternParametersAsObjChanged = Signal() clearFrontendState = Signal() - def __init__(self, parent=None): + def __init__(self, parent=None, interface=None): super().__init__(parent) self.parent = parent self.state = parent.l_parameters - + self._interface = interface self._experiment_parameters = None self._experiment_data_as_xml = "" self.experiment_data = None @@ -37,6 +39,13 @@ def __init__(self, parent=None): self._experiment_skipped = False self.experiments = self._defaultExperiments() self.clearFrontendState.connect(self.onClearFrontendState) + self.spin_polarized = False + self._current_spin_component = 'Sum' + self._refine_sum = True + self._refine_diff = True + self._refine_up = False + self._refine_down = False + self.fn_aggregate = self.pol_sum def _defaultExperiment(self): return { @@ -44,11 +53,102 @@ def _defaultExperiment(self): "color": "#00a3e3" } + def _loadExperimentCif(self, file_url): + print("+ _loadExperimentCif") + file_path = generalizePath(file_url) + block = cif.read(file_path).sole_block() + + # Get experiment type + # Set default experiment type: powder1DCWunp + self.parent.l_sample.experimentType = 'powder1DCWunp' + # Check if powder1DCWpol + value = block.find_value("_diffrn_radiation_polarization") + if value is not None: + self.parent.l_sample.experimentType = 'powder1DCWpol' + # Check if powder1DTOFunp + # ... + # Check if powder1DTOFpol + # ... + + # Get diffraction radiation parameters + pattern_parameters = self.parent.l_sample._sample.pattern + value = block.find_value("_diffrn_radiation_polarization") + if value is not None: + pattern_parameters.beam.polarization = float(value) + value = block.find_value("_diffrn_radiation_efficiency") + if value is not None: + pattern_parameters.beam.efficiency = float(value) + + # Get pattern parameters + pattern_parameters = self.parent.l_sample._sample.pattern + value = block.find_value("_setup_offset_2theta") + if value is not None: + pattern_parameters.zero_shift = float(value) + value = block.find_value("_setup_field") + if value is not None: + pattern_parameters.field = float(value) + + # Get instrumental parameters + instrument_parameters = self.parent.l_sample._sample.parameters + value = block.find_value("_setup_wavelength") + if value is not None: + instrument_parameters.wavelength = float(value) + value = block.find_value("_pd_instr_resolution_u") + if value is not None: + instrument_parameters.resolution_u = float(value) + value = block.find_value("_pd_instr_resolution_v") + if value is not None: + instrument_parameters.resolution_v = float(value) + value = block.find_value("_pd_instr_resolution_w") + if value is not None: + instrument_parameters.resolution_w = float(value) + value = block.find_value("_pd_instr_resolution_x") + if value is not None: + instrument_parameters.resolution_x = float(value) + value = block.find_value("_pd_instr_resolution_y") + if value is not None: + instrument_parameters.resolution_y = float(value) + + # Get phase parameters + sample_phase_labels = self.parent.l_phase.phases.phase_names + experiment_phase_labels = list(block.find_loop("_phase_label")) + experiment_phase_scales = np.fromiter(block.find_loop("_phase_scale"), float) + for (phase_label, phase_scale) in zip(experiment_phase_labels, experiment_phase_scales): + if phase_label in sample_phase_labels: + self.parent.l_phase.phases[phase_label].scale = phase_scale + + # Get data + data = self.state._data.experiments[0] + # Polarized case + data.x = np.fromiter(block.find_loop("_pd_meas_2theta"), float) + data.y = np.fromiter(block.find_loop("_pd_meas_intensity_up"), float) + data.e = np.fromiter(block.find_loop("_pd_meas_intensity_up_sigma"), float) + data.yb = np.fromiter(block.find_loop("_pd_meas_intensity_down"), float) + data.eb = np.fromiter(block.find_loop("_pd_meas_intensity_down_sigma"), float) + self.spin_polarized = True + # Unpolarized case + if not np.any(data.y): + data.x = np.fromiter(block.find_loop("_pd_meas_2theta"), float) + data.y = np.fromiter(block.find_loop("_pd_meas_intensity"), float) + data.e = np.fromiter(block.find_loop("_pd_meas_intensity_sigma"), float) + data.yb = np.zeros(len(data.y)) + data.eb = np.zeros(len(data.e)) + self.spin_polarized = False + self.setPolarized(self.spin_polarized) + return data + def _loadExperimentData(self, file_url): print("+ _loadExperimentData") file_path = generalizePath(file_url) data = self.state._data.experiments[0] - data.x, data.y, data.e = np.loadtxt(file_path, unpack=True) + try: + data.x, data.y, data.e, data.yb, data.eb = np.loadtxt(file_path, unpack=True) + self.setPolarized(True) + except Exception as e: + data.x, data.y, data.e = np.loadtxt(file_path, unpack=True) + data.yb = np.zeros(len(data.y)) + data.eb = np.zeros(len(data.e)) + self.setPolarized(False) return data def _experimentDataParameters(self, data): @@ -62,12 +162,40 @@ def _experimentDataParameters(self, data): } return parameters - def experimentDataXYZ(self): - return (self._experiment_data.x, self._experiment_data.y, self._experiment_data.e) # noqa: E501 - def _defaultExperiments(self): return [] + def refinement(self): + return {"sum": self._refine_sum, "diff": self._refine_diff, "up": self._refine_up, "down": self._refine_down} + + def refinement_methods(self): + return {self.pol_sum: self._refine_sum, self.pol_diff: self._refine_diff, self.pol_up: self._refine_up, self.pol_down: self._refine_down} + + def setPolarized(self, polarized: bool): + if self.spin_polarized == polarized: + return False + current_type = self.parent.l_sample.experimentType + if 'TOF' in current_type: + return False # no polarized for TOF + + self.spin_polarized = polarized + if polarized: + if 'unp' in current_type: + current_type = current_type.replace('unp', 'pol') + elif 'pol' in current_type: + return False # no change + else: + # old style unpolarized + current_type = current_type + "pol" + else: + if 'pol' in current_type: + current_type = current_type.replace('pol', 'unp') + + self.parent.l_sample.experimentType = current_type + # need to recalculate the profile + self.state._updateCalculatedData() + return True + def experimentLoaded(self, loaded: bool): if self._experiment_loaded == loaded: return @@ -86,6 +214,15 @@ def experimentDataAsObj(self): def _setExperimentDataAsXml(self): self._experiment_data_as_xml = dicttoxml(self.experiments, attr_type=True).decode() # noqa: E501 + def addExperimentDataFromCif(self, file_url): + self._experiment_data = self._loadExperimentCif(file_url) + self.state._data.experiments[0].name = pathlib.Path(file_url).stem + self.experiments = [{'name': experiment.name} for experiment in self.state._data.experiments] + self.experimentLoaded(True) + self.experimentSkipped(False) + # need to update parameters in all the places. + self.parent.l_phase.structureParametersChanged.emit() + def addExperimentDataFromXye(self, file_url): self._experiment_data = self._loadExperimentData(file_url) self.state._data.experiments[0].name = pathlib.Path(file_url).stem @@ -93,11 +230,24 @@ def addExperimentDataFromXye(self, file_url): self.experimentLoaded(True) self.experimentSkipped(False) + def addBackgroundDataFromCif(self, file_url): + file_path = generalizePath(file_url) + block = cif.read(file_path).sole_block() + # Get background + background_2thetas = np.fromiter(block.find_loop("_pd_background_2theta"), float) + background_intensities = np.fromiter(block.find_loop("_pd_background_intensity"), float) + self.parent.l_background.addPoints(background_2thetas, background_intensities) + self.parent.l_background._setAsXml() + self.parent.l_plotting1d.bokehBackgroundDataObjChanged.emit() + def removeExperiment(self): if len(self.parent.l_sample._sample.pattern.backgrounds) > 0: self.parent.l_background.removeAllPoints() self.parent.l_fitting.removeAllConstraints() + self.setPolarized(False) + self._current_spin_component = 'Sum' self.experiments.clear() + self._experiment_data = None self.experimentLoaded(False) self.experimentSkipped(False) @@ -110,12 +260,23 @@ def _onExperimentLoadedChanged(self): def setCurrentExperimentDatasetName(self, name): self.parent.l_phase.setCurrentExperimentDatasetName(name) + def initializeBackground(self): + self.parent.l_plotting1d.setMeasuredData( + self._experiment_data.x, + self._experiment_data.y + self._experiment_data.yb, + self._experiment_data.e + self._experiment_data.eb) + + self.parent.proxy.parameters.simulationParametersAsObj = \ + json.dumps(self._experiment_parameters) + self.parent.l_background.initializeContainer() + def _onExperimentDataAdded(self): print("***** _onExperimentDataAdded") + # default settings are up+down self.parent.l_plotting1d.setMeasuredData( self._experiment_data.x, - self._experiment_data.y, - self._experiment_data.e) + self._experiment_data.y + self._experiment_data.yb, + self._experiment_data.e + self._experiment_data.eb) self._experiment_parameters = \ self._experimentDataParameters(self._experiment_data) @@ -136,4 +297,103 @@ def _onPatternParametersChanged(self): self.patternParametersAsObjChanged.emit() def onClearFrontendState(self): - self.parent.l_plotting1d.clearFrontendState() \ No newline at end of file + self.parent.l_plotting1d.clearFrontendState() + + def spinComponent(self): + return self._current_spin_component + + @staticmethod + def pol_sum(a, b): + return a + b + + @staticmethod + def pol_diff(a, b): + return a - b + + @staticmethod + def pol_up(a, b): + return a + + @staticmethod + def pol_down(a, b): + return b + + def setSpinComponent(self, component=None): + if self._current_spin_component == component: + return False + if component is not None: + self._current_spin_component = component + + phase_label = self.parent.l_phase.phases.phase_names[0] + components = self._interface.get_phase_components(phase_label) + calc_y = components['components']['up'] + calc_yb = components['components']['down'] + bg = self._interface.get_component('f_background') * 2.0 + + self.fn_aggregate = self.pol_sum + has_experiment = self._experiment_data is not None + if self._current_spin_component == 'Sum': + if has_experiment: + y = self._experiment_data.y + self._experiment_data.yb + e = self._experiment_data.e + self._experiment_data.eb + sim_y = calc_y + calc_yb + bg + self.fn_aggregate = self.pol_sum + elif self._current_spin_component == 'Difference': + if has_experiment: + y = self._experiment_data.y - self._experiment_data.yb + e = self._experiment_data.e + self._experiment_data.eb + bg = np.zeros_like(bg) + sim_y = calc_y - calc_yb + self.fn_aggregate = self.pol_diff + elif self._current_spin_component == 'Up': + if has_experiment: + y = self._experiment_data.y + e = self._experiment_data.e + bg = bg / 2 + sim_y = calc_y + bg + self.fn_aggregate = self.pol_up + elif self._current_spin_component == 'Down': + if has_experiment: + y = self._experiment_data.yb + e = self._experiment_data.eb + bg = bg / 2 + sim_y = calc_yb + bg + self.fn_aggregate = self.pol_down + else: + return False + + if has_experiment: + sim_x = self._experiment_data.x + else: + sim_x = self.state.sim_x() + self.parent.l_plotting1d.setBackgroundData(sim_x, bg) + if has_experiment: + self.parent.l_plotting1d.setMeasuredData(self._experiment_data.x, y, e) + + self.parent.l_plotting1d.setCalculatedData(sim_x, sim_y) + + return has_experiment + + def refineSum(self): + return self._refine_sum + + def setRefineSum(self, value): + self._refine_sum = value + + def refineDiff(self): + return self._refine_diff + + def setRefineDiff(self, value): + self._refine_diff = value + + def refineUp(self): + return self._refine_up + + def setRefineUp(self, value): + self._refine_up = value + + def refineDown(self): + return self._refine_down + + def setRefineDown(self, value): + self._refine_down = value diff --git a/easyDiffractionApp/Logic/Fitting.py b/easyDiffractionApp/Logic/Fitting.py index ddc29115..84756546 100644 --- a/easyDiffractionApp/Logic/Fitting.py +++ b/easyDiffractionApp/Logic/Fitting.py @@ -4,8 +4,11 @@ from PySide2.QtCore import Signal, QObject, QThread +import numpy as np + from threading import Thread +from easyDiffractionLib.interface import InterfaceFactory as Calculator from easyCore.Fitting.Fitting import Fitter as CoreFitter from easyCore.Fitting.Constraints import ObjConstraint, NumericConstraint @@ -56,7 +59,7 @@ def __init__(self, parent=None, interface=None): self.finished.connect(self.onSuccess) self.failed.connect(self.onFailed) - def fit_threading(self): + def fit_nonpolar(self): data = self.data method = self._current_minimizer_method_name @@ -72,15 +75,65 @@ def fit_threading(self): 'weights': weights, 'method': method } + + local_kwargs = {} if method == 'least_squares': kwargs['minimizer_kwargs'] = {'diff_step': 1e-5} + + # save some kwargs on the interface object for use in the calculator + self.interface._InterfaceFactoryTemplate__interface_obj.saved_kwargs = local_kwargs try: res = self.fitter.fit(x, y, **kwargs) + except Exception as ex: self.failed.emit(str(ex)) return self.finished.emit(res) + def fit_polar(self): + data = self.data + method = self._current_minimizer_method_name + self._fit_finished = False + self.fitStarted.emit() + exp_data = data.experiments[0] + x = exp_data.x + + refinement = self.parent.l_experiment.refinement_methods() + targets = [component for component in refinement if refinement[component]] + try: + x_, y_, fit_func = self.interface().generate_pol_fit_func(x, exp_data.y, exp_data.yb, targets) + except Exception as ex: + raise NotImplementedError('This is not implemented for this calculator yet') + weights = 1/exp_data.e + weights = np.tile(weights, len(targets)) + + kwargs = { + 'weights': weights, + 'method': method + } + + local_kwargs = {} + if method == 'least_squares': + kwargs['minimizer_kwargs'] = {'diff_step': 1e-5} + + # save some kwargs on the interface object for use in the calculator + # TODO FIX THIS THIS IS NOT THE WAY TO DO IT :-/ + self.interface._InterfaceFactoryTemplate__interface_obj.saved_kwargs = local_kwargs + try: + obj = self.fitter.fit_object + fitter = CoreFitter(obj, fit_func) + res = fitter.fit(x_, y_, **kwargs) + except Exception as ex: + self.failed.emit(str(ex)) + return + self.finished.emit(res) + + def fit_threading(self): + if self.parent.l_experiment.spin_polarized: + self.fit_polar() + else: + self.fit_nonpolar() + def setFailedFitResults(self): self._fit_results = _defaultFitResults() self._fit_results['success'] = 'Failure' # not None but a string @@ -114,6 +167,9 @@ def joinFitThread(self): def finishFit(self): self._fit_finished = True self.fitFinished.emit() + # TODO: remove once background is correctly implemented in polarized + if self.parent.l_experiment.spin_polarized: + self.parent.l_experiment.setSpinComponent() # must re-instantiate the thread object self.fit_thread = Thread(target=self.fit_threading) @@ -199,6 +255,7 @@ def setCurrentCalculatorIndex(self, new_index: int): self.interface.switch(new_name) # recreate the fitter object with the new interface self.fitter = CoreFitter(self.parent.l_sample._sample, self.interface.fit_func) + self.parent.l_sample._sample.update_bindings() self.currentCalculatorChanged.emit() print("***** _onCurrentCalculatorChanged") diff --git a/easyDiffractionApp/Logic/LogicController.py b/easyDiffractionApp/Logic/LogicController.py index 6d23ebbc..4f88077a 100644 --- a/easyDiffractionApp/Logic/LogicController.py +++ b/easyDiffractionApp/Logic/LogicController.py @@ -40,7 +40,7 @@ def __init__(self, parent): def initializeLogics(self): self.l_state = StateLogic(self, interface=self.interface) self.l_parameters = ParametersLogic(self, interface=self.interface) - self.l_experiment = ExperimentLogic(self) + self.l_experiment = ExperimentLogic(self, interface=self.interface) self.l_phase = PhaseLogic(self, interface=self.interface) self.l_sample = SampleLogic(self, interface=self.interface) self.l_fitting = FittingLogic(self, interface=self.interface) diff --git a/easyDiffractionApp/Logic/Parameters.py b/easyDiffractionApp/Logic/Parameters.py index 98975a44..073425ab 100644 --- a/easyDiffractionApp/Logic/Parameters.py +++ b/easyDiffractionApp/Logic/Parameters.py @@ -16,7 +16,6 @@ from easyDiffractionApp.Logic.DataStore import DataSet1D, DataStore - class ParametersLogic(QObject): """ """ @@ -69,24 +68,33 @@ def _defaultData(self): data.append( DataSet1D( name='PND', - x=x_data, y=np.zeros_like(x_data), - x_label='2theta (deg)', y_label='Intensity', + x=x_data, + y=np.zeros_like(x_data), + yb=np.zeros_like(x_data), + x_label='2theta (deg)', + y_label='Intensity', data_type='experiment' ) ) data.append( DataSet1D( name='{:s} engine'.format(self._interface_name), - x=x_data, y=np.zeros_like(x_data), - x_label='2theta (deg)', y_label='Intensity', + x=x_data, + y=np.zeros_like(x_data), + yb=np.zeros_like(x_data), + x_label='2theta (deg)', + y_label='Intensity', data_type='simulation' ) ) data.append( DataSet1D( name='Difference', - x=x_data, y=np.zeros_like(x_data), - x_label='2theta (deg)', y_label='Difference', + x=x_data, + y=np.zeros_like(x_data), + yb=np.zeros_like(x_data), + x_label='2theta (deg)', + y_label='Difference', data_type='simulation' ) ) @@ -106,7 +114,8 @@ def simulationParametersAsObj(self, json_str): def _defaultPatternParameters(self): return { "scale": 1.0, - "zero_shift": 0.0 + "zero_shift": 0.0, + "field": 0.0 } def _setPatternParametersAsObj(self): @@ -124,7 +133,7 @@ def _defaultInstrumentParameters(self): "resolution_v": -0.01, "resolution_w": 0.01, "resolution_x": 0.0, - "resolution_y": 0.0 + "resolution_y": 0.0, } def _setInstrumentParametersAsObj(self): @@ -153,6 +162,7 @@ def _setIconifiedLabels(self): # Modify current label label = label.replace(".background.", ".") label = label.replace("Uiso.Uiso", "Uiso") + label = label.replace("Ciso.chi_11", "Ciso") label = label.replace("fract_", "fract.") label = label.replace("length_", "length.") label = label.replace("angle_", "angle.") @@ -161,6 +171,7 @@ def _setIconifiedLabels(self): # Modify previous label previousLabel = previousLabel.replace(".background.", ".") previousLabel = previousLabel.replace("Uiso.Uiso", "Uiso") + previousLabel = previousLabel.replace("Ciso.chi_11", "Ciso") previousLabel = previousLabel.replace("fract_", "fract.") previousLabel = previousLabel.replace("length_", "length.") previousLabel = previousLabel.replace("angle_", "angle.") @@ -191,6 +202,7 @@ def _setIconifiedLabels(self): list[i] = list[i].replace("angle", f'less-than') list[i] = list[i].replace("atoms", f'atom') list[i] = list[i].replace("adp", f'arrows-alt') + list[i] = list[i].replace("msp", f'arrows-alt') list[i] = list[i].replace("fract", f'map-marker-alt') list[i] = list[i].replace("resolution", f'grip-lines-vertical') list[i] = list[i].replace("point_background", f'wave-square') @@ -200,6 +212,7 @@ def _setIconifiedLabels(self): list[i] = list[i].replace("angle", f'less-than') list[i] = list[i].replace("atoms", f'atom') list[i] = list[i].replace("adp", f'arrows-alt') + list[i] = list[i].replace("msp", f'arrows-alt') list[i] = list[i].replace("fract", f'map-marker-alt') list[i] = list[i].replace("resolution", f'grip-lines-vertical') list[i] = list[i].replace("point_background", f'wave-square') @@ -231,8 +244,10 @@ def _setParametersAsObj(self): continue # rename some groups of parameters and add experimental dataset name + par_path = par_path.replace('Instrument1DCWPolParameters.', f'Instrument.