From 44a7767f5c608902c87cacaa8fa2615cef5e6342 Mon Sep 17 00:00:00 2001 From: Tieqiong Zhang Date: Tue, 14 Jan 2025 01:44:03 -0500 Subject: [PATCH 1/7] fix: released user manual img not showing --- doc/manual/html/readme.txt | 2 - doc/source/conf.py | 2 +- doc/source/manual.rst | 2 +- .../manual_resources}/pdfgui.html | 50 +++++++++---------- 4 files changed, 27 insertions(+), 29 deletions(-) delete mode 100644 doc/manual/html/readme.txt rename doc/{manual/html => source/manual_resources}/pdfgui.html (99%) diff --git a/doc/manual/html/readme.txt b/doc/manual/html/readme.txt deleted file mode 100644 index cf60cf43..00000000 --- a/doc/manual/html/readme.txt +++ /dev/null @@ -1,2 +0,0 @@ -This directory need to be relatively the same as doc/build/html/manual from -doc/source/_static/images diff --git a/doc/source/conf.py b/doc/source/conf.py index cc57882a..ec3f312b 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -158,7 +158,7 @@ # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the documentation. -# html_extra_path = [] +html_extra_path = ['images'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. diff --git a/doc/source/manual.rst b/doc/source/manual.rst index 9667d818..fa6b1192 100644 --- a/doc/source/manual.rst +++ b/doc/source/manual.rst @@ -13,4 +13,4 @@ Resources used - :download:`Nanoparticle structure ` .. raw:: html - :file: ../manual/html/pdfgui.html + :file: manual_resources/pdfgui.html diff --git a/doc/manual/html/pdfgui.html b/doc/source/manual_resources/pdfgui.html similarity index 99% rename from doc/manual/html/pdfgui.html rename to doc/source/manual_resources/pdfgui.html index 5c4a963f..24219aeb 100644 --- a/doc/manual/html/pdfgui.html +++ b/doc/source/manual_resources/pdfgui.html @@ -1069,7 +1069,7 @@

2.2 Creating a simple fit using a preexisting structure file exercise a preexisting structure file Ni.stru is to be loaded.

-images/fig2-01 +images/fig2-01

Figure 2.1: PDFgui window with fit tree and Plot Control panels to the left and current action panel to the right. The fit tree panel features the current fit @@ -1103,7 +1103,7 @@

2.2 Creating a simple fit using a preexisting structure file were collected at 300 K.

-images/fig2-02 +images/fig2-02

Figure 2.2: Appearance of a PDFgui window after a PDF dataset is loaded. The Fit Tree panel features the current fit, loaded Ni structure, and loaded Ni PDF @@ -1137,7 +1137,7 @@

2.2 Creating a simple fit using a preexisting structure file rightmost “quick-plot” button in the tool bar.

-images/fig2-03 +images/fig2-03

Figure 2.3: Adjusting data set related configuration. @@ -1168,7 +1168,7 @@

2.2 Creating a simple fit using a preexisting structure file Figure 2.4.

-images/fig2-04 +images/fig2-04

Figure 2.4: Setting up the refinement parameters and constraints. @@ -1187,7 +1187,7 @@

2.2 Creating a simple fit using a preexisting structure file

-images/fig2-05 +images/fig2-05

Figure 2.5: Setting up the refinement parameters and constraints. @@ -1210,7 +1210,7 @@

2.2 Creating a simple fit using a preexisting structure file that the parameter assignment is done correctly.

-images/fig2-06 +images/fig2-06

Figure 2.6: Reviewing the fit parameters and conditions. @@ -1231,7 +1231,7 @@

2.2 Creating a simple fit using a preexisting structure file illustrated in Figure 2.7.

-images/fig2-07 +images/fig2-07

Figure 2.7: While the refinement is running, the refinement progress is displayed in the PDFfit2 Output panel. @@ -1252,7 +1252,7 @@

2.2 Creating a simple fit using a preexisting structure file may make it difficult to reproduce the fit.

-images/fig2-08 +images/fig2-08

Figure 2.8: Updating the set of initial values of refined parameters. @@ -1267,13 +1267,13 @@

2.2 Creating a simple fit using a preexisting structure file fitting is in progress, the content will be updated after each fit iteration.