{self.parent.l_experiment.experimentDataAsObj()[0]["name"]}.') par_path = par_path.replace('Instrument1DCWParameters.', f'Instrument.{self.parent.l_experiment.experimentDataAsObj()[0]["name"]}.') par_path = par_path.replace('Instrument1DTOFParameters.', f'Instrument.{self.parent.l_experiment.experimentDataAsObj()[0]["name"]}.') + par_path = par_path.replace('PolPowder1DParameters.', f'Instrument.{self.parent.l_experiment.experimentDataAsObj()[0]["name"]}.') par_path = par_path.replace('Powder1DParameters.', f'Instrument.{self.parent.l_experiment.experimentDataAsObj()[0]["name"]}.') par_path = par_path.replace('.sigma0', '.resolution_sigma0') par_path = par_path.replace('.sigma1', '.resolution_sigma1') @@ -312,6 +327,19 @@ def _parameterObj(self, obj_id: str): obj = borg.map.get_item_by_key(obj_id) return obj + def sim_x(self): + """ + Rerurn the x-axis of the simulated data. + """ + params = self._simulation_parameters_as_obj + x_min = float(params['x_min']) + x_max = float(params['x_max']) + x_step = float(params['x_step']) + num_points = int((x_max - x_min) / x_step + 1) + simx = np.linspace(x_min, x_max, num_points) + return simx + + #################################################################################################################### # Calculated data #################################################################################################################### @@ -329,15 +357,20 @@ def _updateCalculatedData(self): sim.x = exp.x elif self.parent.l_experiment._experiment_skipped: - params = self._simulation_parameters_as_obj - x_min = float(params['x_min']) - x_max = float(params['x_max']) - x_step = float(params['x_step']) - num_points = int((x_max - x_min) / x_step + 1) - sim.x = np.linspace(x_min, x_max, num_points) - - sim.y = self._interface.fit_func(sim.x) - self.plotCalculatedDataSignal.emit((sim.x, sim.y)) + sim.x = self.sim_x() + + kwargs = {} + if self.parent.l_experiment.spin_polarized: + fn = self.parent.l_experiment.fn_aggregate + kwargs["pol_fn"] = fn + # save some kwargs on the interface object for use in the calculator + # self._interface._InterfaceFactoryTemplate__interface_obj.saved_kwargs = local_kwargs + + sim.y = self._interface.fit_func(sim.x, **kwargs) + if self.parent.l_experiment.spin_polarized: + self.parent.l_experiment.setSpinComponent() + else: + self.plotCalculatedDataSignal.emit((sim.x, sim.y)) for phase_index, phase_name in enumerate([str(phase._borg.map.convert_id(phase).int) for phase in self.parent.l_phase.phases]): hkl = self._interface.get_hkl(x_array=sim.x, phase_name=phase_name, encoded_name=True) @@ -346,19 +379,18 @@ def _updateCalculatedData(self): if 'time' in hkl.keys(): self.plotBraggDataSignal.emit((phase_index, hkl['time'], hkl['h'], hkl['k'], hkl['l'])) # noqa: E501 - def defaultSimulationParams(exp_type='powder1DCW', jsonify=True): - if exp_type == 'powder1DCW': + if 'powder1DCW' in exp_type: params = { - 'x_min': 10, - 'x_max': 120, + 'x_min': 20, + 'x_max': 140, 'x_step': 0.1 } - elif exp_type == 'powder1DTOF': + elif 'powder1DTOF' in exp_type: params = { 'x_min': 5000, - 'x_max': 60000, - 'x_step': 50 + 'x_max': 17000, + 'x_step': 10 } else: raise AttributeError('Unknown Experiment type') diff --git a/easyDiffractionApp/Logic/Phase.py b/easyDiffractionApp/Logic/Phase.py index f5a1d9a0..7e57efe4 100644 --- a/easyDiffractionApp/Logic/Phase.py +++ b/easyDiffractionApp/Logic/Phase.py @@ -10,6 +10,8 @@ from easyCore import np, borg from easyDiffractionLib import Phases, Phase, Lattice, Site, SpaceGroup +from easyCrystallography.Components.AtomicDisplacement import AtomicDisplacement +from easyCrystallography.Components.Susceptibility import MagneticSusceptibility from easyCrystallography.Symmetry.tools import SpacegroupInfo from easyApp.Logic.Utils.Utils import generalizePath @@ -30,11 +32,12 @@ def __init__(self, parent=None, interface=None): self.parent = parent self._interface = interface self.state = parent.l_parameters - self.phases = Phases(interface=interface) + self.phases = Phases() self._phases_as_obj = [] self._phases_as_xml = "" self._phases_as_cif = "" self._current_phase_index = 0 + self.has_msp = False #################################################################################################################### #################################################################################################################### @@ -71,17 +74,17 @@ def addDefaultPhase(self): idx = known_phases.count(default_phase.name) default_phase.name = default_phase.name + str(idx) # print('Disabling scale') - # default_phase.scale.enabled = False + default_phase.scale.fixed = True self.phases.append(default_phase) borg.stack.enabled = True @staticmethod def _defaultPhase(): - space_group = SpaceGroup.from_pars('P 42/n c m') - cell = Lattice.from_pars(8.56, 8.56, 6.12, 90, 90, 90) - atom = Site.from_pars(label='Cl1', specie='Cl', fract_x=0.125, fract_y=0.167, fract_z=0.107) # noqa: E501 - atom.add_adp('Uiso', Uiso=0.0) - phase = Phase('Dichlorine', spacegroup=space_group, cell=cell) + space_group = SpaceGroup.from_pars('F d -3:2') + cell = Lattice.from_pars(5.0, 3.0, 4.0, 90, 90, 90) + adp = AtomicDisplacement("Uiso") + atom = Site(label='O', specie='O', fract_x=0.0, fract_y=0.0, fract_z=0.0, adp=adp) + phase = Phase('Test', spacegroup=space_group, cell=cell) phase.add_atom(atom) return phase @@ -140,6 +143,7 @@ def _setCurrentSpaceGroup(self, new_name: str): if phases[self._current_phase_index].spacegroup.space_group_HM_name == new_name: # noqa: E501 return phases[self._current_phase_index].spacegroup.space_group_HM_name = new_name # noqa: E501 + self._updateCalculatedData() def updateParameters(self): self.parent.parametersChanged.emit() @@ -228,12 +232,15 @@ def setCurrentSpaceGroupSetting(self, new_number: int): def addDefaultAtom(self): index = len(self.phases[0].atoms.atom_labels) + 1 label = f'Label{index}' - atom = Site.from_pars(label=label, - specie='O', - fract_x=0.05, - fract_y=0.05, - fract_z=0.05) - atom.add_adp('Uiso', Uiso=0.0) + adp = AtomicDisplacement("Uiso") + msp = MagneticSusceptibility("Ciso") + atom = Site(label=label, + specie='Cl', + fract_x=0.5, + fract_y=0.5, + fract_z=0.5, + adp=adp, + msp=msp) self.phases[self._current_phase_index].add_atom(atom) self.updateParameters() @@ -255,15 +262,20 @@ def addSampleFromCif(self, cif_url): phases = Phases.from_cif_file(cif_path) self.phases.interface = self._interface for phase in phases: - # print('Disabling scale') - # phase.scale.enabled = False + phase.scale.fixed = True self.phases.append(phase) + # see if MSP is present (or just default) + msps = [hasattr(atom, 'msp') for atom in phase.atoms] # noqa: E501 + self.has_msp = any(msps) self.phasesReplaced.emit() borg.stack.enabled = True def getCurrentPhaseName(self): return self.phases[self._current_phase_index].name + def hasMsp(self): + return self.has_msp + def setCurrentPhaseName(self, name): if self.phases[self._current_phase_index].name == name: return diff --git a/easyDiffractionApp/Logic/Plotting1d.py b/easyDiffractionApp/Logic/Plotting1d.py index cbf4363e..1c96d768 100644 --- a/easyDiffractionApp/Logic/Plotting1d.py +++ b/easyDiffractionApp/Logic/Plotting1d.py @@ -216,7 +216,10 @@ def setBackgroundData(self, xarray, yarray): if not xarray.size: return interp_func = scipy.interpolate.interp1d(xarray, yarray, fill_value="extrapolate") - self._setBackgroundDataArrays(self._measured_xarray, interp_func(self._measured_xarray)) + extrapolated_y = interp_func(self._measured_xarray) + if len(extrapolated_y) == 0: + return + self._setBackgroundDataArrays(self._measured_xarray, extrapolated_y) self._setBokehBackgroundDataObj() self._setBokehPhasesDataObj() if self.currentLib == 'qtcharts': @@ -305,8 +308,24 @@ def _setBokehPhasesDataObj(self): for phase_index in range(len(self.parent.l_phase.phases)): # skip this step with try-except block until instrumental parameters are defined/loaded try: - yarray = self._interface.get_calculated_y_for_phase(phase_index) - if self._background_yarray.size: + if not self.parent.l_experiment.spin_polarized: + yarray = self._interface.get_calculated_y_for_phase(phase_index) + is_diff = False + else: + phases_y = list(self._interface.get_component('phases').values())[phase_index] + component = self.parent.l_experiment.spinComponent() + is_diff = False + if component == "Sum": + yarray = phases_y["components"]["up"] + phases_y["components"]["down"] + elif component == "Difference": + yarray = phases_y["components"]["up"] - phases_y["components"]["down"] + is_diff = True + elif component == "Up": + yarray = phases_y["components"]["up"] + elif component == "Down": + yarray = phases_y["components"]["down"] + + if self._background_yarray.size and not is_diff: self._bokeh_phases_data_obj[f'{phase_index}'] = { 'x': Plotting1dLogic.aroundX(self._calculated_xarray), 'y_upper': Plotting1dLogic.aroundY(yarray + self._background_yarray), diff --git a/easyDiffractionApp/Logic/Project.py b/easyDiffractionApp/Logic/Project.py index 4ac36c0a..7b8fde4e 100644 --- a/easyDiffractionApp/Logic/Project.py +++ b/easyDiffractionApp/Logic/Project.py @@ -41,9 +41,10 @@ def __init__(self, parent=None , interface=None): self._project_info = self._defaultProjectInfo() self._project_created = False self._state_changed = False + self._read_only = False self._report = "" - self._currentProjectPath = os.path.expanduser("~") + self._currentProjectPath = os.path.join(os.path.expanduser("~"), 'TestProject') #################################################################################################################### #################################################################################################################### @@ -93,18 +94,22 @@ def _defaultProjectInfo(self): def projectExamplesAsXml(self): model = [ - {"name": "PbSO4", "description": "neutrons, powder, constant wavelength, 1D, D1@ILL", + {"name": "PbSO4", "description": "neutrons, powder, constant wavelength, D1A@ILL", "path": "../Resources/Examples/PbSO4/project.json"}, - {"name": "Co2SiO4", "description": "neutrons, powder, constant wavelength, 1D, D20@ILL", + {"name": "Co2SiO4", "description": "neutrons, powder, constant wavelength, D20@ILL", "path": "../Resources/Examples/Co2SiO4/project.json"}, - {"name": "Dy3Al5O12", "description": "neutrons, powder, constant wavelength, 1D, G41@LLB", + {"name": "Dy3Al5O12", "description": "neutrons, powder, constant wavelength, G41@LLB", "path": "../Resources/Examples/Dy3Al5O12/project.json"}, - {"name": "CeCuAl3", "description": "neutrons, powder, time-of-flight, 1D, Polaris@ISIS", + {"name": "CeCuAl3", "description": "neutrons, powder, time-of-flight, Polaris@ISIS", "path": "../Resources/Examples/CeCuAl3/project.json"}, - {"name": "Na2Ca3Al2F14", "description": "neutrons, powder, time-of-flight, 1D, Osiris@ISIS", + {"name": "Na2Ca3Al2F14", "description": "neutrons, powder, time-of-flight, Osiris@ISIS", "path": "../Resources/Examples/Na2Ca3Al2F14/project.json"}, - {"name": "Si3N4", "description": "neutrons, powder, multi-phase, 1D, 3T2@LLB", - "path": "../Resources/Examples/Si3N4/project.json"} + {"name": "Si3N4", "description": "neutrons, powder, constant wavelength, multi-phase, 3T2@LLB", + "path": "../Resources/Examples/Si3N4/project.json"}, + {"name": "Fe3O4", "description": "neutrons, powder, constant wavelength, polarised, 6T2@LLB", + "path": "../Resources/Examples/Fe3O4/project.json"}, + {"name": "Ho2Ti2O7", "description": "neutrons, powder, constant wavelength, polarised, VIP@LLB", + "path": "../Resources/Examples/Ho2Ti2O7/project.json"} ] xml = dicttoxml(model, attr_type=False) xml = xml.decode() @@ -192,8 +197,12 @@ def _loadProject(self): # send signal to tell the proxy we changed phases self.phasesEnabled.emit() self.phasesAsObjChanged.emit() - # self.structureParametersChanged.emit() - self.parent.l_background._setAsXml() + + # project info + self._project_info = descr['project_info'] + + # read only flag + self._read_only = descr['read_only'] # experiment if 'experiments' in descr: @@ -202,15 +211,25 @@ def _loadProject(self): self.parent.l_parameters._data.experiments[0].x = np.array(descr['experiments'][0]) self.parent.l_parameters._data.experiments[0].y = np.array(descr['experiments'][1]) self.parent.l_parameters._data.experiments[0].e = np.array(descr['experiments'][2]) + if(len(descr['experiments']) > 3): + self.parent.l_parameters._data.experiments[0].yb = np.array(descr['experiments'][3]) + self.parent.l_parameters._data.experiments[0].eb = np.array(descr['experiments'][4]) + self.parent.l_experiment.spin_polarized = True + else: + length = len(self.parent.l_parameters._data.experiments[0].y) + self.parent.l_parameters._data.experiments[0].yb = np.zeros(length) + self.parent.l_parameters._data.experiments[0].eb = np.zeros(length) + self.parent.l_experiment.spin_polarized = False self.parent.l_experiment._experiment_data = self.parent.l_parameters._data.experiments[0] self.parent.l_experiment.experiments = [{'name': descr['project_info']['experiments']}] self.parent.l_experiment.setCurrentExperimentDatasetName(descr['project_info']['experiments']) - + self.parent.l_experiment.setPolarized(self.parent.l_experiment.spin_polarized) # send signal to tell the proxy we changed experiment self.experimentDataAdded.emit() - self.parent.parametersChanged.emit() + self.parent.l_background.onAsObjChanged() + if self.parent.l_experiment.spin_polarized: + self.parent.l_experiment.setSpinComponent() self.experimentLoadedChanged.emit() - else: # delete existing experiment self.parent.l_experiment.removeExperiment() @@ -219,8 +238,6 @@ def _loadProject(self): self.parent.l_experiment.experimentSkipped(True) self.parent.l_experiment.experimentSkippedChanged.emit() - # project info - self._project_info = descr['project_info'] new_minimizer_settings = descr.get('minimizer', None) if new_minimizer_settings is not None: @@ -251,8 +268,13 @@ def saveProject(self): experiments_y = self.parent.l_parameters._data.experiments[0].y experiments_e = self.parent.l_parameters._data.experiments[0].e descr['experiments'] = [experiments_x, experiments_y, experiments_e] + if self.parent.l_experiment.spin_polarized: + experiments_yb = self.parent.l_parameters._data.experiments[0].yb + experiments_eb = self.parent.l_parameters._data.experiments[0].eb + descr['experiments'] += [experiments_yb, experiments_eb] descr['experiment_skipped'] = self.parent.l_experiment._experiment_skipped + descr['read_only'] = self._read_only descr['project_info'] = self._project_info descr['interface'] = self._interface.current_interface_name @@ -280,6 +302,7 @@ def resetState(self): self.projectInfoChanged.emit() self.project_save_filepath = "" self.removeExperiment.emit() + self.parent.l_fitting.setCurrentCalculatorIndex(0) if self.parent.l_phase.samplesPresent(): self.parent.l_phase.removeAllPhases() self.reset.emit() diff --git a/easyDiffractionApp/Logic/Proxies/Background.py b/easyDiffractionApp/Logic/Proxies/Background.py index c9e5daf0..2e330033 100644 --- a/easyDiffractionApp/Logic/Proxies/Background.py +++ b/easyDiffractionApp/Logic/Proxies/Background.py @@ -32,8 +32,8 @@ def