-images/fig2-09 +images/fig2-09

Figure 2.9: An example of PDFgui plotting capabilities: displaying a fit.

-images/fig2-10 +images/fig2-10

Figure 2.10: An example of PDFgui plotting capabilities: displaying a parameter. @@ -1284,7 +1284,7 @@

2.2 Creating a simple fit using a preexisting structure file file, or saved along with the entire project for future reference.

-images/fig2-11 +images/fig2-11

Figure 2.11: Using “Journal” feature can be a convenient way for taking notes. @@ -1406,7 +1406,7 @@

3.1 Building structure model using crystal symmetry

sites with the proper symmetry.

-images/fig3-01 +images/fig3-01

Figure 3.1: Expanding the unit cell using space group information. @@ -1435,7 +1435,7 @@

3.1 Building structure model using crystal symmetry

identical to these described in Creating a simple fit using a preexisting structure file.

-images/fig3-02 +images/fig3-02

Figure 3.2: Setting up symmetry constraints to be used in a refinement. @@ -1472,7 +1472,7 @@

3.2 Calculating PDF from a structure

set is loaded, as shown in Figure 3.3.

-images/fig3-03 +images/fig3-03

Figure 3.3: An example of the calculation configuration panel. @@ -1582,7 +1582,7 @@

3.3.1 Multistage fitting

parameter is not yet refined. An example of this is shown in Figure 3.4.

-images/fig3-04 +images/fig3-04

Figure 3.4: An example of linked fits. The output of a converged fit will be fed into the succeeding fit in the sequence as an input. @@ -1678,7 +1678,7 @@

3.3.2 Sequential fitting of incremental r-series

is done, you can review the results using the plot control.

-images/fig3-05 +images/fig3-05

Figure 3.5: Appearance of the setup panel for specifying an incremental r-series fit conditions. @@ -1741,7 +1741,7 @@

3.3.3 Sequential fitting of temperature series

The data can be ordered by temperature by clicking the “Temperature” header.

-images/fig3-06 +images/fig3-06

Figure 3.6: Setting up a T-series sequential refinement for LaMnO3. Ordering by temperature will ensure that the fits are linked correctly. @@ -1768,7 +1768,7 @@

3.3.3 Sequential fitting of temperature series

the plot of Uiso(20) vs T.

-images/fig3-07 +images/fig3-07

Figure 3.7: Displaying the refinement results as a function of external parameter: T-series refinement of LaMnO3, example of isotropic ADP of @@ -1828,7 +1828,7 @@

3.3.4 Sequential fitting of doping series

previous example.

-images/fig3-08 +images/fig3-08

Figure 3.8: After loading of the Ca-doping data series of LaMnO3 system, proper doping assignment needs to be carried out, as the doping levels introspected @@ -1872,7 +1872,7 @@

3.3.4 Sequential fitting of doping series

sequential refinement of the doping series.

-images/fig3-09 +images/fig3-09

Figure 3.9: Sequence of refined parameters, such as lattice constants, can be plotted vs doping using PDFgui plotting facilities. Figure features lattice @@ -2049,7 +2049,7 @@

3.4 Nanoparticle structure

Quantitative size-dependent structure and strain determination of CdSe nanoparticles using atomic pair distribution function analysis.

-images/fig3-10 +images/fig3-10

Figure 3.10: Fitting the structure of a nanoparticle: 3nm CdSe nanoparticle example. @@ -2141,7 +2141,7 @@

4.1 PDF plotting

-images/fig4-01 +images/fig4-01

Figure 4.1: Plotting window featuring Rw vs refinement step for Ni example. The basic functionality for manipulating the plot is provided through icons @@ -2185,7 +2185,7 @@

4.2 Displaying the structure

An example Ni structure visualization with AtomEye is shown in Figure 4.2.

-images/fig4-02 +images/fig4-02

Figure 4.2: Using AtomEye functionality (if installed on your system) for 3D visualization of the initial and refined PDF structures: example of Ni @@ -2511,7 +2511,7 @@

Renamed variables

(float Å^-1, default 0 Å^-1, qsig in PDFFIT)
PDF Gaussian dampening envelope due to limited Q-resolution. Not applied when equal to zero. The Gaussian envelope is of the form -

images/eq-01.png

+

images/eq-01.png

Dataset: qbroad
@@ -2627,7 +2627,7 @@

5.4 PDF peak width

the motion can be strongly correlated leading to a sharpening of the first peak(s) in the observed PDF. PDFfit2 provides three different correction terms for the PDF peak width. The final width is given by -

images/eq-02.png

+

images/eq-02.png

Here the primed sigma is the peak width without correlation, which is computed from the anisotropic displacement parameters. The first two terms correct for the effects of correlated motion. Within the scope of the users From f3fcd454dfdc504d22a0193d19f2cdacedad43d4 Mon Sep 17 00:00:00 2001 From: Tieqiong Zhang Date: Tue, 14 Jan 2025 01:45:56 -0500 Subject: [PATCH 2/7] trigger doc release --- .github/workflows/publish-docs-on-release.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/publish-docs-on-release.yml b/.github/workflows/publish-docs-on-release.yml index e56e7010..7db784b9 100644 --- a/.github/workflows/publish-docs-on-release.yml +++ b/.github/workflows/publish-docs-on-release.yml @@ -1,6 +1,7 @@ name: Deploy Documentation on Release on: + pull_request: release: types: [published] workflow_dispatch: From 4c9f194c79984937bc36136f9011eb2e5c1496bc Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 14 Jan 2025 06:47:06 +0000 Subject: [PATCH 3/7] [pre-commit.ci] auto fixes from pre-commit hooks --- doc/source/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/conf.py b/doc/source/conf.py index ec3f312b..73026b4a 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -158,7 +158,7 @@ # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the documentation. -html_extra_path = ['images'] +html_extra_path = ["images"] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. From c1a52c76389de4134ecd170e31b0cf44f9ef5f9d Mon Sep 17 00:00:00 2001 From: Tieqiong Zhang Date: Thu, 16 Jan 2025 00:40:39 -0500 Subject: [PATCH 4/7] trigger doc release --- .github/workflows/publish-docs-on-release.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/publish-docs-on-release.yml b/.github/workflows/publish-docs-on-release.yml index 7db784b9..dade44ae 100644 --- a/.github/workflows/publish-docs-on-release.yml +++ b/.github/workflows/publish-docs-on-release.yml @@ -1,7 +1,7 @@ name: Deploy Documentation on Release on: - pull_request: + push: release: types: [published] workflow_dispatch: @@ -13,4 +13,3 @@ jobs: project: diffpy.pdfgui c_extension: false headless: true - python_version: 3.12 From 45b6d7575cc98a01fa8a3aba9c352e7d1b92e782 Mon Sep 17 00:00:00 2001 From: Tieqiong Zhang Date: Thu, 16 Jan 2025 00:43:23 -0500 Subject: [PATCH 5/7] back to 3.12 --- .github/workflows/publish-docs-on-release.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/publish-docs-on-release.yml b/.github/workflows/publish-docs-on-release.yml index dade44ae..38f24b62 100644 --- a/.github/workflows/publish-docs-on-release.yml +++ b/.github/workflows/publish-docs-on-release.yml @@ -13,3 +13,4 @@ jobs: project: diffpy.pdfgui c_extension: false headless: true + python_version: 3.12 From 8915272608a364b8bdfc9e84c85ae73433feef7f Mon Sep 17 00:00:00 2001 From: Tieqiong Zhang Date: Thu, 16 Jan 2025 00:51:19 -0500 Subject: [PATCH 6/7] fix path --- doc/source/manual_resources/pdfgui.html | 50 ++++++++++++------------- 1 file changed, 25 insertions(+), 25 deletions(-) diff --git a/doc/source/manual_resources/pdfgui.html b/doc/source/manual_resources/pdfgui.html index 24219aeb..774ae074 100644 --- a/doc/source/manual_resources/pdfgui.html +++ b/doc/source/manual_resources/pdfgui.html @@ -1069,7 +1069,7 @@