setDefaultPoints(self): self.logic.setDefaultPoints() @Slot() - def addPoint(self): - self.logic.addPoint() + def addDefaultPoint(self): + self.logic.addDefaultPoint() @Slot(str) def removePoint(self, point_name: str): diff --git a/easyDiffractionApp/Logic/Proxies/Experiment.py b/easyDiffractionApp/Logic/Proxies/Experiment.py index 0d680755..48edb712 100644 --- a/easyDiffractionApp/Logic/Proxies/Experiment.py +++ b/easyDiffractionApp/Logic/Proxies/Experiment.py @@ -3,6 +3,8 @@ # SPDX-License-Identifier: BSD-3-Clause # © 2021-2022 Contributors to the easyDiffraction project +import os + from PySide2.QtCore import QObject, Signal, Slot, Property @@ -44,6 +46,56 @@ def setCurrentExperimentDatasetName(self, name): #################################################################################################################### #################################################################################################################### + @Property(bool, notify=experimentLoadedChanged) + def isSpinPolarized(self): + return self.logic.spin_polarized + + @Property(str, notify=experimentLoadedChanged) + def spinComponent(self): + return self.logic.spinComponent() + + @Slot('QVariant') + def setSpinPolarization(self, spin_polarized): + if self.logic.setPolarized(spin_polarized): + self.experimentLoadedChanged.emit() + + @Slot('QVariant') + def setSpinComponent(self, component): + if self.logic.setSpinComponent(component): + self.experimentLoadedChanged.emit() + + @Property(bool, notify=experimentLoadedChanged) + def refineSum(self): + return self.logic.refineSum() + + @refineSum.setter + def refineSum(self, value): + self.logic.setRefineSum(value) + + @Property(bool, notify=experimentLoadedChanged) + def refineDiff(self): + return self.logic.refineDiff() + + @refineDiff.setter + def refineDiff(self, value): + self.logic.setRefineDiff(value) + + @Property(bool, notify=experimentLoadedChanged) + def refineUp(self): + return self.logic.refineUp() + + @refineUp.setter + def refineUp(self, value): + self.logic.setRefineUp(value) + + @Property(bool, notify=experimentLoadedChanged) + def refineDown(self): + return self.logic.refineDown() + + @refineDown.setter + def refineDown(self, value): + self.logic.setRefineDown(value) + @Property(str, notify=experimentDataAsXmlChanged) def experimentDataAsXml(self): return self.logic._experiment_data_as_xml @@ -63,7 +115,27 @@ def _onExperimentDataChanged(self): #################################################################################################################### @Slot(str) - def addExperimentDataFromXye(self, file_url): + def addExperimentData(self, file_url): + _, file_extension = os.path.splitext(file_url) + if file_extension == '.cif': + print(f"Reading '{file_extension}' file") + self._addExperimentDataFromCif(file_url) + elif file_extension in ('.xye', '.xys'): + print(f"Reading '{file_extension}' file") + self._addExperimentDataFromXye(file_url) + elif file_extension == '.xy': + print(f"We are working on supporting '{file_extension}' files") + else: + print(f"This file extension is not supported: '{file_extension}'") + + def _addExperimentDataFromCif(self, file_url): + self.logic.addExperimentDataFromCif(file_url) + self.logic.initializeBackground() + self.logic.addBackgroundDataFromCif(file_url) + self.logic._onExperimentDataAdded() + self.experimentLoadedChanged.emit() + + def _addExperimentDataFromXye(self, file_url): self.logic.addExperimentDataFromXye(file_url) self.logic._onExperimentDataAdded() self.experimentLoadedChanged.emit() diff --git a/easyDiffractionApp/Logic/Proxies/Phase.py b/easyDiffractionApp/Logic/Proxies/Phase.py index 0edfc980..09264119 100644 --- a/easyDiffractionApp/Logic/Proxies/Phase.py +++ b/easyDiffractionApp/Logic/Proxies/Phase.py @@ -186,6 +186,10 @@ def addDefaultAtom(self): def removeAtom(self, atom_label: str): self.logic.removeAtom(atom_label) + @Property(bool, notify=currentPhaseChanged) + def hasMsp(self): + return self.logic.hasMsp() + #################################################################################################################### # Current phase #################################################################################################################### diff --git a/easyDiffractionApp/Logic/Proxies/Plotting1d.py b/easyDiffractionApp/Logic/Proxies/Plotting1d.py index fd2e1c08..45b0c692 100644 --- a/easyDiffractionApp/Logic/Proxies/Plotting1d.py +++ b/easyDiffractionApp/Logic/Proxies/Plotting1d.py @@ -137,3 +137,4 @@ def lineSeriesCustomReplace(self, line_series, points): @Slot(int, str, result='QBrush') def verticalLine(self, size, color): return self.logic.verticalLine(size, color) + diff --git a/easyDiffractionApp/Logic/Proxies/Project.py b/easyDiffractionApp/Logic/Proxies/Project.py index 1a459142..258182dd 100644 --- a/easyDiffractionApp/Logic/Proxies/Project.py +++ b/easyDiffractionApp/Logic/Proxies/Project.py @@ -72,18 +72,19 @@ def saveProject(self): def loadProjectAs(self, filepath): self.logic._loadProjectAs(filepath) self.stateChanged.emit(False) + self.parent.fitting.calculatorListChanged.emit() @Slot() def loadProject(self): self.logic._loadProject() - # self._background_proxy.onAsObjChanged() self.stateChanged.emit(False) + self.parent.fitting.calculatorListChanged.emit() @Slot(str) def loadExampleProject(self, filepath): self.logic._loadProjectAs(filepath) - self.currentProjectPath = '--- EXAMPLE ---' self.stateChanged.emit(False) + self.parent.fitting.calculatorListChanged.emit() @Property(str, notify=dummySignal) def projectFilePath(self): @@ -103,6 +104,10 @@ def resetState(self): self.logic.stateHasChanged(False) self.stateChanged.emit(False) + @Property(bool, notify=projectCreatedChanged) + def readOnly(self): + return self.logic._read_only + @Property(bool, notify=stateChanged) def stateHasChanged(self): return self.logic._state_changed diff --git a/easyDiffractionApp/Logic/Sample.py b/easyDiffractionApp/Logic/Sample.py index 6d140d99..2654da55 100644 --- a/easyDiffractionApp/Logic/Sample.py +++ b/easyDiffractionApp/Logic/Sample.py @@ -7,7 +7,8 @@ from easyDiffractionLib.sample import Sample from easyDiffractionLib.Profiles.P1D import Instrument1DCWParameters from easyDiffractionLib.Profiles.P1D import Instrument1DTOFParameters -from easyDiffractionLib.Profiles.P1D import Powder1DParameters +from easyDiffractionLib.Profiles.P1D import Instrument1DCWPolParameters +from easyDiffractionLib.Profiles.P1D import Powder1DParameters, PolPowder1DParameters class SampleLogic(QObject): @@ -28,12 +29,8 @@ def __init__(self, parent=None, interface=None): #################################################################################################################### #################################################################################################################### - def _defaultCWSample(self): - sample = Sample( - phases=self._phases.phases, - parameters=Instrument1DCWParameters.default(), - pattern=Powder1DParameters.default(), - interface=self._interface) + def _defaultParameters(self, sample): + # return Instrument1DCWParameters.default() sample.pattern.zero_shift = 0.0 sample.pattern.scale = 100.0 sample.parameters.wavelength = 1.912 @@ -44,11 +41,32 @@ def _defaultCWSample(self): sample.parameters.resolution_y = 0.0 # 0.0961 return sample + def _defaultCWSample(self): + sample = Sample( + phases=self._phases.phases, + parameters=Instrument1DCWParameters(), + pattern=Powder1DParameters(), + interface=self._interface) + self._defaultParameters(sample) + return sample + + def _defaultCWPolSample(self): + # sample = super()._defaultCWSample() + sample = Sample( + phases=self._phases.phases, + parameters=Instrument1DCWPolParameters(), + pattern=PolPowder1DParameters(), + interface=self._interface) + self._defaultParameters(sample) + sample.pattern.beam.polarization = 0.0 + sample.pattern.beam.efficiency = 100.0 + return sample + def _defaultTOFSample(self): sample = Sample( phases=self._phases.phases, - parameters=Instrument1DTOFParameters.default(), - pattern=Powder1DParameters.default(), + parameters=Instrument1DTOFParameters(), + pattern=Powder1DParameters(), interface=self._interface) sample.pattern.zero_shift = 0.0 sample.pattern.scale = 100.0 @@ -70,7 +88,9 @@ def _defaultTOFSample(self): @property def experimentType(self): exp_type = None - if issubclass(type(self._sample.parameters), Instrument1DCWParameters): + if issubclass(type(self._sample.parameters), Instrument1DCWPolParameters): + exp_type = 'powder1DCWpol' + elif issubclass(type(self._sample.parameters), Instrument1DCWParameters): exp_type = 'powder1DCW' elif issubclass(type(self._sample.parameters), Instrument1DTOFParameters): exp_type = 'powder1DTOF' @@ -80,15 +100,16 @@ def experimentType(self): @experimentType.setter def experimentType(self, new_exp_type: str): - phases = self._phases.phases - pattern = self._sample.pattern - - if new_exp_type == 'powder1DCW': - params = Instrument1DCWParameters.default() + if new_exp_type == 'powder1DCWpol': + self._sample = self._defaultCWPolSample() + elif new_exp_type == 'powder1DCWunp' or new_exp_type == 'powder1DCW': self._sample = self._defaultCWSample() - elif new_exp_type == 'powder1DTOF': - params = Instrument1DTOFParameters.default() + if new_exp_type == 'powder1DCW': + new_exp_type = 'powder1DCWunp' + elif new_exp_type == 'powder1DTOFunp' or new_exp_type == 'powder1DTOF': self._sample = self._defaultTOFSample() + if new_exp_type == 'powder1DTOF': + new_exp_type = 'powder1DTOFunp' else: raise AttributeError('Unknown Experiment type') @@ -98,12 +119,7 @@ def experimentType(self, new_exp_type: str): interfaces = self._interface.interface_compatability(test_str) interface.switch(interfaces[0]) - self._sample = Sample( - phases=phases, - parameters=params, - pattern=pattern, - interface=self._interface) + self._sample.interface = interface self.parent.l_phase.phasesAsObjChanged.emit() self.parent.proxy.fitting.calculatorListChanged.emit() - #self.parent.parametersChanged.emit() diff --git a/easyDiffractionApp/Logic/Stack.py b/easyDiffractionApp/Logic/Stack.py index af1119ac..12269837 100644 --- a/easyDiffractionApp/Logic/Stack.py +++ b/easyDiffractionApp/Logic/Stack.py @@ -6,7 +6,7 @@ from easyCore import borg from easyCore.Objects.Groups import BaseCollection -from easyCore.Objects.Base import BaseObj +from easyCore.Objects.ObjectClasses import BaseObj from easyDiffractionLib import Phases, Phase diff --git a/examples/CIFs/CeCuAl.cif b/examples/CIFs/CeCuAl.cif deleted file mode 100644 index 5b4c07c4..00000000 --- a/examples/CIFs/CeCuAl.cif +++ /dev/null @@ -1,25 +0,0 @@ -data_CeCuAl - -_cell_length_a 4.25678 -_cell_length_b 4.25678 -_cell_length_c 10.63386 -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 90.0 -_space_group_name_H-M_alt 'I 4 m m' - -loop_ -_atom_site_label -_atom_site_type_symbol -_atom_site_occupancy -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -_atom_site_adp_type -_atom_site_U_iso_or_equiv -Ce Ce 1.0 0.0 0.0 0.0 Uiso 0.00589 -Cu1 Cu 0.925 0.0 0.0 0.63224 Uiso 0.0083 -Al1 Al 0.075 0.0 0.0 0.63224 Uiso 0.0083 -Cu2 Cu 0.044 0.0 0.0 0.40437 Uiso 0.0097 -Al2 Al 0.956 0.0 0.0 0.40437 Uiso 0.0097 -Al3 Al 0.986 0.0 0.5 0.24981 Uiso 0.00707 diff --git a/examples/CIFs/Cl2.cif b/examples/CIFs/Cl2.cif deleted file mode 100644 index 089116fe..00000000 --- a/examples/CIFs/Cl2.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_Dichlorine - -_cell_length_a 8.56(1) -_cell_length_b 8.56(1) -_cell_length_c 6.12(1) -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 90.0 -_space_group_name_H-M_alt 'P 42/n c m' -_space_group.IT_coordinate_system_code 1 - -loop_ - _atom_site_label - _atom_site_type_symbol - _atom_site_occupancy - _atom_site_fract_x - _atom_site_fract_y - _atom_site_fract_z - _atom_site_adp_type - _atom_site_U_iso_or_equiv - Cl1 Cl 1.0 0.125 0.167 0.107(1) Uiso 0.0 \ No newline at end of file diff --git a/examples/CIFs/Co2SiO4.cif b/examples/CIFs/Co2SiO4.cif deleted file mode 100644 index c34ec260..00000000 --- a/examples/CIFs/Co2SiO4.cif +++ /dev/null @@ -1,26 +0,0 @@ -data_Co2SiO4 - -_cell_length_a 10.28(2) -_cell_length_b 6.03(1) -_cell_length_c 4.75(1) -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 90.0 -_space_group_name_H-M_alt 'P n m a' - -loop_ - _atom_site_label - _atom_site_type_symbol - _atom_site_occupancy - _atom_site_fract_x - _atom_site_fract_y - _atom_site_fract_z - _atom_site_adp_type - _atom_site_U_iso_or_equiv - Co1 Co 1.0 0.0 0.0 0.0 Uiso 0.0 - Co2 Co 1.0 0.279(2) 0.25 0.985(2) Uiso 0.0 - Si Si 1.0 0.094(1) 0.25 0.429(2) Uiso 0.0 - O1 O 1.0 0.091(2) 0.25 0.771(2) Uiso 0.0 - O2 O 1.0 0.448(2) 0.25 0.217(2) Uiso 0.0 - O3 O 1.0 0.164(2) 0.032(2) 0.28(1) Uiso 0.0 - diff --git a/examples/CIFs/Dichlorine.cif b/examples/CIFs/Dichlorine.cif deleted file mode 100644 index f176e705..00000000 --- a/examples/CIFs/Dichlorine.cif +++ /dev/null @@ -1,21 +0,0 @@ -data_Dichlorine - -_cell_length_a 8.56 -_cell_length_b 8.56 -_cell_length_c 6.12 -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 90.0 -_space_group_name_H-M_alt 'P 42/n c m' -_space_group.IT_coordinate_system_code 1 - -loop_ - _atom_site_label - _atom_site_type_symbol - _atom_site_occupancy - _atom_site_fract_x - _atom_site_fract_y - _atom_site_fract_z - _atom_site_adp_type - _atom_site_U_iso_or_equiv - Cl1 Cl 1.0 0.125 0.167 0.107 Uiso 0.0 diff --git a/examples/CIFs/Dy3Al5O12.cif b/examples/CIFs/Dy3Al5O12.cif deleted file mode 100644 index 8b4549af..00000000 --- a/examples/CIFs/Dy3Al5O12.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_Dy3Al5O12 - -_cell_length_a 11.8(1) -_cell_length_b 11.8 -_cell_length_c 11.8 -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 90.0 -_space_group_name_H-M_alt 'I a -3 d' - -loop_ - _atom_site_label - _atom_site_type_symbol - _atom_site_occupancy - _atom_site_fract_x - _atom_site_fract_y - _atom_site_fract_z - _atom_site_adp_type - _atom_site_U_iso_or_equiv - Dy Dy3+ 1.0 0.125 0.0 0.25 Uiso 0.0 - Al1 Al3+ 1.0 0.375 0.0 0.25 Uiso 0.0 - Al2 Al3+ 1.0 0.0 0.0 0.0 Uiso 0.0 - O O2- 1.0 0.0306(2) 0.05(2) 0.648(2) Uiso 0.0 - diff --git a/examples/CIFs/Ho2TiO7.cif b/examples/CIFs/Ho2TiO7.cif deleted file mode 100644 index 5ae0a2c7..00000000 --- a/examples/CIFs/Ho2TiO7.cif +++ /dev/null @@ -1,25 +0,0 @@ -data_Ho2Ti2O7 - -_cell_length_a 10.26594(8) -_cell_length_b 10.26594(8) -_cell_length_c 10.26594(8) -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 90.0 -_space_group_name_H-M_alt 'F d -3 m' -_space_group.IT_coordinate_system_code 2 - -loop_ - _atom_site_label - _atom_site_type_symbol - _atom_site_occupancy - _atom_site_fract_x - _atom_site_fract_y - _atom_site_fract_z - _atom_site_adp_type - _atom_site_U_iso_or_equiv - Ho Ho3+ 1.0 0.5 0.5 0.5 Uiso 0.0 - Ti Ti3+ 1.0 0.0 0.0 0.0 Uiso 0.0 - O1 O2- 1.0 0.32850(0) 0.125 0.125 Uiso 0.0 - O2 O2- 1.0 0.375 0.375 0.375 Uiso 0.0 - diff --git a/examples/CIFs/PbSO4.cif b/examples/CIFs/PbSO4.cif deleted file mode 100644 index 4e7ad534..00000000 --- a/examples/CIFs/PbSO4.