2.2 Creating a simple fit using a preexisting structure file exercise a preexisting structure file Ni.stru is to be loaded.

-images/fig2-01 +images/fig2-01

Figure 2.1: PDFgui window with fit tree and Plot Control panels to the left and current action panel to the right. The fit tree panel features the current fit @@ -1103,7 +1103,7 @@

2.2 Creating a simple fit using a preexisting structure file were collected at 300 K.

-images/fig2-02 +images/fig2-02

Figure 2.2: Appearance of a PDFgui window after a PDF dataset is loaded. The Fit Tree panel features the current fit, loaded Ni structure, and loaded Ni PDF @@ -1137,7 +1137,7 @@

2.2 Creating a simple fit using a preexisting structure file rightmost “quick-plot” button in the tool bar.

-images/fig2-03 +images/fig2-03

Figure 2.3: Adjusting data set related configuration. @@ -1168,7 +1168,7 @@

2.2 Creating a simple fit using a preexisting structure file Figure 2.4.

-images/fig2-04 +images/fig2-04

Figure 2.4: Setting up the refinement parameters and constraints. @@ -1187,7 +1187,7 @@

2.2 Creating a simple fit using a preexisting structure file

-images/fig2-05 +images/fig2-05

Figure 2.5: Setting up the refinement parameters and constraints. @@ -1210,7 +1210,7 @@

2.2 Creating a simple fit using a preexisting structure file that the parameter assignment is done correctly.

-images/fig2-06 +images/fig2-06

Figure 2.6: Reviewing the fit parameters and conditions. @@ -1231,7 +1231,7 @@

2.2 Creating a simple fit using a preexisting structure file illustrated in Figure 2.7.

-images/fig2-07 +images/fig2-07

Figure 2.7: While the refinement is running, the refinement progress is displayed in the PDFfit2 Output panel. @@ -1252,7 +1252,7 @@

2.2 Creating a simple fit using a preexisting structure file may make it difficult to reproduce the fit.

-images/fig2-08 +images/fig2-08

Figure 2.8: Updating the set of initial values of refined parameters. @@ -1267,13 +1267,13 @@

2.2 Creating a simple fit using a preexisting structure file fitting is in progress, the content will be updated after each fit iteration.

-images/fig2-09 +images/fig2-09

Figure 2.9: An example of PDFgui plotting capabilities: displaying a fit.

-images/fig2-10 +images/fig2-10

Figure 2.10: An example of PDFgui plotting capabilities: displaying a parameter. @@ -1284,7 +1284,7 @@

2.2 Creating a simple fit using a preexisting structure file file, or saved along with the entire project for future reference.

-images/fig2-11 +images/fig2-11

Figure 2.11: Using “Journal” feature can be a convenient way for taking notes. @@ -1406,7 +1406,7 @@

3.1 Building structure model using crystal symmetry

sites with the proper symmetry.

-images/fig3-01 +images/fig3-01

Figure 3.1: Expanding the unit cell using space group information. @@ -1435,7 +1435,7 @@

3.1 Building structure model using crystal symmetry

identical to these described in Creating a simple fit using a preexisting structure file.

-images/fig3-02 +images/fig3-02

Figure 3.2: Setting up symmetry constraints to be used in a refinement. @@ -1472,7 +1472,7 @@

3.2 Calculating PDF from a structure

set is loaded, as shown in Figure 3.3.

-images/fig3-03 +images/fig3-03

Figure 3.3: An example of the calculation configuration panel. @@ -1582,7 +1582,7 @@

3.3.1 Multistage fitting

parameter is not yet refined. An example of this is shown in Figure 3.4.

-images/fig3-04 +images/fig3-04

Figure 3.4: An example of linked fits. The output of a converged fit will be fed into the succeeding fit in the sequence as an input. @@ -1678,7 +1678,7 @@

3.3.2 Sequential fitting of incremental r-series

is done, you can review the results using the plot control.

-images/fig3-05 +images/fig3-05

Figure 3.5: Appearance of the setup panel for specifying an incremental r-series fit conditions. @@ -1741,7 +1741,7 @@

3.3.3 Sequential fitting of temperature series

The data can be ordered by temperature by clicking the “Temperature” header.

-images/fig3-06 +images/fig3-06

Figure 3.6: Setting up a T-series sequential refinement for LaMnO3. Ordering by temperature will ensure that the fits are linked correctly. @@ -1768,7 +1768,7 @@

3.3.3 Sequential fitting of temperature series

the plot of Uiso(20) vs T.

-images/fig3-07 +images/fig3-07

Figure 3.7: Displaying the refinement results as a function of external parameter: T-series refinement of LaMnO3, example of isotropic ADP of @@ -1828,7 +1828,7 @@

3.3.4 Sequential fitting of doping series

previous example.

-images/fig3-08 +images/fig3-08

Figure 3.8: After loading of the Ca-doping data series of LaMnO3 system, proper doping assignment needs to be carried out, as the doping levels introspected @@ -1872,7 +1872,7 @@

3.3.4 Sequential fitting of doping series

sequential refinement of the doping series.

-images/fig3-09 +images/fig3-09

Figure 3.9: Sequence of refined parameters, such as lattice constants, can be plotted vs doping using PDFgui plotting facilities. Figure features lattice @@ -2049,7 +2049,7 @@

3.4 Nanoparticle structure

Quantitative size-dependent structure and strain determination of CdSe nanoparticles using atomic pair distribution function analysis.

-images/fig3-10 +images/fig3-10

Figure 3.10: Fitting the structure of a nanoparticle: 3nm CdSe nanoparticle example. @@ -2141,7 +2141,7 @@

4.1 PDF plotting

-images/fig4-01 +images/fig4-01

Figure 4.1: Plotting window featuring Rw vs refinement step for Ni example. The basic functionality for manipulating the plot is provided through icons @@ -2185,7 +2185,7 @@

4.2 Displaying the structure

An example Ni structure visualization with AtomEye is shown in Figure 4.2.

-images/fig4-02 +images/fig4-02

Figure 4.2: Using AtomEye functionality (if installed on your system) for 3D visualization of the initial and refined PDF structures: example of Ni @@ -2511,7 +2511,7 @@

Renamed variables

(float Å^-1, default 0 Å^-1, qsig in PDFFIT)
PDF Gaussian dampening envelope due to limited Q-resolution. Not applied when equal to zero. The Gaussian envelope is of the form -

images/eq-01.png

+

images/eq-01.png

Dataset: qbroad
@@ -2627,7 +2627,7 @@

5.4 PDF peak width

the motion can be strongly correlated leading to a sharpening of the first peak(s) in the observed PDF. PDFfit2 provides three different correction terms for the PDF peak width. The final width is given by -