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_PbSO4 - -_cell_length_a 8.48 -_cell_length_b 5.398 -_cell_length_c 6.958 -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 90.0 -_space_group_name_H-M_alt 'P n m a' - -loop_ - _atom_site_label - _atom_site_type_symbol - _atom_site_occupancy - _atom_site_fract_x - _atom_site_fract_y - _atom_site_fract_z - _atom_site_adp_type - _atom_site_U_iso_or_equiv - Pb Pb 1.0 0.1882 0.25 0.167 Uiso 0.01 - S S 1.0 0.063 0.25 0.686 Uiso 0.01 - O1 O 1.0 -0.095 0.25 0.6 Uiso 0.01 - O2 O 1.0 0.181 0.25 0.543 Uiso 0.01 - O3 O 1.0 0.085 0.026 0.806 Uiso 0.01 diff --git a/examples/CIFs/SrTiO3.cif b/examples/CIFs/SrTiO3.cif deleted file mode 100644 index 9a0deeb1..00000000 --- a/examples/CIFs/SrTiO3.cif +++ /dev/null @@ -1,24 +0,0 @@ -data_SrTiO3 - -_cell_length_a 5.5202(2) -_cell_length_b 5.5202(2) -_cell_length_c 7.8067(3) -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 90.0 -_space_group_name_H-M_alt 'P b n m' - -loop_ - _atom_site_label - _atom_site_type_symbol - _atom_site_occupancy - _atom_site_fract_x - _atom_site_fract_y - _atom_site_fract_z - _atom_site_adp_type - _atom_site_U_iso_or_equiv - Sr Sr 1.0 0.0 0.0 0.25 Uiso 0.0 - Ti Ti 1.0 0.5 0.0 0.0 Uiso 0.0 - O1 O 1.0 0.0 0.5 0.25 Uiso 0.0 - O2 O 1.0 0.75 0.25 0.0 Uiso 0.0 - diff --git a/examples/CIFs/multi.cif b/examples/CIFs/multi.cif deleted file mode 100644 index d2d7b0d3..00000000 --- a/examples/CIFs/multi.cif +++ /dev/null @@ -1,51 +0,0 @@ -data_Co2SiO4 - -_cell_length_a 10.28 -_cell_length_b 6.03 -_cell_length_c 4.75 -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 90.0 -_space_group_name_H-M_alt 'P n m a' - -loop_ -_atom_site_label -_atom_site_type_symbol -_atom_site_occupancy -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -_atom_site_adp_type -_atom_site_U_iso_or_equiv -Co1 Co 1.0 0.0 0.0 0.0 Uiso 0.0 -Co2 Co 1.0 0.279(2) 0.25 0.985(2) Uiso 0.0 -Si Si 1.0 0.094(1) 0.25 0.429(2) Uiso 0.0 -O1 O 1.0 0.091(2) 0.25 0.771(2) Uiso 0.0 -O2 O 1.0 0.448(2) 0.25 0.217(2) Uiso 0.0 -O3 O 1.0 0.164(2) 0.032(2) 0.28(1) Uiso 0.0 - -data_CeCuAl - -_cell_length_a 4.25678 -_cell_length_b 4.25678 -_cell_length_c 10.63386 -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 90.0 -_space_group_name_H-M_alt 'I 4 m m' - -loop_ -_atom_site_label -_atom_site_type_symbol -_atom_site_occupancy -_atom_site_fract_x -_atom_site_fract_y -_atom_site_fract_z -_atom_site_adp_type -_atom_site_U_iso_or_equiv -Ce Ce 1.0 0.0 0.0 0.0 Uiso 0.00589 -Cu1 Cu 0.925 0.0 0.0 0.63224 Uiso 0.0083 -Al1 Al 0.075 0.0 0.0 0.63224 Uiso 0.0083 -Cu2 Cu 0.044 0.0 0.0 0.40437 Uiso 0.0097 -Al2 Al 0.956 0.0 0.0 0.40437 Uiso 0.0097 -Al3 Al 0.986 0.0 0.5 0.24981 Uiso 0.00707 diff --git a/examples/MultiPhases/Si3N4/project.cif b/examples/MultiPhases/Si3N4/project.cif deleted file mode 100644 index cc470ca9..00000000 --- a/examples/MultiPhases/Si3N4/project.cif +++ /dev/null @@ -1,5 +0,0 @@ -_name Si3N4 -_short_description 'diffraction, powder, 1D' -_samples 'Si3N4_alpha, Si3N4_beta' -_experiments '3T2@LLB' -_modified '02.12.2021 10:15' diff --git a/examples/MultiPhases/Si3N4/samples/Si3N4_alpha.cif b/examples/MultiPhases/Si3N4/samples/Si3N4_alpha.cif deleted file mode 100644 index db9d86cd..00000000 --- a/examples/MultiPhases/Si3N4/samples/Si3N4_alpha.cif +++ /dev/null @@ -1,26 +0,0 @@ -data_Si3N4_alpha - -_space_group_name_H-M_alt 'P 3 1 c' - -_cell_length_a 7.751856 -_cell_length_b 7.751856 -_cell_length_c 5.619506 -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 120.0 - -loop_ - _atom_site_label - _atom_site_type_symbol - _atom_site_occupancy - _atom_site_fract_x - _atom_site_fract_y - _atom_site_fract_z - _atom_site_adp_type - _atom_site_U_iso_or_equiv - Si1 Si 1.0 0.08185 0.51180 0.65958 Uiso 0.01 - Si2 Si 1.0 0.25323 0.16763 0.45090 Uiso 0.01 - N1 N 1.0 0.65512 0.61058 0.43269 Uiso 0.01 - N2 N 1.0 0.31514 0.31865 0.69801 Uiso 0.01 - N3 N 1.0 0.33333 0.66667 0.60394 Uiso 0.01 - N4 N 1.0 0.00000 0.00000 0.45292 Uiso 0.01 diff --git a/examples/MultiPhases/Si3N4/samples/Si3N4_beta.cif b/examples/MultiPhases/Si3N4/samples/Si3N4_beta.cif deleted file mode 100644 index 3d0be16d..00000000 --- a/examples/MultiPhases/Si3N4/samples/Si3N4_beta.cif +++ /dev/null @@ -1,23 +0,0 @@ -data_Si3N4_beta - -_space_group_name_H-M_alt 'P 63/m' - -_cell_length_a 7.605376 -_cell_length_b 7.605376 -_cell_length_c 2.907065 -_cell_angle_alpha 90.0 -_cell_angle_beta 90.0 -_cell_angle_gamma 120.0 - -loop_ - _atom_site_label - 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"degree", - "enabled": false, - "@id": "51184919879197574599512993194894434709" + "value": 90.0, + "@id": "140822947190314826395851075244309460790", + "enabled": false }, "angle_beta": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "angle_beta", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -116,15 +114,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "189152488073825551097941177992755351924" + "value": 90.0, + "@id": "216723154934804487642855589132515093266", + "enabled": false }, "angle_gamma": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "angle_gamma", - "value": 90.0, "error": 0.0, 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345.626, - 337.315 + 337.315, + 332.164, + 314.331, + 318.669, + 308.42, + 324.075, + 311.954, + 313.37, + 321.858, + 313.214, + 343.578, + 348.168, + 372.395, + 391.587, + 396.806, + 402.523, + 379.443, + 365.573, + 355.291, + 330.554, + 324.034, + 330.168, + 327.327, + 323.518, + 309.467, + 305.262, + 296.831, + 316.12, + 316.63, + 304.865, + 320.122, + 319.289, + 317.628, + 320.572, + 356.18, + 326.039, + 330.711, + 332.282, + 348.51, + 360.975, + 348.378, + 358.167, + 372.137, + 351.657, + 353.808, + 332.974, + 340.623, + 321.17, + 313.959, + 325.698, + 308.461, + 286.357, + 293.202, + 293.753, + 295.325, + 292.733, + 298.512, + 318.009, + 303.572, + 324.292, + 332.137, + 355.565, + 398.393, + 487.333, + 605.511, + 697.787, + 769.353, + 817.299, + 825.785, + 758.145, + 695.043, + 569.475, + 476.77, + 417.69, + 408.55, + 405.288, + 466.552, + 495.121, + 516.095, + 534.109, + 541.226, + 522.32, + 498.541, + 465.616, + 434.174, + 399.149, + 366.152, + 349.739, + 349.137, + 311.732, + 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+ 294.968, + 306.917, + 270.436, + 271.103, + 277.896, + 277.557, + 273.946, + 296.738, + 289.103, + 299.678, + 301.884, + 318.856, + 314.676, + 332.129, + 338.793, + 335.431, + 329.89, + 328.038, + 325.383 ], [ 10.79, @@ -5352,20 +5662,221 @@ 8.792, 8.401, 7.896, - 7.769 + 7.769, + 7.742, + 7.52, + 7.566, + 7.461, + 7.643, + 7.489, + 7.534, + 7.629, + 7.52, + 7.891, + 7.96, + 8.197, + 8.499, + 8.63, + 8.748, + 8.348, + 8.144, + 8.003, + 7.761, + 7.627, + 7.748, + 7.69, + 7.606, + 7.473, + 7.386, + 7.332, + 7.51, + 7.537, + 7.398, + 7.573, + 7.445, + 7.787, + 7.477, + 7.982, + 7.649, + 7.701, + 7.736, + 7.868, + 8.084, + 7.92, + 8.005, + 8.209, + 7.978, + 7.99, + 7.824, + 8.04, + 7.737, + 7.601, + 7.649, + 7.442, + 7.19, + 7.26, + 7.258, + 7.297, + 7.22, + 7.32, + 7.523, + 7.391, + 7.614, + 7.705, + 7.993, + 8.419, + 9.341, + 10.423, + 11.198, + 11.692, + 12.103, + 12.173, + 11.605, + 11.171, + 10.132, + 9.246, + 8.646, + 8.569, + 8.546, + 9.18, + 9.488, + 9.847, + 10.008, + 9.96, + 9.663, + 9.509, + 9.128, + 8.819, + 8.451, + 8.083, + 7.878, + 7.87, + 7.46, + 7.434, + 7.187, + 7.471, + 7.197, + 7.08, + 7.255, + 7.296, + 7.224, + 7.381, + 7.348, + 7.61, + 8.079, + 8.261, + 8.757, + 8.977, + 9.281, + 9.184, + 9.084, + 9.103, + 9.076, + 9.128, + 8.953, + 9.156, + 9.364, + 9.502, + 9.843, + 9.789, + 9.679, + 9.57, + 9.114, + 8.995, + 8.778, + 8.75, + 9.24, + 9.24, + 9.811, + 10.155, + 10.099, + 10.401, + 10.385, + 10.27, + 9.954, + 9.714, + 9.46, + 9.342, + 9.318, + 9.241, + 9.496, + 9.146, + 9.44, + 9.28, + 9.113, + 9.164, + 8.812, + 8.404, + 7.995, + 7.788, + 7.513, + 7.622, + 7.38, + 7.3, + 7.346, + 6.963, + 7.09, + 7.116, + 6.466, + 9.402, + 6.707, + 7.328, + 7.344, + 7.467, + 7.659, + 7.514, + 7.853, + 7.875, + 8.154, + 8.143, + 8.281, + 8.192, + 8.268, + 8.464, + 8.248, + 8.451, + 8.32, + 8.391, + 8.401, + 8.095, + 7.915, + 7.773, + 7.458, + 7.416, + 7.364, + 7.281, + 7.373, + 7.023, + 6.721, + 7.154, + 7.21, + 6.598, + 7.266, + 7.296, + 7.127, + 7.245, + 7.491, + 7.368, + 7.531, + 7.885, + 7.691, + 7.39, + 8.008, + 7.109 ] ], "experiment_skipped": false, + "read_only": false, "project_info": { "name": "Co2SiO4", - "short_description": "diffraction, powder, 1D", + "short_description": "neutrons, powder, constant wavelength, D20@ILL", "samples": "Co2SiO4", "experiments": "D20@ILL", - "modified": "26.04.2021 17:46" + "modified": "20.07.2022 08:20" }, "interface": "CrysPy", "minimizer": { "engine": "lmfit", - "method": "leastsq" + "method": "least_squares" } } diff --git a/examples/PdCw1d/Co2SiO4/samples/Co2SiO4.cif b/examples/PdCw1d/Co2SiO4/samples/Co2SiO4.cif index 25f96404..c78b15a8 100644 --- a/examples/PdCw1d/Co2SiO4/samples/Co2SiO4.cif +++ b/examples/PdCw1d/Co2SiO4/samples/Co2SiO4.cif @@ -1,11 +1,10 @@ data_Co2SiO4 -_space_group_name_H-M_ref 'P n m a' -_space_group_IT_coordinate_system_code abc +_space_group_name_H-M_alt 'P n m a' -_cell_length_a 10.28() -_cell_length_b 6.03() -_cell_length_c 4.75() +_cell_length_a 10.3100 +_cell_length_b 6.0045 +_cell_length_c 4.7872 _cell_angle_alpha 90.0 _cell_angle_beta 90.0 _cell_angle_gamma 90.0 @@ -18,7 +17,7 @@ _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy _atom_site_adp_type -_atom_site_u_iso_or_equiv +_atom_site_U_iso_or_equiv Co1 Co 0.0 0.0 0.0 1.0 Uiso 0.004 Co2 Co 0.279 0.25 0.985 1.0 Uiso 0.007 Si Si 0.094 0.25 0.429 1.0 Uiso 0.005 diff --git a/examples/PdCw1d/Dy3Al5O12/project.cif b/examples/PdCw1d/Dy3Al5O12/project.cif index dcc1612f..94bca08e 100644 --- a/examples/PdCw1d/Dy3Al5O12/project.cif +++ b/examples/PdCw1d/Dy3Al5O12/project.cif @@ -1,5 +1,5 @@ _name Dy3Al5O12 -_short_description 'diffraction, powder, 1D' +_short_description 'neutrons, powder, constant wavelength, G41@LLB' _samples 'Dy3Al5O12' _experiments 'G41@LLB' _modified '26.04.2021 20:07' diff --git a/examples/PdCw1d/Dy3Al5O12/project.json b/examples/PdCw1d/Dy3Al5O12/project.json index 2160ff48..2e615887 100644 --- a/examples/PdCw1d/Dy3Al5O12/project.json +++ b/examples/PdCw1d/Dy3Al5O12/project.json @@ -4,47 +4,45 @@ "@class": "Sample", "@version": "0.0.1", "phases": { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phases", "@version": "0.0.1", "name": "Phases", "data": [ { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phase", "@version": "0.0.1", "name": "Dy3Al5O12", "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", "@class": "SpaceGroup", - "@version": "0.0.1", + "@version": "0.1.0", "_space_group_HM_name": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.0.1", + "@version": "0.2.2", "name": "_space_group_HM_name", - "value": "I a -3 d", + "value": "I a -3 d:1", "units": "dimensionless", "description": "Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_name_H-M_alt.html", "display_name": "_space_group_HM_name", "enabled": true, - "@id": "244438963110265392754211283835678565150" + "@id": "29214101360585411911591445881576148800" }, - "interface": null, "setting": "", - "@id": "189827113577734163747069165382571363789" + "@id": "286981274392192463488439017875314105906" }, "cell": { "@module": "easyCrystallography.Components.Lattice", "@class": "PeriodicLattice", - "@version": "0.0.1", + "@version": "0.1.0", "length_a": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "length_a", - "value": 11.8993, "error": 0.0, "min": 0, "max": Infinity, @@ -52,15 +50,15 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "@id": "117787400006272866550408224938148610151", + "value": 11.8993, + "@id": "205275846955820659600226090102179059750", "enabled": true }, "length_b": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "length_b", - "value": 11.8993, "error": 0.0, "min": 0, "max": Infinity, @@ -68,15 +66,15 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "@id": "339598709096884380215056222607118371974", + "value": 11.8993, + "@id": "120220800643955197686488654000435124176", "enabled": false }, "length_c": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "length_c", - "value": 11.8993, "error": 0.0, "min": 0, "max": Infinity, @@ -84,15 +82,15 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "@id": "52887480189221381562823462813835005123", + "value": 11.8993, + "@id": "193429044294434803972816913633079082278", "enabled": false }, "angle_alpha": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "angle_alpha", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -100,15 +98,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "@id": "223740939447894539894375442949434831064", + "value": 90.0, + "@id": "129931072237923508169515371158306016380", "enabled": false }, "angle_beta": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "angle_beta", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -116,15 +114,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "@id": "29993304974595014458622938804671030063", + "value": 90.0, + "@id": "171854791705225383384237977202407192940", "enabled": false }, "angle_gamma": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "angle_gamma", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -132,163 +130,154 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "@id": "289320941814827973957687123833676019860", + "value": 90.0, + "@id": "268550261311219579378162222960839187437", "enabled": false }, "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", "@class": "SpaceGroup", - "@version": "0.0.1", + "@version": "0.1.0", "_space_group_HM_name": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.0.1", + "@version": "0.2.2", "name": "_space_group_HM_name", - "value": "I a -3 d", "units": "dimensionless", "description": "Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_name_H-M_alt.html", "display_name": "_space_group_HM_name", "enabled": true, - "@id": "244438963110265392754211283835678565150" + "value": "I a -3 d:1", + "@id": "29214101360585411911591445881576148800" }, - "interface": null, "setting": "", - "@id": "189827113577734163747069165382571363789" + "@id": "286981274392192463488439017875314105906" }, - "interface": null, - "@id": "179262843888073344101938373505544369509" + "@id": "253867573042298902042293604743743390364" }, "atoms": { - "@module": "easyCrystallography.Components.Site", + "@module": "easyDiffractionLib.components.site", "@class": "Atoms", "@version": "0.0.1", "name": "atoms", "data": [ { - "@module": "easyCrystallography.Components.Site", + "@module": "easyDiffractionLib.components.site", "@class": "Site", "@version": "0.0.1", "label": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.0.1", + "@version": "0.2.2", "name": "label", - "value": "Dy", "units": "dimensionless", "description": "A unique identifier for a particular site in the crystal", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_label.html", "display_name": "label", "enabled": true, - "@id": "193944229157770363077924382233955135776" + "value": "Dy", + "@id": "59263958248139732529982124187128387829" }, "specie": { "@module": "easyCrystallography.Components.Specie", "@class": "Specie", - "@version": "0.0.1", - "specie": { - "@module": "easyCrystallography.Elements.periodic_table", - "@class": "Species", - "element": "Dy", - "oxidation_state": 3.0 - }, + "@version": "0.1.0", + "specie": "Dy3+", "value": "Dy3+", "units": "dimensionless", - "@id": "163881136803873119527473265596207167023" + "@id": "259497135664051532847616224677694475293" }, "occupancy": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "occupancy", - "value": 1.0, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "description": "The fraction of the atom type present at this site.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_occupancy.html", + "value": 1.0, "units": "dimensionless", - "@id": "89510636051693886129653350507603738885", + "@id": "318594791160914637287088520662724560373", "enabled": true }, "fract_x": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "fract_x", - "value": 0.125, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "description": "Atom-site coordinate as fractions of the unit cell length.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", + "value": 0.125, "units": "dimensionless", - "@id": "166496842203343248248968841814370714382", + "@id": "126192475085321928999193216412350747152", "enabled": true }, "fract_y": { - "@module": "easyCore.Objects.Base", + "@module": 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"current_exp" } ], - "@id": "314985552432917253903333235674120820989" + "@id": "209083206686172266003775848654529324710" }, - "interface": null, - "@id": "125147637640647704652536314743757431554" + "@id": "284371294898928399503916843093403628476" }, "name": "easySample", - "@id": "334641578196303554733207034843996810864" + "@id": "192914271704940946233612181312397697661" }, "experiments": [ [ @@ -3668,16 +3644,17 @@ ] ], "experiment_skipped": false, + "read_only": false, "project_info": { "name": "Dy3Al5O12", - "short_description": "diffraction, powder, 1D", + "short_description": "neutrons, powder, constant wavelength, G41@LLB", "samples": "Dy3Al5O12", "experiments": "G41@LLB", - "modified": "26.04.2021 20:07" + "modified": "01.06.2022 16:34" }, "interface": "CrysPy", "minimizer": { "engine": "lmfit", - "method": "leastsq" + "method": "least_squares" } } diff --git a/examples/PdCw1d/Dy3Al5O12/samples/Dy3Al5O12.cif b/examples/PdCw1d/Dy3Al5O12/samples/Dy3Al5O12.cif index 72ce67d3..c2af934a 100644 --- a/examples/PdCw1d/Dy3Al5O12/samples/Dy3Al5O12.cif +++ b/examples/PdCw1d/Dy3Al5O12/samples/Dy3Al5O12.cif @@ -1,6 +1,6 @@ data_Dy3Al5O12 -_cell_length_a 11.8() +_cell_length_a 11.8 _cell_length_b 11.8 _cell_length_c 11.8 _cell_angle_alpha 90.0 diff --git a/examples/PdCw1d/PbSO4/project.cif b/examples/PdCw1d/PbSO4/project.cif index e6f9c3a6..f0325aa5 100644 --- a/examples/PdCw1d/PbSO4/project.cif +++ b/examples/PdCw1d/PbSO4/project.cif @@ -1,5 +1,5 @@ _name PbSO4 -_short_description 'diffraction, powder, 1D' +_short_description 'neutrons, powder, constant wavelength, D1A@ILL' _samples 'PbSO4' _experiments 'D1A@ILL' _modified '26.04.2021 12:46' diff --git a/examples/PdCw1d/PbSO4/project.json b/examples/PdCw1d/PbSO4/project.json index beb10da9..254c3759 100644 --- a/examples/PdCw1d/PbSO4/project.json +++ b/examples/PdCw1d/PbSO4/project.json @@ -4,63 +4,61 @@ "@class": "Sample", "@version": "0.0.1", "phases": { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phases", "@version": "0.0.1", "name": "Phases", "data": [ { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phase", "@version": "0.0.1", "name": "PbSO4", "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", "@class": "SpaceGroup", - "@version": "0.0.1", + "@version": "0.1.0", "_space_group_HM_name": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.0.1", + "@version": "0.2.2", "name": "_space_group_HM_name", - "value": "P n m a", + "value": "P n m a:abc", "units": "dimensionless", "description": "Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting.", "url": 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"enabled": true, - "@id": "78570807957815705415902192294156126083" + "value": 8.4774, + "@id": "10971425981967737184650235645406766924", + "enabled": true }, "length_b": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "length_b", - "value": 5.396587488764175, "error": 0.0, "min": 0, "max": Infinity, @@ -68,15 +66,15 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "190077505831356677494429456762614169949" + "value": 5.396, + "@id": "307679075055753684987562388239036674011", + "enabled": true }, "length_c": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "length_c", - "value": 6.957814737950935, "error": 0.0, "min": 0, "max": Infinity, @@ -84,15 +82,15 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "31002191715379837232482174997841266130" + "value": 6.957, + "@id": "43198596658802343767843434680670335454", + "enabled": true }, "angle_alpha": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "angle_alpha", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -100,15 +98,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "112911982988727070449763831112419597364" + "value": 90.0, + "@id": "87081486690993477241190035210247325150", + "enabled": false }, "angle_beta": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "angle_beta", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -116,15 +114,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "187918726403921120415238932037380075165" + "value": 90.0, + "@id": "293291295444280922208323006932792085825", + "enabled": false }, "angle_gamma": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.0.1", + "@version": "0.2.2", "name": "angle_gamma", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -132,163 +130,154 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": 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+_short_description 'neutrons, powder, constant wavelength, multi-phase, 3T2@LLB' +_samples 'Si3N4_alpha, Si3N4_beta' +_experiments '3T2@LLB' +_modified '01.02.2022 10:16' diff --git a/examples/MultiPhases/Si3N4/project.json b/examples/PdCw1d/Si3N4/project.json similarity index 85% rename from examples/MultiPhases/Si3N4/project.json rename to examples/PdCw1d/Si3N4/project.json index f5ffbbe4..d2ae0637 100644 --- a/examples/MultiPhases/Si3N4/project.json +++ b/examples/PdCw1d/Si3N4/project.json @@ -4,15 +4,15 @@ "@class": "Sample", "@version": "0.0.1", "phases": { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phases", - "@version": "0.1.0", + "@version": "0.0.1", "name": "Phases", "data": [ { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phase", - "@version": "0.1.0", + "@version": "0.0.1", "name": "Si3N4_alpha", "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", @@ -21,7 +21,7 @@ "_space_group_HM_name": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "value": "P 3 1 c:r", "units": "dimensionless", @@ -29,10 +29,10 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_name_H-M_alt.html", "display_name": "_space_group_HM_name", "enabled": true, - "@id": "323241945591398306874692827938017348414" + "@id": "86303283277332365658229310607173746582" }, "setting": "", - "@id": "193046138044008511252559169148005569223" + "@id": "231959193280068587934112480710157782826" }, "cell": { "@module": "easyCrystallography.Components.Lattice", @@ -41,25 +41,24 @@ "length_a": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_a", - "value": 7.750937232235225, - "error": 7.813047787239839e-05, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "181991401382169934454776876765019937644" + "value": 7.75092882, + "@id": "296829975319484471340458433109455693563", + "enabled": true }, "length_b": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_b", - "value": 7.750937232235225, "error": 0.0, "min": 0, "max": Infinity, @@ -67,31 +66,31 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": false, - "@id": "257940179990375812233766193926225676842" + "value": 7.75092882, + "@id": "268411233507208252474429892848405077841", + "enabled": false }, "length_c": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_c", - "value": 5.6188624843154455, - "error": 6.571632875487679e-05, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "189377729326982989681979976614458164367" + "value": 5.61886556, + "@id": "207905530962558145358553910299546199405", + "enabled": true }, "angle_alpha": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_alpha", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -99,15 +98,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "129490205601582203133786442515140839093" + "value": 90.0, + "@id": "228430533379346032942186159257947728019", + "enabled": false }, "angle_beta": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_beta", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -115,15 +114,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "96058479203997940850338664668269508403" + "value": 90.0, + "@id": "91560787151282548333066320410523472702", + "enabled": false }, "angle_gamma": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_gamma", - "value": 120.0, "error": 0.0, "min": 0, "max": Infinity, @@ -131,8 +130,9 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "211244524058489656596228457777796015872" + "value": 120.0, + "@id": "146616716845168454195790472462586600855", + "enabled": false }, "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", @@ -141,7 +141,7 @@ "_space_group_HM_name": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "units": "dimensionless", "description": "Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting.", @@ -149,27 +149,27 @@ "display_name": "_space_group_HM_name", "enabled": true, "value": "P 3 1 c:r", - "@id": "323241945591398306874692827938017348414" + "@id": "86303283277332365658229310607173746582" }, "setting": "", - "@id": "193046138044008511252559169148005569223" + "@id": "231959193280068587934112480710157782826" }, - "@id": "285240588659650940043575158590322239931" + "@id": "155976119202582527829072713301365514991" }, "atoms": { - "@module": "easyCrystallography.Components.Site", + "@module": "easyDiffractionLib.components.site", "@class": "Atoms", - "@version": "0.1.0", + "@version": "0.0.1", "name": "atoms", "data": [ { - "@module": "easyCrystallography.Components.Site", + "@module": "easyDiffractionLib.components.site", "@class": "Site", - "@version": "0.1.0", + "@version": "0.0.1", "label": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "label", "units": "dimensionless", "description": "A unique identifier for a particular site in the crystal", @@ -177,85 +177,80 @@ "display_name": "label", "enabled": true, "value": "Si1", - "@id": "170995106079168173347706073583030598591" + "@id": "252349893550166803735678459796943282036" }, "specie": { "@module": "easyCrystallography.Components.Specie", "@class": "Specie", "@version": "0.1.0", - "specie": { - "@module": "easyCrystallography.Elements.periodic_table", - "@class": "Specie", - "element": "Si", - "oxidation_state": 0.0 - }, + "specie": "Si", "value": "Si", "units": "dimensionless", - "@id": "234508008732212473267666677214933190504" + "@id": "11812382042399330309843614236793936949" }, "occupancy": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "occupancy", - "value": 1.0, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "description": "The fraction of the atom type present at this site.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_occupancy.html", + "value": 1.0, "units": "dimensionless", - "enabled": true, - "@id": 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"url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", + "value": 0.5118, "units": "dimensionless", - "enabled": true, - "@id": "320174685589061908372241494433418146960" + "@id": "154523197434132623578813101565243670751", + "enabled": true }, "fract_z": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_z", - "value": 0.65958, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "description": "Atom-site coordinate as fractions of the unit cell length.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", + "value": 0.65958, "units": "dimensionless", - "enabled": true, - "@id": "56493226233657170190197221031529925558" + "@id": "21929278650781288798970206598930600828", + "enabled": true }, "adp": { "@module": "easyCrystallography.Components.AtomicDisplacement", @@ -264,15 +259,15 @@ "adp_type": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "adp_type", "units": "dimensionless", - "description": "A standard code used to describe the type of atomic displacement parameters used for the site.", - "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_adp_type.html", + "description": "", + "url": "", "display_name": "adp_type", "enabled": true, "value": "Uiso", - "@id": "172993164894525169466453747509971684783" + "@id": "142315435170661291784100900126307511497" }, "adp_class": { "@module": "easyCrystallography.Components.AtomicDisplacement", @@ -281,33 +276,33 @@ "Uiso": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "Uiso", - "value": 0.0018430490936811675, - "error": 0.000378241223340326, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "The standard anisotropic atomic displacement components in angstroms squared which appear in the structure-factor term.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_U_iso_or_equiv.html", "units": "angstrom ** 2", - "enabled": true, - "@id": "93550894432416978203527030270631656274" + "value": 0.0018421, + "@id": "17393123368801072202484554015097240857", + "enabled": true }, - "@id": "205352601965746492012165534649173455318" + "@id": "24322348403683779888283149117420195814" }, - "@id": "123396978013611077015265835198678291083" + "@id": "85509183444002604028206669150297724325" }, - "@id": "266121421336683548397269686472031201735" + "@id": "187310347499425504790110682256281912221" }, { - "@module": "easyCrystallography.Components.Site", + "@module": "easyDiffractionLib.components.site", "@class": "Site", - "@version": "0.1.0", + "@version": "0.0.1", "label": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "label", "units": 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"https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_occupancy.html", + "value": 1.0, "units": "dimensionless", - "enabled": true, - "@id": "115875901419425049555728384163446195043" + "@id": "126931383050637456248122413463949022818", + "enabled": true }, "fract_x": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_x", - "value": 0.25323, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "description": "Atom-site coordinate as fractions of the unit cell length.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", + "value": 0.25323, "units": "dimensionless", - "enabled": true, - "@id": "223175656991958107460577145275923945560" + "@id": "40200420925349677944070442226812858457", + "enabled": true }, "fract_y": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_y", - 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+ "enabled": true }, "adp": { "@module": "easyCrystallography.Components.AtomicDisplacement", @@ -402,15 +392,15 @@ "adp_type": { "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "adp_type", "units": "dimensionless", - "description": "A standard code used to describe the type of atomic displacement parameters used for the site.", - "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_adp_type.html", + "description": "", + "url": "", "display_name": "adp_type", "enabled": true, "value": "Uiso", - "@id": "213177797075153259404784878100742452587" + "@id": "151171284128110554879142502312134722760" }, "adp_class": { "@module": "easyCrystallography.Components.AtomicDisplacement", @@ -419,33 +409,33 @@ "Uiso": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "Uiso", - "value": 0.0034646717289629073, - "error": 0.00026438570328856693, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "The standard anisotropic atomic displacement components in angstroms squared which appear in the structure-factor term.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_U_iso_or_equiv.html", "units": "angstrom ** 2", - "enabled": true, - "@id": "145255688554219708217828878170996790243" + "value": 0.003458, + "@id": "185052766137140738180645084979222725289", + "enabled": true }, - "@id": "337484231039320030318344771660382399242" + "@id": "56344661108164507286648759202622020171" }, - "@id": "30130521937761812133875468903437821999" + "@id": "21136421175602015407056336627384946193" }, - "@id": "261103540248458796841086735004145025482" + "@id": "68744825672669990404314748085362650051" }, { - "@module": "easyCrystallography.Components.Site", + "@module": "easyDiffractionLib.components.site", "@class": "Site", - "@version": "0.1.0", + 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"Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_beta", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -1116,15 +1085,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "241162298318023015198418751187885240411" + "value": 90.0, + "@id": "234721781392059050688462352116675172853", + "enabled": false }, "angle_gamma": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_gamma", - "value": 120.0, "error": 0.0, "min": 0, "max": Infinity, @@ -1132,8 +1101,9 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "92696310242075230774651188791041052047" + "value": 120.0, 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"description": "Atom-site coordinate as fractions of the unit cell length.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", + "value": 0.17522, "units": "dimensionless", - "enabled": true, - "@id": "14611810905869702491788383966094102166" + "@id": "275306018601597034850816313822853798781", + "enabled": true }, "fract_y": { "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "fract_y", - "value": 0.76977, "error": 0.0, "min": -Infinity, "max": Infinity, "fixed": true, "description": "Atom-site coordinate as fractions of the unit cell length.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_fract_.html", + "value": 0.76977, "units": "dimensionless", - "enabled": true, - "@id": "320499471465753129497396138026008327481" + "@id": "154744872509314936668289571339815942324", + "enabled": true }, "fract_z": { "@module": "easyCore.Objects.Variable", 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+ "@id": "87230681367240879358362504412675971857", "linked_experiment": "current_exp" } ], - "@id": "59436888496241803269443684628306727418" + "@id": "67593751496468925824576400934378232582" }, - "@id": "91809965133523759693155732921215412530" + "@id": "164617770833469586882890467553663414791" }, "name": "easySample", - "@id": "195262697602864733544803148452188384260" + "@id": "132659903369418757236213243635775850216" }, "experiments": [ [ @@ -9432,12 +9387,13 @@ ] ], "experiment_skipped": false, + "read_only": false, "project_info": { "name": "Si3N4", - "short_description": "diffraction, powder, 1D", - "samples": "Si3N4_alpha, Si3N4_beta", + "short_description": "neutrons, powder, constant wavelength, multi-phase, 3T2@LLB", + "samples": "Si3N4_alpha", "experiments": "3T2@LLB", - "modified": "02.12.2021 10:16" + "modified": "02.06.2022 15:07" }, "interface": "CrysPy", "minimizer": { diff --git a/examples/PdCw1d/Si3N4/samples/Si3N4_alpha.cif b/examples/PdCw1d/Si3N4/samples/Si3N4_alpha.cif new file mode 100644 index 00000000..e776a4cd --- /dev/null +++ b/examples/PdCw1d/Si3N4/samples/Si3N4_alpha.cif @@ -0,0 +1,25 @@ +data_Si3N4_alpha + +_cell_length_a 7.75092882 +_cell_length_b 7.75092882 +_cell_length_c 5.61886556 +_cell_angle_alpha 90.0 +_cell_angle_beta 90.0 +_cell_angle_gamma 120.0 +_space_group_name_H-M_alt 'P 3 1 c' + +loop_ +_atom_site_label +_atom_site_type_symbol +_atom_site_occupancy +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +_atom_site_adp_type +_atom_site_U_iso_or_equiv +Si1 Si 1.0 0.0819 0.5118 0.65958 Uiso 0.0018421 +Si2 Si 1.0 0.25323 0.16763 0.4509 Uiso 0.003458 +N1 N 1.0 0.65512 0.61058 0.43269 Uiso 0.00484863 +N2 N 1.0 0.31514 0.31865 0.69801 Uiso 0.00501808 +N3 N 1.0 0.33333333 0.66666667 0.60394 Uiso 0.00490371 +N4 N 1.0 0.0 0.0 0.45292 Uiso 0.00487042 diff --git a/examples/PdCw1d/Si3N4/samples/Si3N4_beta.cif b/examples/PdCw1d/Si3N4/samples/Si3N4_beta.cif new file mode 100644 index 00000000..8815502f --- /dev/null +++ b/examples/PdCw1d/Si3N4/samples/Si3N4_beta.cif @@ -0,0 +1,22 @@ +data_Si3N4_beta + +_cell_length_a 7.60375657 +_cell_length_b 7.60375657 +_cell_length_c 2.9066949 +_cell_angle_alpha 90.0 +_cell_angle_beta 90.0 +_cell_angle_gamma 120.0 +_space_group_name_H-M_alt 'P 63/m' + +loop_ +_atom_site_label +_atom_site_type_symbol +_atom_site_occupancy +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +_atom_site_adp_type +_atom_site_U_iso_or_equiv +Si Si 1.0 0.17522 0.76977 0.25 Uiso 0.00301531 +N1 N 1.0 0.33131 0.0312 0.25 Uiso 0.00660646 +N2 N 1.0 0.33333333 0.66666667 0.25 Uiso 0.01067827 diff --git a/examples/PdCw1dPol/Fe3O4/experiments/PolNPD5T.cif b/examples/PdCw1dPol/Fe3O4/experiments/PolNPD5T.cif new file mode 100644 index 00000000..c1636bf1 --- /dev/null +++ b/examples/PdCw1dPol/Fe3O4/experiments/PolNPD5T.cif @@ -0,0 +1,356 @@ +data_PolNPD5T + +_setup_wavelength 2.4 +_setup_field 5.0 +_setup_offset_2theta 0.360 + +_pd_instr_resolution_u 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+_atom_site_label +_atom_site_type_symbol +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +_atom_site_occupancy +_atom_site_adp_type +_atom_site_U_iso_or_equiv +Fe3A Fe3+ 0.125 0.125 0.125 1.0 Uiso 0.0 +Fe3B Fe3+ 0.5 0.5 0.5 1.0 Uiso 0.0 +O O2- 0.25521 0.25521 0.25521 1.0 Uiso 0.0 + +loop_ +_atom_site_susceptibility_label +_atom_site_susceptibility_chi_type +_atom_site_susceptibility_chi_11 +_atom_site_susceptibility_chi_22 +_atom_site_susceptibility_chi_33 +_atom_site_susceptibility_chi_12 +_atom_site_susceptibility_chi_13 +_atom_site_susceptibility_chi_23 +Fe3A Cani -0.8463 -0.8463 -0.8463 0.0 0.0 0.0 +Fe3B Cani 0.7651 0.7651 0.7651 0.0 0.0 0.0 + +loop_ +_atom_site_scat_label +_atom_site_scat_lande +_atom_site_scat_kappa +Fe3A 2.0 1.0 +Fe3B 2.0 1.0 diff --git a/examples/PdCw1dPol/Ho2Ti2O7/experiments/VIP@LLB-5K5T.cif b/examples/PdCw1dPol/Ho2Ti2O7/experiments/VIP@LLB-5K5T.cif new file mode 100644 index 00000000..b7542ea6 --- /dev/null +++ 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673.4 23.99 578.5 23.48 +80.4 715.34 24.45 631.24 24.0 +80.6 625.41 23.98 627.0 23.99 +80.8 659.25 24.3 600.44 24.0 +81.0 617.92 24.1 526.94 23.63 +81.2 643.9 24.21 551.74 23.72 +81.4 610.43 24.05 570.73 23.84 +81.6 687.21 25.11 535.41 24.27 +81.8 604.92 24.92 559.32 24.65 +82.0 589.97 24.97 499.26 24.46 diff --git a/examples/PdCw1dPol/Ho2Ti2O7/project.cif b/examples/PdCw1dPol/Ho2Ti2O7/project.cif new file mode 100644 index 00000000..178299c3 --- /dev/null +++ b/examples/PdCw1dPol/Ho2Ti2O7/project.cif @@ -0,0 +1,5 @@ +_name Ho2Ti2O7 +_short_description 'neutrons, powder, constant wavelength, polarised, VIP@LLB' +_samples 'Ho2Ti2O7' +_experiments 'VIP@LLB-5K5T' +_modified '24.05.2022 09:52' diff --git a/examples/PdCw1dPol/Ho2Ti2O7/project.json b/examples/PdCw1dPol/Ho2Ti2O7/project.json new file mode 100644 index 00000000..dfdba957 --- /dev/null +++ b/examples/PdCw1dPol/Ho2Ti2O7/project.json @@ -0,0 +1,3571 @@ +{ + "sample": { + "@module": "easyDiffractionLib.sample", + "@class": 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+_cell_angle_alpha 90.0 +_cell_angle_beta 90.0 +_cell_angle_gamma 90.0 + +loop_ +_atom_site_label +_atom_site_type_symbol +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +_atom_site_occupancy +_atom_site_adp_type +_atom_site_U_iso_or_equiv +Ho Ho3+ 0.5 0.5 0.5 1.0 Uiso 0.0 +Ti Ti3+ 0.0 0.0 0.0 1.0 Uiso 0.0 +O1 O2- 0.32858 0.125 0.125 1.0 Uiso 0.0 +O2 O2- 0.375 0.375 0.375 1.0 Uiso 0.0 + +loop_ +_atom_site_susceptibility_label +_atom_site_susceptibility_chi_type +_atom_site_susceptibility_chi_11 +_atom_site_susceptibility_chi_22 +_atom_site_susceptibility_chi_33 +_atom_site_susceptibility_chi_12 +_atom_site_susceptibility_chi_13 +_atom_site_susceptibility_chi_23 +Ho Cani 3.826 3.826 3.826 3.738 3.738 3.738 + +loop_ +_atom_site_scat_label +_atom_site_scat_lande +_atom_site_scat_kappa +Ho 2.0 1.0 diff --git a/examples/PdTof1d/CeCuAl/project.cif b/examples/PdTof1d/CeCuAl/project.cif deleted file mode 100644 index 45c6c0ec..00000000 --- a/examples/PdTof1d/CeCuAl/project.cif +++ /dev/null @@ -1,5 +0,0 @@ -_name CeCuAl -_short_description 'diffraction, powder, time-of-flight, 1D' -_samples CeCuAl -_experiments data -_modified '17.08.2021 12:09' \ No newline at end of file diff --git a/easyDiffractionApp/Gui/Resources/Examples/CeCuAl3/experiments/Polaris@ISIS.xye b/examples/PdTof1d/CeCuAl3/experiments/data.xye similarity index 100% rename from easyDiffractionApp/Gui/Resources/Examples/CeCuAl3/experiments/Polaris@ISIS.xye rename to examples/PdTof1d/CeCuAl3/experiments/data.xye diff --git a/examples/PdTof1d/CeCuAl3/project.cif b/examples/PdTof1d/CeCuAl3/project.cif new file mode 100644 index 00000000..7c662197 --- /dev/null +++ b/examples/PdTof1d/CeCuAl3/project.cif @@ -0,0 +1,5 @@ +_name CeCuAl3 +_short_description 'neutrons, powder, time-of-flight, Polaris@ISIS' +_samples CeCuAl3 +_experiments Polaris@ISIS +_modified '01.06.2022 17:37' \ No newline at end of file diff --git a/examples/PdTof1d/CeCuAl/project.json b/examples/PdTof1d/CeCuAl3/project.json similarity index 88% rename from examples/PdTof1d/CeCuAl/project.json rename to examples/PdTof1d/CeCuAl3/project.json index 1f79d2ce..80a733de 100644 --- a/examples/PdTof1d/CeCuAl/project.json +++ b/examples/PdTof1d/CeCuAl3/project.json @@ -4,24 +4,24 @@ "@class": "Sample", "@version": "0.0.1", "phases": { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phases", - "@version": "0.1.0", + "@version": "0.0.1", "name": "Phases", "data": [ { - "@module": "easyCrystallography.Structures.Phase", + "@module": "easyDiffractionLib.components.phase", "@class": "Phase", - "@version": "0.1.0", - "name": "CeCuAl", + "@version": "0.0.1", + "name": "CeCuAl3", "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", "@class": "SpaceGroup", "@version": "0.1.0", "_space_group_HM_name": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "value": "I 4 m m:1", "units": "dimensionless", @@ -29,37 +29,36 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ispace_group_name_H-M_alt.html", "display_name": "_space_group_HM_name", "enabled": true, - "@id": "1954026808476057484795678994665585426" + "@id": "92511438978541827671077057099865312947" }, "setting": "", - "@id": "44789896278723749053908744180303440237" + "@id": "222565624025825627389897792174009768146" }, "cell": { "@module": "easyCrystallography.Components.Lattice", "@class": "PeriodicLattice", "@version": "0.1.0", "length_a": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_a", - "value": 4.27, - "error": 2.0752675942694823e-05, + "error": 0.0, "min": 0, "max": Infinity, - "fixed": false, + "fixed": true, "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "118045009364869044973170781511273166304" + "value": 4.25678, + "@id": "234672620443661706452513332120214942559", + "enabled": true }, "length_b": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_b", - "value": 4.27, "error": 0.0, "min": 0, "max": Infinity, @@ -67,15 +66,15 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": false, - "@id": "42007859955892896734917527366386201765" + "value": 4.25678, + "@id": "85425776782285712451290302618592709094", + "enabled": false }, "length_c": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "length_c", - "value": 10.63386, "error": 0.0, "min": 0, "max": Infinity, @@ -83,15 +82,15 @@ "description": "Unit-cell length of the selected structure in angstroms.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_length_.html", "units": "angstrom", - "enabled": true, - "@id": "68169772586211830516861638269023208503" + "value": 10.63386, + "@id": "246279696135347528533794717361986971866", + "enabled": true }, "angle_alpha": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_alpha", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -99,15 +98,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "4630849066711794743137328798001489149" + "value": 90.0, + "@id": "219381851216903354666585703465148778448", + "enabled": false }, "angle_beta": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_beta", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -115,15 +114,15 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "66253765475231088010157595782508792770" + "value": 90.0, + "@id": "161908189792929465044933349045501351867", + "enabled": false }, "angle_gamma": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "angle_gamma", - "value": 90.0, "error": 0.0, "min": 0, "max": Infinity, @@ -131,17 +130,18 @@ "description": "Unit-cell angle of the selected structure in degrees.", "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_angle_.html", "units": "degree", - "enabled": false, - "@id": "307275569813681036997629556649432231944" + "value": 90.0, + "@id": "188615872074363214500782718002580593354", + "enabled": false }, "spacegroup": { "@module": "easyCrystallography.Components.SpaceGroup", "@class": "SpaceGroup", "@version": "0.1.0", "_space_group_HM_name": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "_space_group_HM_name", "units": "dimensionless", "description": "Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting.", @@ -149,27 +149,27 @@ "display_name": "_space_group_HM_name", "enabled": true, "value": "I 4 m m:1", - "@id": "1954026808476057484795678994665585426" + "@id": "92511438978541827671077057099865312947" }, "setting": "", - "@id": "44789896278723749053908744180303440237" + "@id": "222565624025825627389897792174009768146" }, - "@id": "89910516919152965396035682529018462299" + "@id": "251035681628978485508314653975561393149" }, "atoms": { - "@module": "easyCrystallography.Components.Site", + "@module": "easyDiffractionLib.components.site", "@class": "Atoms", - "@version": "0.1.0", + "@version": "0.0.1", "name": "atoms", "data": [ { - "@module": "easyCrystallography.Components.Site", + "@module": "easyDiffractionLib.components.site", "@class": "Site", - "@version": "0.1.0", + "@version": "0.0.1", "label": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Descriptor", - "@version": "0.1.0", + "@version": "0.2.2", "name": "label", "units": "dimensionless", "description": "A unique identifier for a particular site in the crystal", @@ -177,28 +177,22 @@ "display_name": "label", "enabled": true, "value": "Ce", - "@id": "158532580964058414357553556705444514942" + "@id": "165246873119695638909545137623096722509" }, "specie": { "@module": "easyCrystallography.Components.Specie", "@class": "Specie", "@version": "0.1.0", - "specie": { - "@module": "easyCrystallography.Elements.periodic_table", - "@class": "Specie", - "element": "Ce", - "oxidation_state": 0.0 - }, + "specie": "Ce", "value": "Ce", "units": "dimensionless", - "@id": "23620732596045583427782748585275765405" + "@id": "134562065958884847521548820369120732621" }, "occupancy": { - "@module": "easyCore.Objects.Base", + "@module": "easyCore.Objects.Variable", "@class": "Parameter", - "@version": "0.1.0", + "@version": "0.2.2", "name": "occupancy", - "value": 1.0, "error": 0.0, "min": -Infinity, "max": Infinity, @@ -207,14 +201,14 @@ "url": "https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_occupancy.html", "units": "dimensionless", "enabled": true, - "@id": 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a/easyDiffractionApp/Gui/Resources/Examples/Na2Ca3Al2F14/samples/Na2Ca3Al2F14.cif b/examples/PdTof1d/Na2Ca3Al2F14/samples/Na2Ca3Al2F14.cif similarity index 100% rename from easyDiffractionApp/Gui/Resources/Examples/Na2Ca3Al2F14/samples/Na2Ca3Al2F14.cif rename to examples/PdTof1d/Na2Ca3Al2F14/samples/Na2Ca3Al2F14.cif diff --git a/pyproject.toml b/pyproject.toml index 59c52700..f0dfacdf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = 'poetry.masonry.api' [tool.poetry] name = 'easyDiffractionApp' -version = '0.8.3-beta' +version = '0.8.4-beta' description = 'Making diffraction data analysis and modelling easy.' license = 'BSD-3-Clause' authors = ['Andrew Sazonov', 'Simon Ward', 'Piotr Rozyczko'] @@ -22,7 +22,7 @@ url = "https://easyscience.github.io/pypi/" secondary = true [tool.poetry.dependencies] -python = '^3.7, <3.9' +python = '^3.8, <3.9' darkdetect = '^0.3.1' pyobjc-core = { version = '^7.1', platform = 'darwin' } pyobjc-framework-cocoa = { version = '^7.1', platform = 'darwin' } @@ -32,21 +32,21 @@ easyApp = { git = 'https://github.com/easyScience/easyApp.git', rev = 'master' } #[tool.poetry.dev-dependencies] # PyInstaller -pyinstaller = '4.5.1' # 4.6-4.7 give "ModuleNotFoundError: No module named 'pip'" on Ubuntu, when run app +pyinstaller = '4.5.1' # 4.6-5.2 give "ModuleNotFoundError: No module named 'pip'" on Ubuntu, when run app #pyinstaller = { git = 'https://github.com/pyinstaller/pyinstaller.git', rev = 'develop' } pywin32-ctypes = { version = '^0.2.0', platform = 'win32' } pypiwin32 = { version = '^223', platform = 'win32' } -pefile = { version = '^2019.4.18', platform = 'win32' } +pefile = { version = '^2022.5.30', platform = 'win32' } # Misc toml = '^0.10.2' requests = '^2.25.1' dephell_licenses = '^0.1.7' ffmpeg-python = '^0.2.0' mss = '^6.1.0' -#opencv-python = '^4.5.1' opencv-python = '4.5.1.48' -google-trans-new = "^1.1.9" +google-trans-new = '^1.1.9' gTTS = '^2.2.2' +gemmi = '^0.5.4' [tool.poetry.scripts] easyDiffraction = 'easyDiffractionApp.main:main' @@ -54,7 +54,7 @@ easyDiffraction = 'easyDiffractionApp.main:main' # CUSTOM CONFIG [release] -app_name = 'easyDiffraction' +app_name = 'EasyDiffraction' tag_template = 'v{VERSION}' title_template = 'Version {VERSION} ({DATE})' description_file = 'RELEASE.md' @@ -72,14 +72,18 @@ download = '.ci/download' screenshots = '.ci/screenshots' build = '.ci/build' distribution = '.ci/distribution' -certificates_path = 'Certificates' [ci.scripts] silent_install = 'SilentInstall.js' package_install = 'InstallerInstallScript.js' config_control = 'InstallerControlScript.js' config_style = 'style.qss' -certificate_name = 'ESS_cert' + +[ci.codesign] +bundle_id = 'org.easyscience.easydiffraction' + +[ci.codesign.macos] +identity = 'Developer ID Application: European Spallation Source Eric (W2AG9MPZ43)' [ci.app.icon] dir = ['Gui', 'Resources', 'Logo'] @@ -90,7 +94,7 @@ file_ext = { macos = '.icns', ubuntu = '.png', windows = '.ico' } build_dir_suffix = 'Setup' repository_dir_suffix = 'Repos' os = { macos = 'macOS', ubuntu = 'Linux', windows = 'Windows' } # Should be the same as GH actions ${{ runner.os }} -arch = { macos = 'x86-64', ubuntu = 'x86-64', windows = 'x86-32' } +arch = { macos = 'x64', ubuntu = 'x64', windows = 'x64' } file_ext = { macos = '.app', ubuntu = '', windows = '.exe' } maintenance_tool_suffix = 'MaintenanceTool' maintenance_file = 'signedmaintenancetool.exe' @@ -160,16 +164,16 @@ manual_exclude = [ 'mfc*', 'msvcp*', 'VCRUNTIME*', '*Qt*Scxml*', '*Qt*Sensors*', '*Qt*Sql*', '*Qt*VirtualKeyboard*', '*Qt*Wayland*' ] [ci.qtifw.setup] -version = '4.1.0' +version = '4.4.1' https_mirrors = ['download.qt.io', 'ftp.fau.de/qtproject', 'mirrors.dotsrc.org/qtproject'] base_path = 'official_releases/qt-installer-framework' file_name_base = 'QtInstallerFramework' -file_platform = { macos = 'macOS-x86_64', ubuntu = 'linux-x64', windows = 'windows-x86' } +file_platform = { macos = 'macOS-x64', ubuntu = 'linux-x64', windows = 'windows-x64' } file_ext = { macos = 'dmg', ubuntu = 'run', windows = 'exe' } installation_path = { macOS = '/Users/runner/Qt', Linux = '/home/runner/Qt', Windows = 'C:\Qt' } [ci.ffmpeg.macos] # https://evermeet.cx/ffmpeg/ffmpeg-4.3.zip -version = '4.3.1' +version = '5.0.1' base_url = 'https://evermeet.cx/ffmpeg' file_name_base = 'ffmpeg-' file_ext = '.zip' diff --git a/tests/PbSO4/project.json b/tests/PbSO4/project.json index ec3b8afa..5f5b4294 100644 --- a/tests/PbSO4/project.json +++ b/tests/PbSO4/project.json @@ -7278,7 +7278,7 @@ } ], "instrument_parameters": { - "@module": "easyDiffractionLib.Elements.Experiments.Experiment", + "@module": "easyDiffractionLib.elements.Experiments.Experiment", "@class": "Pars1D", "@version": "0.0.1", "wavelength": { diff --git a/tests/polar/experiment.xye b/tests/polar/experiment.xye new file mode 100644 index 00000000..bc668d07 --- /dev/null +++ b/tests/polar/experiment.xye @@ -0,0 +1,388 @@ +4.6 626.97 93.64 413.31 90.64 +4.8 708.72 91.83 749.57 92.55 +5.0 718.07 89.38 575.64 87.29 +5.2 679.62 86.86 595.28 85.63 +5.4 683.03 84.66 580.64 83.17 +5.6 727.63 83.54 705.12 83.16 +5.8 709.16 83.16 653.77 82.39 +6.0 765.5 81.54 654.01 79.82 +6.2 813.4 80.76 865.23 81.57 +6.4 613.4 78.81 727.05 80.57 +6.6 530.91 76.38 458.89 75.37 +6.8 892.05 79.61 610.54 75.48 +7.0 932.68 79.59 733.16 76.68 +7.2 1611.08 89.13 863.58 79.1 +7.4 3505.62 109.22 1711.89 88.84 +7.6 5658.21 131.62 2033.16 95.3 +7.8 5454.61 124.07 2091.49 91.29 +8.0 3593.33 88.07 1460.03 68.68 +8.2 1720.63 70.73 906.5 61.95 +8.4 974.33 61.94 877.03 60.86 +8.6 1670.12 68.42 1546.15 67.16 +8.8 2380.65 76.38 2531.38 77.76 +9.0 2816.17 80.7 2649.69 79.25 +9.2 2271.4 72.72 2171.75 71.75 +9.4 1246.23 62.53 1157.09 61.57 +9.6 674.62 56.73 593.59 55.76 +9.8 690.47 55.49 574.28 54.09 +10.0 650.11 54.77 447.35 52.21 +10.2 497.37 53.33 447.73 52.69 +10.4 549.61 52.2 475.87 51.27 +10.6 619.58 53.45 436.48 51.27 +10.8 631.83 52.53 653.12 52.77 +11.0 459.72 51.33 493.73 51.79 +11.2 439.19 51.03 571.14 52.61 +11.4 455.23 51.0 406.06 50.45 +11.6 538.38 50.19 536.0 50.17 +11.8 573.93 46.73 579.49 46.81 +12.0 502.59 37.94 624.97 39.05 +12.2 382.09 37.94 483.5 38.88 +12.4 548.98 38.74 632.66 39.48 +12.6 759.49 40.63 910.88 41.91 +12.8 938.97 42.75 1051.91 43.68 +13.0 966.57 41.93 1127.24 43.23 +13.2 883.26 40.74 887.27 40.78 +13.4 599.7 38.5 592.61 38.42 +13.6 501.64 37.63 467.09 37.31 +13.8 406.53 37.28 396.74 37.19 +14.0 443.33 36.77 448.14 36.81 +14.2 397.42 36.61 482.8 37.39 +14.4 574.92 37.05 536.58 36.71 +14.6 672.48 38.06 514.49 36.69 +14.8 1218.7 42.36 956.73 40.3 +15.0 2038.32 48.33 1581.72 45.19 +15.2 2473.27 51.42 1823.2 47.18 +15.4 2408.49 51.36 1607.34 46.02 +15.6 1924.68 47.46 1161.06 42.19 +15.8 1843.13 46.2 916.4 39.55 +16.0 1535.92 40.56 739.87 35.15 +16.2 1223.09 38.0 704.68 34.3 +16.4 781.62 34.78 576.06 33.25 +16.6 619.03 33.13 497.22 32.16 +16.8 505.57 31.83 598.13 32.55 +17.0 513.34 31.68 462.2 31.27 +17.2 489.86 31.63 426.67 31.16 +17.4 451.39 31.36 501.7 31.76 +17.6 508.04 31.77 475.44 31.52 +17.8 581.81 32.38 541.25 32.05 +18.0 562.86 32.51 906.08 34.98 +18.2 766.89 33.35 1573.5 38.62 +18.4 817.74 33.59 2054.02 41.36 +18.6 796.7 33.16 1995.08 40.81 +18.8 750.51 32.89 1463.24 37.67 +19.0 484.9 31.53 800.24 33.81 +19.2 612.94 32.68 679.12 33.16 +19.4 781.23 34.38 676.61 33.67 +19.6 1289.18 38.78 876.5 36.32 +19.8 2615.92 46.49 1533.95 40.91 +20.0 4003.54 51.29 2123.31 42.79 +20.2 4419.98 50.0 2327.75 41.09 +20.4 3733.59 46.73 1967.75 38.7 +20.6 2353.72 39.82 1378.38 34.74 +20.8 1232.64 32.87 838.03 30.55 +21.0 766.54 29.84 696.61 29.41 +21.2 641.73 28.8 530.86 28.07 +21.4 527.51 27.72 561.44 27.95 +21.6 530.99 28.18 446.06 27.62 +21.8 490.1 28.25 494.58 28.27 +22.0 514.55 29.3 500.51 29.22 +22.2 533.06 32.35 467.21 31.99 +22.4 648.52 35.82 582.96 35.5 +22.6 917.85 38.65 732.61 37.78 +22.8 1039.3 39.21 799.88 38.09 +23.0 939.74 37.64 802.83 36.98 +23.2 699.73 35.78 518.17 34.86 +23.4 775.6 35.29 659.02 34.71 +23.6 928.82 36.02 793.95 35.33 +23.8 1633.96 37.75 1023.04 34.74 +24.0 2188.94 38.83 1296.8 34.47 +24.2 2444.96 38.05 1446.82 33.24 +24.4 2116.27 32.38 1214.12 28.23 +24.6 1543.45 29.04 942.93 26.11 +24.8 977.04 26.34 667.36 24.66 +25.0 628.41 24.67 492.07 23.89 +25.2 487.43 24.15 480.94 24.11 +25.4 497.39 24.17 447.33 23.88 +25.6 647.35 25.27 465.6 24.25 +25.8 1052.79 27.22 625.33 24.98 +26.0 1649.1 29.87 849.44 25.96 +26.2 2207.57 32.63 1046.96 27.24 +26.4 2333.0 32.98 1095.76 27.27 +26.6 2142.82 32.02 1004.78 26.64 +26.8 1673.56 29.65 836.33 25.43 +27.0 1322.86 27.92 765.03 24.99 +27.2 1287.82 27.03 830.93 24.66 +27.4 1472.66 28.48 1048.04 26.34 +27.6 1567.65 29.09 1103.57 26.79 +27.8 1574.07 29.08 1100.41 26.74 +28.0 1399.46 27.96 1031.16 26.08 +28.2 1030.61 26.35 743.96 24.8 +28.4 758.88 24.54 606.56 23.69 +28.6 628.06 23.52 556.65 23.12 +28.8 445.17 21.95 382.78 21.6 +29.0 449.58 21.93 467.35 22.03 +29.2 503.8 22.35 448.32 22.03 +29.4 509.06 22.33 546.19 22.53 +29.6 497.25 22.31 507.6 22.37 +29.8 490.91 21.67 560.91 22.05 +30.0 462.58 22.04 470.28 22.09 +30.2 561.88 22.53 470.89 22.02 +30.4 611.56 22.93 457.03 22.07 +30.6 801.05 24.01 517.54 22.48 +30.8 996.87 24.87 583.47 22.7 +31.0 1032.46 24.83 530.61 22.22 +31.2 964.6 24.52 545.47 22.32 +31.4 813.86 24.21 450.4 22.26 +31.6 686.45 23.58 412.7 22.08 +31.8 549.7 22.98 454.26 22.45 +32.0 422.51 22.74 341.25 22.29 +32.2 395.75 22.67 454.49 22.99 +32.4 505.26 22.81 514.08 22.85 +32.6 592.33 23.73 597.95 23.76 +32.8 578.01 23.9 627.39 24.15 +33.0 690.8 24.41 637.12 24.14 +33.2 904.55 24.59 776.17 23.95 +33.4 963.1 24.19 867.92 23.74 +33.6 1014.36 24.24 828.51 23.38 +33.8 1026.12 24.2 829.64 23.28 +34.0 835.89 23.52 712.27 22.92 +34.2 763.65 22.83 579.33 21.9 +34.4 633.36 21.85 547.65 21.4 +34.6 522.38 21.3 495.49 21.16 +34.8 468.79 20.78 426.16 20.56 +35.0 516.68 21.05 450.68 20.7 +35.2 517.87 21.25 468.35 20.99 +35.4 564.38 21.54 497.42 21.18 +35.6 659.37 21.96 554.5 21.41 +35.8 739.31 22.34 640.63 21.83 +36.0 780.55 22.82 714.19 22.49 +36.2 813.37 22.41 736.49 22.03 +36.4 824.91 22.94 682.31 22.22 +36.6 699.62 22.55 579.61 21.93 +36.8 648.17 22.53 553.46 22.05 +37.0 618.88 22.13 477.1 21.39 +37.2 616.44 22.19 463.55 21.39 +37.4 606.81 22.1 436.42 21.22 +37.6 760.71 22.67 510.51 21.4 +37.8 823.09 23.34 539.36 21.91 +38.0 1037.79 24.07 670.68 22.32 +38.2 1246.18 23.53 772.13 21.5 +38.4 1453.93 24.36 901.2 22.05 +38.6 1511.67 24.69 929.03 22.29 +38.8 1552.58 24.28 959.34 21.89 +39.0 1442.43 24.36 875.0 22.0 +39.2 1255.67 23.54 811.69 21.64 +39.4 1091.87 23.01 718.89 21.39 +39.6 994.66 22.68 794.16 21.81 +39.8 951.74 22.64 758.71 21.8 +40.0 965.42 22.32 805.74 21.64 +40.2 1014.54 22.55 825.05 21.74 +40.4 1103.25 23.07 834.5 21.91 +40.6 1184.43 23.15 847.84 21.69 +40.8 1163.32 23.0 841.6 21.6 +41.0 1189.78 22.82 840.43 21.29 +41.2 1103.75 22.47 744.38 20.87 +41.4 987.65 21.68 651.18 20.18 +41.6 895.73 21.68 550.27 20.08 +41.8 770.71 21.06 536.03 19.96 +42.0 739.94 20.69 566.98 19.86 +42.2 611.68 20.21 497.18 19.66 +42.4 579.35 20.14 496.71 19.75 +42.6 674.59 20.47 612.71 20.18 +42.8 799.77 21.0 660.72 20.36 +43.0 918.99 21.8 759.38 21.07 +43.2 970.8 21.71 813.78 21.02 +43.4 989.3 21.27 775.88 20.34 +43.6 935.56 21.05 741.83 20.21 +43.8 858.98 20.78 653.32 19.86 +44.0 747.31 19.91 644.53 19.46 +44.2 612.06 19.8 536.06 19.45 +44.4 593.74 19.54 552.9 19.36 +44.6 530.94 19.27 489.24 19.07 +44.8 528.63 19.13 500.05 19.0 +45.0 469.52 19.06 430.64 18.87 +45.2 534.29 19.03 473.4 18.74 +45.4 525.74 19.05 434.18 18.61 +45.6 550.94 19.36 430.33 18.78 +45.8 506.21 19.46 369.13 18.8 +46.0 552.6 19.45 408.85 18.76 +46.2 553.46 19.66 382.02 18.84 +46.4 687.62 19.99 445.8 18.86 +46.6 788.41 20.57 527.19 19.39 +46.8 865.62 21.07 582.79 19.8 +47.0 989.21 21.73 621.68 20.12 +47.2 1036.96 21.86 704.48 20.41 +47.4 1098.85 22.19 779.26 20.82 +47.6 1102.77 22.26 749.03 20.76 +47.8 1075.87 21.73 806.1 20.6 +48.0 1080.76 22.09 777.22 20.78 +48.2 966.23 21.67 775.51 20.84 +48.4 931.75 21.65 720.35 20.71 +48.6 951.5 21.58 724.42 20.58 +48.8 1002.48 21.72 756.01 20.64 +49.0 1031.25 20.95 788.1 19.94 +49.2 1069.0 21.06 796.87 19.93 +49.4 1083.97 21.42 778.77 20.16 +49.6 1064.51 21.38 774.61 20.16 +49.8 974.36 21.06 687.69 19.84 +50.0 951.34 20.77 694.11 19.66 +50.2 804.2 20.45 559.25 19.39 +50.4 714.32 19.84 494.37 18.89 +50.6 623.51 19.99 430.84 19.13 +50.8 586.16 19.9 364.58 18.88 +51.0 543.88 19.66 424.13 19.12 +51.2 488.87 19.43 342.94 18.76 +51.4 447.83 19.32 354.02 18.9 +51.6 513.26 19.42 340.74 18.63 +51.8 460.48 19.29 365.78 18.86 +52.0 478.07 19.69 385.82 19.27 +52.2 469.2 19.64 416.23 19.4 +52.4 457.61 19.69 420.67 19.53 +52.6 436.64 19.66 387.2 19.42 +52.8 469.28 19.9 363.95 19.42 +53.0 454.48 19.45 393.31 19.17 +53.2 433.11 19.83 384.81 19.61 +53.4 452.99 19.92 393.66 19.66 +53.6 460.91 20.11 385.75 19.77 +53.8 479.42 20.05 372.58 19.56 +54.0 514.08 20.17 406.62 19.69 +54.2 520.71 20.18 373.26 19.53 +54.4 556.73 20.36 444.45 19.87 +54.6 640.13 20.93 460.57 20.15 +54.8 772.45 21.23 619.57 20.56 +55.0 745.57 21.06 596.61 20.42 +55.2 827.09 21.06 654.5 20.32 +55.4 863.2 19.97 682.19 19.24 +55.6 816.19 19.45 712.54 19.04 +55.8 802.26 19.82 725.82 19.5 +56.0 762.03 19.72 668.88 19.34 +56.2 748.92 19.44 690.69 19.19 +56.4 764.06 19.41 674.79 19.05 +56.6 673.13 19.15 624.78 18.95 +56.8 658.88 18.93 591.05 18.65 +57.0 656.83 18.95 574.08 18.59 +57.2 647.48 19.0 549.5 18.58 +57.4 632.71 19.01 532.24 18.58 +57.6 579.93 18.76 485.92 18.35 +57.8 559.33 18.67 495.27 18.41 +58.0 578.68 18.69 409.25 17.96 +58.2 584.81 18.83 417.08 18.11 +58.4 575.37 19.05 432.76 18.46 +58.6 603.54 19.11 447.21 18.45 +58.8 640.61 19.32 474.09 18.6 +59.0 684.9 19.35 529.04 18.68 +59.2 710.68 19.57 544.5 18.87 +59.4 787.38 19.55 615.82 18.84 +59.6 809.81 20.02 642.48 19.34 +59.8 823.77 19.97 695.08 19.44 +60.0 826.28 20.05 698.82 19.54 +60.2 838.05 20.14 678.24 19.49 +60.4 754.59 19.7 635.75 19.21 +60.6 714.59 19.58 604.37 19.14 +60.8 688.71 19.42 583.78 19.01 +61.0 696.51 19.61 582.59 19.13 +61.2 675.24 19.53 569.0 19.08 +61.4 613.01 19.43 457.24 18.76 +61.6 637.1 19.31 470.77 18.6 +61.8 544.48 19.14 396.37 18.5 +62.0 516.27 18.73 352.58 18.03 +62.2 455.27 18.93 362.03 18.51 +62.4 474.72 19.0 379.43 18.6 +62.6 456.16 18.89 383.13 18.55 +62.8 466.05 18.86 356.88 18.37 +63.0 456.94 18.38 326.35 17.84 +63.2 440.41 18.02 354.34 17.65 +63.4 512.77 18.29 418.84 17.88 +63.6 488.59 18.45 414.36 18.14 +63.8 548.22 18.59 454.19 18.17 +64.0 630.73 18.73 492.07 18.14 +64.2 605.66 18.78 437.66 18.07 +64.4 659.66 18.98 516.44 18.38 +64.6 782.99 19.1 592.39 18.33 +64.8 839.92 19.7 625.32 18.81 +65.0 919.4 19.95 696.39 19.04 +65.2 924.99 20.01 707.15 19.14 +65.4 1017.5 20.21 801.94 19.36 +65.6 1000.25 20.27 785.1 19.42 +65.8 1035.91 20.12 838.97 19.36 +66.0 1062.77 20.26 814.77 19.29 +66.2 1023.34 20.31 820.36 19.51 +66.4 950.9 20.05 786.3 19.38 +66.6 901.83 19.85 723.91 19.11 +66.8 858.09 19.68 703.26 19.04 +67.0 788.71 19.33 663.21 18.81 +67.2 818.61 19.15 622.0 18.35 +67.4 731.56 19.16 609.02 18.65 +67.6 699.64 19.07 587.8 18.58 +67.8 615.29 18.76 508.89 18.3 +68.0 584.64 18.69 450.59 18.11 +68.2 610.66 18.77 481.61 18.19 +68.4 515.66 18.57 438.07 18.22 +68.6 566.21 18.84 513.38 18.61 +68.8 557.98 19.09 489.74 18.8 +69.0 590.37 19.1 496.35 18.68 +69.2 602.21 19.1 494.58 18.61 +69.4 610.71 19.04 558.7 18.8 +69.6 631.87 19.24 495.94 18.65 +69.8 614.17 19.33 526.89 18.93 +70.0 591.01 19.73 555.2 19.57 +70.2 682.02 19.9 570.09 19.41 +70.4 671.82 19.93 558.63 19.42 +70.6 620.64 19.65 564.74 19.4 +70.8 672.9 19.91 521.03 19.23 +71.0 623.43 19.82 521.46 19.37 +71.2 650.8 20.39 527.79 19.83 +71.4 656.9 20.31 562.97 19.88 +71.6 610.22 20.36 494.24 19.83 +71.8 570.86 20.2 472.73 19.73 +72.0 576.21 20.21 466.77 19.7 +72.2 611.69 20.39 520.16 19.97 +72.4 659.55 20.73 527.62 20.12 +72.6 614.16 20.83 557.11 20.54 +72.8 639.04 21.14 550.08 20.71 +73.0 596.43 20.82 572.05 20.7 +73.2 557.56 20.74 532.2 20.61 +73.4 562.18 20.65 539.59 20.54 +73.6 614.91 20.34 573.38 20.15 +73.8 648.89 20.81 601.64 20.6 +74.0 644.83 20.9 598.98 20.67 +74.2 647.35 20.85 604.49 20.66 +74.4 625.47 20.75 583.45 20.56 +74.6 659.67 20.98 571.6 20.56 +74.8 598.98 20.63 555.6 20.43 +75.0 649.05 21.1 590.07 20.82 +75.2 720.45 21.57 600.83 21.01 +75.4 704.04 21.52 644.58 21.24 +75.6 639.5 21.38 591.09 21.14 +75.8 681.64 21.39 628.85 21.15 +76.0 717.42 21.59 602.84 21.04 +76.2 691.49 21.53 616.86 21.16 +76.4 666.95 21.93 634.47 21.77 +76.6 670.42 22.02 540.49 21.38 +76.8 627.38 21.94 483.2 21.22 +77.0 554.07 21.69 521.92 21.53 +77.2 578.27 21.76 535.31 21.53 +77.4 603.68 21.85 443.49 21.07 +77.6 612.98 22.41 433.23 21.49 +77.8 636.95 22.6 496.25 21.89 +78.0 602.01 22.52 449.83 21.72 +78.2 605.13 22.55 514.09 22.08 +78.4 618.76 22.5 485.65 21.8 +78.6 583.18 22.41 487.78 21.93 +78.8 586.35 22.52 510.53 22.15 +79.0 633.06 23.39 538.35 22.92 +79.2 668.07 23.68 592.58 23.3 +79.4 673.48 23.59 539.33 22.89 +79.6 620.36 23.39 568.03 23.12 +79.8 697.11 23.49 609.58 23.03 +80.0 696.35 23.69 559.43 23.0 +80.2 673.4 23.99 578.5 23.48 +80.4 715.34 24.45 631.24 24.0 +80.6 625.41 23.98 627.0 23.99 +80.8 659.25 24.3 600.44 24.0 +81.0 617.92 24.1 526.94 23.63 +81.2 643.9 24.21 551.74 23.72 +81.4 610.43 24.05 570.73 23.84 +81.6 687.21 25.11 535.41 24.27 +81.8 604.92 24.92 559.32 24.65 +82.0 589.97 24.97 499.26 24.46 diff --git a/tests/polar/structure.cif b/tests/polar/structure.cif new file mode 100644 index 00000000..5e786367 --- /dev/null +++ b/tests/polar/structure.cif @@ -0,0 +1,42 @@ +data_Ho2Ti2O7 + +_space_group_name_h-m_ref 'F d -3 m' +_space_group_it_coordinate_system_code 2 + +_cell_length_a 10.26594(88) +_cell_length_b 10.26594(88) +_cell_length_c 10.26594(88) +_cell_angle_alpha 90.0 +_cell_angle_beta 90.0 +_cell_angle_gamma 90.0 + +loop_ +_atom_site_label +_atom_site_type_symbol +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +_atom_site_occupancy +_atom_site_adp_type +_atom_site_U_iso_or_equiv +Ho Ho3+ 0.5 0.5 0.5 1.0 Uiso 0.0 +Ti Ti3+ 0.0 0.0 0.0 1.0 Uiso 0.0 +O1 O2- 0.32858 0.125 0.125 1.0 Uiso 0.0 +O2 O2- 0.375 0.375 0.375 1.0 Uiso 0.0 + +loop_ +_atom_site_susceptibility_label +_atom_site_susceptibility_chi_type +_atom_site_susceptibility_chi_11 +_atom_site_susceptibility_chi_22 +_atom_site_susceptibility_chi_33 +_atom_site_susceptibility_chi_12 +_atom_site_susceptibility_chi_13 +_atom_site_susceptibility_chi_23 +Ho Cani 0.1() 0.1 0.1 0.1() 0.1 0.1 + +loop_ +_atom_site_scat_label +_atom_site_scat_lande +_atom_site_scat_kappa +Ho 2.0 1.0 diff --git a/tools/Scripts/Config.py b/tools/Scripts/Config.py index 4170bf95..c3b56a52 100644 --- a/tools/Scripts/Config.py +++ b/tools/Scripts/Config.py @@ -12,10 +12,11 @@ class Config(): - def __init__(self): + def __init__(self, branch_name=None): # Main self.__dict__ = Functions.config() self.os = Functions.osName() + self.branch_name = branch_name # Application self.app_version = self.__dict__['tool']['poetry']['version'] @@ -41,23 +42,19 @@ def __init__(self): self.setup_file_ext = self.__dict__['ci']['app']['setup']['file_ext'][self.os] self.setup_full_name = f'{self.setup_name}{self.setup_file_ext}' self.setup_exe_path = os.path.join(self.dist_dir, self.setup_full_name) - self.maintenancetool_file = os.path.join(self.__dict__['ci']['project']['subdirs']['certificates_path'], - self.__dict__['ci']['app']['setup']['maintenance_file']) + + # Artifacts + self.setup_zip_path_short = self.setupZipPathShort() + self.setup_zip_path = self.setupZipPath() + self.video_tutorial_path = self.videoTutorialPath() # Application repository self.repository_dir_suffix = self.__dict__['ci']['app']['setup']['repository_dir_suffix'] # Project - self.package_name = f'{self.app_name}App' + self.package_name = self.__dict__['tool']['poetry']['name'] self.license_file = self.__dict__['ci']['project']['license_file'] - # Certificates - self.certificate_path = os.path.join(self.__dict__['ci']['project']['subdirs']['certificates_path'], - self.__dict__['ci']['scripts']['certificate_name'] + "_" + - Functions.osName()[0:3]) - self.certificate_zip_path = os.path.join(self.__dict__['ci']['project']['subdirs']['certificates_path'], - 'Codesigning.zip') - def __getitem__(self, key): return self.__dict__[key] @@ -90,5 +87,28 @@ def installationDirForQtifw(self): dir = os.path.join(dir_shortcut, self.app_name) return dir + def artifactsFileSuffix(self): + if self.branch_name != 'master' and self.branch_name is not None: + return f'_{self.branch_name}' + return '' + + def setupZipPathShort(self): + setup_zip_name = f'{self.setup_name}.zip' + setup_zip_path = os.path.join(self.dist_dir, setup_zip_name) + return setup_zip_path + + def setupZipPath(self): + file_suffix = self.artifactsFileSuffix() + setup_zip_name = f'{self.setup_name}{file_suffix}.zip' + setup_zip_path = os.path.join(self.dist_dir, setup_zip_name) + return setup_zip_path + + def videoTutorialPath(self): + file_suffix = self.artifactsFileSuffix() + video_tutorial_name = f'tutorial_{self.setup_name}{file_suffix}.mp4' + video_tutorial_path = os.path.join(self.dist_dir, video_tutorial_name) + return video_tutorial_path + + if __name__ == "__main__": Config() diff --git a/tools/Scripts/CreateTestVideos.py b/tools/Scripts/CreateTestVideos.py deleted file mode 100755 index 8cd3ea2b..00000000 --- a/tools/Scripts/CreateTestVideos.py +++ /dev/null @@ -1,86 +0,0 @@ -# SPDX-FileCopyrightText: 2022 easyDiffraction contributors -# SPDX-License-Identifier: BSD-3-Clause -# © 2021-2022 Contributors to the easyDiffraction project - -__author__ = "github.com/AndrewSazonov" -__version__ = '0.0.1' - -import os, sys -import ffmpeg -import Functions, Config - - -CONFIG = Config.Config() - -def inputPattern(): - return f'{CONFIG.screenshots_dir}/*.png' - -def outputPath(): - file_suffix = Functions.artifactsFileSuffix(sys.argv[1]) - return os.path.join(CONFIG.dist_dir, f'tutorial{CONFIG.setup_name_suffix}{file_suffix}.mp4') - -def outputOptions(): - # https://trac.ffmpeg.org/wiki/Encode/H.264 - # https://slhck.info/video/2017/02/24/crf-guide.html - # https://kkroening.github.io/ffmpeg-python/ - # https://github.com/kkroening/ffmpeg-python/issues/95 - return { - 'crf': CONFIG['ci']['app']['tutorials']['video']['crf'], - 'preset': CONFIG['ci']['app']['tutorials']['video']['preset'], - 'movflags': CONFIG['ci']['app']['tutorials']['video']['movflags'], - 'pix_fmt': CONFIG['ci']['app']['tutorials']['video']['pix_fmt'] - } - -def fps(): - return CONFIG['ci']['app']['tutorials']['video']['fps'] - -def writeVideo(): - ( - ffmpeg - .input(inputPattern(), pattern_type='glob', framerate=fps()) - .filter('scale', size='1280x768') - .output(outputPath(), **outputOptions()) - .run(overwrite_output=True) - ) - -def ffmpegZippedFileName(): - version = CONFIG['ci']['ffmpeg']['macos']['version'] - file_name_base = CONFIG['ci']['ffmpeg']['macos']['file_name_base'] - file_ext = CONFIG['ci']['ffmpeg']['macos']['file_ext'] - return f'{file_name_base}{version}{file_ext}' - -def ffmpegUnzippedFilePath(): - exe = CONFIG['ci']['ffmpeg']['macos']['exe'] - return os.path.join(CONFIG.download_dir, exe) - -def ffmpegDownloadUrl(): - base_url = CONFIG['ci']['ffmpeg']['macos']['base_url'] - return f'{base_url}/{ffmpegZippedFileName()}' - -def ffmpegDownloadDest(): - return os.path.join(CONFIG.download_dir, f'{ffmpegZippedFileName()}') - -def downloadFfmpeg(): - Functions.downloadFile( - url=ffmpegDownloadUrl(), - destination=ffmpegDownloadDest() - ) - -def unzipFfmpeg(): - if os.path.exists(ffmpegUnzippedFilePath()): - Functions.printNeutralMessage(f'File already exists {ffmpegUnzippedFilePath()}') - return - Functions.unzip(ffmpegDownloadDest(), CONFIG.download_dir) - Functions.addReadPermission(ffmpegUnzippedFilePath()) - -def addDownloadDestToPath(): - path = Functions.environmentVariable('PATH') - download_dest = os.path.abspath(CONFIG.download_dir) - Functions.setEnvironmentVariable('PATH', f'{download_dest}:{path}') - -if __name__ == "__main__": - #downloadFfmpeg() - #unzipFfmpeg() - #addDownloadDestToPath() - #writeVideo() - Functions.copyFile('tutorial.mp4', outputPath()) diff --git a/tools/Scripts/Functions.py b/tools/Scripts/Functions.py index 251150cd..bbe05d8a 100755 --- a/tools/Scripts/Functions.py +++ b/tools/Scripts/Functions.py @@ -326,9 +326,3 @@ def zip(source, destination): sys.exit() else: printSuccessMessage(message) - - -def artifactsFileSuffix(branch_name): - if branch_name != 'master': - return f'_{branch_name}' - return '' diff --git a/tools/Scripts/InstallerControlScript.js b/tools/Scripts/InstallerControlScript.js index bc519217..4ce21d63 100644 --- a/tools/Scripts/InstallerControlScript.js +++ b/tools/Scripts/InstallerControlScript.js @@ -14,8 +14,8 @@ Controller.prototype.IntroductionPageCallback = function() if (installer.isInstaller()) { var msg = "" - msg += "

Welcome to the easyDiffraction Setup Wizard.

" - msg += "

easyDiffraction is a scientific software for modelling and analysis of diffraction data.

" + msg += "

Welcome to the EasyDiffraction Setup Wizard.

" + msg += "

EasyDiffraction is a scientific software for modelling and analysis of diffraction data.

" msg += "

For more details, please visit https://easydiffraction.org

" page.MessageLabel.setText(msg) } diff --git a/tools/Scripts/InstallerInstallScript.js b/tools/Scripts/InstallerInstallScript.js index 0e0fa5f0..f536a2e0 100644 --- a/tools/Scripts/InstallerInstallScript.js +++ b/tools/Scripts/InstallerInstallScript.js @@ -97,15 +97,15 @@ Component.prototype.createOperations = function() component.addOperation( "Copy", - "@TargetDir@/easyDiffraction.desktop", - "@HomeDir@/.local/share/applications/easyDiffraction.desktop" + "@TargetDir@/@ProductName@.desktop", + "@HomeDir@/.local/share/applications/@ProductName@.desktop" ) /* component.addOperation( "Copy", - "@TargetDir@/easyDiffraction.desktop", - "/usr/share/applications/easyDiffraction.desktop" + "@TargetDir@/@ProductName@.desktop", + "/usr/share/applications/@ProductName@.desktop" ) */ } diff --git a/tools/Scripts/MakeInstaller.py b/tools/Scripts/MakeInstaller.py index 87c005da..e40f7020 100644 --- a/tools/Scripts/MakeInstaller.py +++ b/tools/Scripts/MakeInstaller.py @@ -11,7 +11,6 @@ import xml.dom.minidom import dephell_licenses import Functions, Config -import Signatures CONFIG = Config.Config() @@ -251,23 +250,6 @@ def installQtInstallerFramework(): else: Functions.printSuccessMessage(message) -def prepareSignedMaintenanceTool(): - if CONFIG.setup_os != "Windows": - return - try: - message = 'copy and sign MaintenanceTool' - target_dir = CONFIG['ci']['project']['subdirs']['certificates_path'] - target_file = os.path.join(target_dir, "signedmaintenancetool.exe") - # copy MaintenanceTool locally - Functions.copyFile(os.path.join(qtifwDirPath(), "bin", "installerbase.exe" ), target_file) - Signatures.unzipCerts(zip_pass=sys.argv[2]) - Signatures.sign_windows(file_to_sign=target_file, cert_pass=sys.argv[1]) - except Exception as exception: - Functions.printFailMessage(message, exception) - sys.exit(1) - else: - Functions.printSuccessMessage(message) - def createInstallerSourceDir(): try: message = f'create installer source directory {setupBuildDirPath()}' @@ -298,11 +280,6 @@ def createInstallerSourceDir(): Functions.moveDir(source=freezed_app_src, destination=app_data_subsubdir_path) Functions.copyFile(source=CONFIG.license_file, destination=app_data_subsubdir_path) Functions.copyFile(source=CONFIG['release']['changelog_file'], destination=app_data_subsubdir_path) - # TODO: change the handling of failure in all methods in Functions.py so they bubble up exceptions - # TODO: remove this platform conditional once the above is done - if CONFIG.os == 'windows': - Functions.copyFile(source=CONFIG.maintenancetool_file, destination=app_data_subsubdir_path) - # package: docs ##docs_subdir_path = os.path.join(packagesDirPath(), CONFIG['ci']['app']['setup']['build']['docs_package_subdir']) ##docs_data_subsubdir_path = os.path.join(docs_subdir_path, CONFIG['ci']['app']['setup']['build']['data_subsubdir']) @@ -322,8 +299,6 @@ def createInstallerSourceDir(): #Functions.copyDir(source=examples_dir_src, destination=os.path.join(app_data_subsubdir_path, examples_dir_dest)) # TODO: change the handling of failure in all methods in Functions.py so they bubble up exceptions # TODO: remove this platform conditional once the above is done - if CONFIG.os == 'windows': - Functions.copyFile(source=CONFIG.maintenancetool_file, destination=app_data_subsubdir_path) except Exception as exception: Functions.printFailMessage(message, exception) sys.exit(1) @@ -332,7 +307,7 @@ def createInstallerSourceDir(): def createOfflineInstaller(): try: - message = 'create installer' + message = 'create offline installer' qtifw_bin_dir_path = os.path.join(qtifwDirPath(), 'bin') qtifw_binarycreator_path = os.path.join(qtifw_bin_dir_path, 'binarycreator') qtifw_installerbase_path = os.path.join(qtifw_bin_dir_path, 'installerbase') @@ -387,7 +362,6 @@ def addFilesToLocalRepository(): downloadQtInstallerFramework() osDependentPreparation() installQtInstallerFramework() - prepareSignedMaintenanceTool() createInstallerSourceDir() createOfflineInstaller() createOnlineRepositoryLocally() diff --git a/tools/Scripts/RenameTestVideos.py b/tools/Scripts/RenameTestVideos.py new file mode 100755 index 00000000..d3568c69 --- /dev/null +++ b/tools/Scripts/RenameTestVideos.py @@ -0,0 +1,21 @@ +# SPDX-FileCopyrightText: 2021 easyDiffraction contributors +# SPDX-License-Identifier: BSD-3-Clause +# © 2021 Contributors to the easyDiffraction project + +__author__ = "github.com/AndrewSazonov" +__version__ = '0.0.1' + +import os, sys +import Functions, Config + + +CONFIG = Config.Config(sys.argv[1]) + +def inputPath(): + return 'tutorial.mp4' + +def outputPath(): + return CONFIG.video_tutorial_path + +if __name__ == "__main__": + Functions.copyFile(inputPath(), outputPath()) diff --git a/tools/Scripts/RunApp.py b/tools/Scripts/RunApp.py index ccefe506..5dd945bd 100644 --- a/tools/Scripts/RunApp.py +++ b/tools/Scripts/RunApp.py @@ -35,5 +35,6 @@ def runApp(): else: Functions.printSuccessMessage(message) + if __name__ == "__main__": runApp() diff --git a/tools/Scripts/SignAppInstaller.py b/tools/Scripts/SignAppInstaller.py new file mode 100644 index 00000000..9572a946 --- /dev/null +++ b/tools/Scripts/SignAppInstaller.py @@ -0,0 +1,276 @@ +# SPDX-FileCopyrightText: 2021 easyDiffraction contributors +# SPDX-License-Identifier: BSD-3-Clause +# © 2021 Contributors to the easyDiffraction project + +__author__ = "github.com/AndrewSazonov" +__version__ = '0.0.1' + +import os +import sys +import time +import base64 +import Config +import Functions + + +CONFIG = Config.Config(sys.argv[1]) + +MACOS_IDENTITY = CONFIG['ci']['codesign']['macos']['identity'] +MACOS_CERTIFICATE_ENCODED = sys.argv[2] # Encoded content of the certificate.p12 file +MACOS_CERTIFICATE_PASSWORD = sys.argv[3] # Password associated with the certificate.p12 file +APPSTORE_NOTARIZATION_USERNAME = sys.argv[4] # Apple ID (esss.se personal account) added to https://developer.apple.com +APPSTORE_NOTARIZATION_PASSWORD = sys.argv[5] # App specific password for EasyDiffraction from https://appleid.apple.com + +def signLinux(): + Functions.printNeutralMessage('No code signing needed for linux') + return + +def signWindows(): + Functions.printNeutralMessage('Code signing on Windows is not supported yet') + return + +def signMacos(): + try: + ########################## + # Prepare for code signing + ########################## + + message = f'sign code on {CONFIG.os}' + keychain_name = 'codesign.keychain' + keychain_password = 'password' + mac_certificate_fpath = 'certificate.p12' + + try: + sub_message = f'create keychain "{keychain_name}"' + Functions.run( + 'security', 'create-keychain', + '-p', keychain_password, + keychain_name) + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + try: + sub_message = f'set created keychain "{keychain_name}" to be default keychain' + Functions.run( + 'security', 'default-keychain', + '-s', keychain_name) + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + try: + sub_message = f'list keychains' + Functions.run( + 'security', 'list-keychains') + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + try: + sub_message = f'unlock created keychain "{keychain_name}"' + Functions.run( + 'security', 'unlock-keychain', + '-p', keychain_password, + keychain_name) + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + try: + sub_message = f'create certificate file "{mac_certificate_fpath}"' + certificate_decoded = base64.b64decode(MACOS_CERTIFICATE_ENCODED) + with open(mac_certificate_fpath, 'wb') as f: + f.write(certificate_decoded) + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + try: + sub_message = f'import certificate "{mac_certificate_fpath}" to created keychain "{keychain_name}"' + Functions.run( + 'security', 'import', + mac_certificate_fpath, + '-k', keychain_name, + '-P', MACOS_CERTIFICATE_PASSWORD, + '-T', '/usr/bin/codesign') + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + try: + sub_message = f'show certificates' + Functions.run( + 'security', 'find-identity', + '-v') + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + try: + sub_message = f'allow codesign to access certificate key from keychain "{keychain_name}"' + Functions.run( + 'security', 'set-key-partition-list', + '-S', 'apple-tool:,apple:,codesign:', + '-s', + '-k', keychain_password, keychain_name) + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + #################### + # Sign app installer + #################### + + try: + sub_message = f'sign installer app "{CONFIG.setup_exe_path}" with imported certificate' + Functions.run( + 'codesign', + '--deep', # nested code content such as helpers, frameworks, and plug-ins, should be recursively signed + '--force', # replace any existing signature on the path(s) given + '--verbose=1', # set (with a numeric value) or increments the verbosity level of output + '--timestamp', # request that a default Apple timestamp authority server be contacted to authenticate the time of signin + '--options=runtime', # specify a set of option flags to be embedded in the code signature + '--sign', MACOS_IDENTITY, # sign the code at the path(s) given using this identity + CONFIG.setup_exe_path) + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + try: + sub_message = f'verify app signatures for installer "{CONFIG.setup_exe_path}"' + Functions.run( + 'codesign', + '--verify', # verification of code signatures + '--verbose=1', # set (with a numeric value) or increments the verbosity level of output + CONFIG.setup_exe_path) + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + ######################## + # Notarize app installer + ######################## + + try: + sub_message = f'create zip archive "{CONFIG.setup_zip_path_short}" of offline app installer "{CONFIG.setup_exe_path}" for notarization' + #Functions.zip(CONFIG.setup_exe_path, CONFIG.setup_zip_path_short) + Functions.run( + 'ditto', + '-c', + '-k', + '--rsrc', + '--sequesterRsrc', + CONFIG.setup_exe_path, + CONFIG.setup_zip_path_short) + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + try: + sub_message = f'notarize app installer "{CONFIG.setup_zip_path_short}" for distribution outside of the Mac App Store' # Notarize the app by submitting a zipped package of the app bundle + Functions.run( + 'xcrun', 'altool', + '--notarize-app', + '--file', CONFIG.setup_zip_path_short, + '--type', 'macos', + '--primary-bundle-id', CONFIG['ci']['codesign']['bundle_id'], + '--username', APPSTORE_NOTARIZATION_USERNAME, + '--password', APPSTORE_NOTARIZATION_PASSWORD) + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + try: + sub_message = f'delete submitted zip "{CONFIG.setup_zip_path_short}" of notarized app installer' + Functions.removeFile(CONFIG.setup_zip_path_short) + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + ###################### + # Staple app installer + ###################### + + try: + sub_message = f'download and attach (staple) tickets for notarized executables to app installer "{CONFIG.setup_exe_path}"' + time.sleep(180) # Sleep for 3 minutes before calling the stapler to handle notarization lag on Apple server + # Or maybe one could instead get 'RequestUUID' from the previous 'xcrun altool --notarize-app...' output and + # check in the loop until notarization is succeded via 'xcrun altool --notarization-info UUID...'? + # If notarization is in progress, the '--notarization-info' output should contain 'Status: in progress' + # If notarization is succeded, the '--notarization-info' output should contain 'Status: success' + Functions.run( + 'xcrun', 'stapler', + 'staple', CONFIG.setup_exe_path) + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + try: + sub_message = f'verify the stapled tickets of app installer "{CONFIG.setup_exe_path}"' + Functions.run( + 'xcrun', 'stapler', + 'validate', CONFIG.setup_exe_path) + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + try: + sub_message = f'verify notarization of app installer "{CONFIG.setup_exe_path}"' + Functions.run( + 'spctl', + '--assess', + '--vv', + CONFIG.setup_exe_path) + except Exception as sub_exception: + Functions.printFailMessage(sub_message, sub_exception) + sys.exit(1) + else: + Functions.printSuccessMessage(sub_message) + + except Exception as exception: + Functions.printFailMessage(message, exception) + sys.exit(1) + else: + Functions.printSuccessMessage(message) + + +if __name__ == "__main__": + if CONFIG.os == 'ubuntu': + signLinux() + elif CONFIG.os == 'windows': + signWindows() + elif CONFIG.os == 'macos': + signMacos() + else: + raise AttributeError(f"OS '{CONFIG.os}' is not supported") diff --git a/tools/Scripts/Signatures.py b/tools/Scripts/Signatures.py deleted file mode 100644 index 4996dfed..00000000 --- a/tools/Scripts/Signatures.py +++ /dev/null @@ -1,132 +0,0 @@ -# SPDX-FileCopyrightText: 2022 easyDiffraction contributors -# SPDX-License-Identifier: BSD-3-Clause -# © 2021-2022 Contributors to the easyDiffraction project - -import os -import sys -import zipfile -import Config -import Functions - - -CONFIG = Config.Config() - -app_name = CONFIG.app_name -app_url = CONFIG['tool']['poetry']['homepage'] -installer_exe_path = os.path.join(CONFIG.dist_dir, CONFIG.setup_full_name) - -certificates_dir_path = CONFIG['ci']['project']['subdirs']['certificates_path'] -certificate_file_path = CONFIG.certificate_path -certificates_zip_path = CONFIG.certificate_zip_path - - -def unzipCerts(zip_pass=None): - - if zip_pass is None: - zip_pass = sys.argv[2] - - print('* Unzip certificates') - with zipfile.ZipFile(certificates_zip_path) as zf: - zf.extractall( - path=certificates_dir_path, - pwd=bytes(zip_pass, 'utf-8')) - - -def sign_linux(): - print('* No code signing needed for linux') - return - - -def sign_windows(file_to_sign=installer_exe_path, cert_pass=None): - print('* Code signing for windows') - if cert_pass is None: - cert_pass = sys.argv[1] - # using local signtool, since installing the whole SDK is a total overkill - # signtool_exe_path = os.path.join('C:', os.sep, 'Program Files (x86)', 'Windows Kits', '10', 'bin', 'x86', 'signtool.exe') - signtool_exe_path = os.path.join(certificates_dir_path, 'signtool.exe') - - win_certificate_file_path = certificate_file_path + ".pfx" - - print('* Sign code with imported certificate') - Functions.run( - signtool_exe_path, 'sign', # info - https://msdn.microsoft.com/en-us/data/ff551778(v=vs.71) - '/f', win_certificate_file_path, # signing certificate in a file - '/p', cert_pass, # password to use when opening a PFX file - '/d', app_name, # description of the signed content - '/du', app_url, # URL for the expanded description of the signed content - '/t', 'http://timestamp.digicert.com', # URL to a timestamp server - '/v', # display the verbose version of operation and warning messages - '/a', # Select the best signing cert automatically - file_to_sign) - - -def sign_macos(): - print('* Code signing on MacOS is disabled.') - return - keychain_name = 'codesign.keychain' - keychain_password = 'password' - mac_certificate_file_path = certificate_file_path + ".p12" - identity = 'Developer ID Application: European Spallation Source Eric (W2AG9MPZ43)' - - print('* Create keychain') - Functions.run( - 'security', 'create-keychain', - '-p', keychain_password, - keychain_name) - - print('* Set it to be default keychain') - Functions.run( - 'security', 'default-keychain', - '-s', keychain_name) - - print('* List keychains') - Functions.run( - 'security', 'list-keychains') - - print('* Unlock created keychain') - Functions.run( - 'security', 'unlock-keychain', - '-p', keychain_password, - keychain_name) - - print('* Import certificate to created keychain') - Functions.run( - 'security', 'import', - mac_certificate_file_path, - '-k', keychain_name, - '-P', certificate_password, - '-T', '/usr/bin/codesign') - - print('* Show certificates') - Functions.run( - 'security', 'find-identity', - '-v') - - print('* Allow codesign to access certificate key from keychain') - Functions.run( - 'security', 'set-key-partition-list', - '-S', 'apple-tool:,apple:,codesign:', - '-s', - '-k', keychain_password) - - print('* Sign code with imported certificate') - Functions.run( - 'codesign', - '--deep', - '--force', - '--verbose', - # --timestamp URL - '--sign', identity, - installer_exe_path) - - -if __name__ == "__main__": - unzipCerts() - if CONFIG.os == 'ubuntu': - sign_linux() - elif CONFIG.os == 'windows': - sign_windows() - elif CONFIG.os == 'macos': - sign_macos() - else: - raise AttributeError("Incorrect OS") diff --git a/tools/Scripts/ZipArtifacts.py b/tools/Scripts/ZipAppInstaller.py similarity index 65% rename from tools/Scripts/ZipArtifacts.py rename to tools/Scripts/ZipAppInstaller.py index b27abed3..ef0c4f2b 100755 --- a/tools/Scripts/ZipArtifacts.py +++ b/tools/Scripts/ZipAppInstaller.py @@ -9,19 +9,16 @@ import Functions, Config -CONFIG = Config.Config() +CONFIG = Config.Config(sys.argv[1]) def source(): return CONFIG.setup_exe_path def destination(): - file_suffix = Functions.artifactsFileSuffix(sys.argv[1]) - setup_zip_name = f'{CONFIG.setup_name}{file_suffix}.zip' - setup_zip_path = os.path.join(CONFIG.dist_dir, setup_zip_name) - return setup_zip_path + return CONFIG.setup_zip_path -def zip(): +def zipAppInstaller(): Functions.zip(source(), destination()) if __name__ == "__main__": - zip() + zipAppInstaller()