images/eq-02.png

+

images/eq-02.png

Here the primed sigma is the peak width without correlation, which is computed from the anisotropic displacement parameters. The first two terms correct for the effects of correlated motion. Within the scope of the users From 543e952c22ce9676bddf44c97efc270a5d6d8fb0 Mon Sep 17 00:00:00 2001 From: Tieqiong Zhang Date: Thu, 16 Jan 2025 00:59:43 -0500 Subject: [PATCH 7/7] try path --- doc/{source => manual}/images/Makefile | 0 doc/{source => manual}/images/eq-01.png | Bin doc/{source => manual}/images/eq-02.png | Bin doc/{source => manual}/images/fig2-01.png | Bin doc/{source => manual}/images/fig2-02.png | Bin doc/{source => manual}/images/fig2-03.png | Bin doc/{source => manual}/images/fig2-04.png | Bin doc/{source => manual}/images/fig2-05.png | Bin doc/{source => manual}/images/fig2-06.png | Bin doc/{source => manual}/images/fig2-07.png | Bin doc/{source => manual}/images/fig2-08.png | Bin doc/{source => manual}/images/fig2-09.png | Bin doc/{source => manual}/images/fig2-10.png | Bin doc/{source => manual}/images/fig2-11.png | Bin doc/{source => manual}/images/fig3-01.png | Bin doc/{source => manual}/images/fig3-02.png | Bin doc/{source => manual}/images/fig3-03.png | Bin 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a/doc/source/manual_resources/pdfgui.html +++ b/doc/manual/pdfgui.html @@ -1069,7 +1069,7 @@

2.2 Creating a simple fit using a preexisting structure file exercise a preexisting structure file Ni.stru is to be loaded.

-images/fig2-01 +images/fig2-01

Figure 2.1: PDFgui window with fit tree and Plot Control panels to the left and current action panel to the right. The fit tree panel features the current fit @@ -1103,7 +1103,7 @@

2.2 Creating a simple fit using a preexisting structure file were collected at 300 K.

-images/fig2-02 +images/fig2-02

Figure 2.2: Appearance of a PDFgui window after a PDF dataset is loaded. The Fit Tree panel features the current fit, loaded Ni structure, and loaded Ni PDF @@ -1137,7 +1137,7 @@

2.2 Creating a simple fit using a preexisting structure file rightmost “quick-plot” button in the tool bar.

-images/fig2-03 +images/fig2-03

Figure 2.3: Adjusting data set related configuration. @@ -1168,7 +1168,7 @@

2.2 Creating a simple fit using a preexisting structure file Figure 2.4.

-images/fig2-04 +images/fig2-04

Figure 2.4: Setting up the refinement parameters and constraints. @@ -1187,7 +1187,7 @@

2.2 Creating a simple fit using a preexisting structure file

-images/fig2-05 +images/fig2-05

Figure 2.5: Setting up the refinement parameters and constraints. @@ -1210,7 +1210,7 @@

2.2 Creating a simple fit using a preexisting structure file that the parameter assignment is done correctly.

-images/fig2-06 +images/fig2-06

Figure 2.6: Reviewing the fit parameters and conditions. @@ -1231,7 +1231,7 @@

2.2 Creating a simple fit using a preexisting structure file illustrated in Figure 2.7.

-images/fig2-07 +images/fig2-07

Figure 2.7: While the refinement is running, the refinement progress is displayed in the PDFfit2 Output panel. @@ -1252,7 +1252,7 @@

2.2 Creating a simple fit using a preexisting structure file may make it difficult to reproduce the fit.

-images/fig2-08 +images/fig2-08

Figure 2.8: Updating the set of initial values of refined parameters. @@ -1267,13 +1267,13 @@

2.2 Creating a simple fit using a preexisting structure file fitting is in progress, the content will be updated after each fit iteration.

-images/fig2-09 +images/fig2-09

Figure 2.9: An example of PDFgui plotting capabilities: displaying a fit.

-images/fig2-10 +images/fig2-10

Figure 2.10: An example of PDFgui plotting capabilities: displaying a parameter. @@ -1284,7 +1284,7 @@

2.2 Creating a simple fit using a preexisting structure file file, or saved along with the entire project for future reference.

-images/fig2-11 +images/fig2-11

Figure 2.11: Using “Journal” feature can be a convenient way for taking notes. @@ -1406,7 +1406,7 @@

3.1 Building structure model using crystal symmetry

sites with the proper symmetry.

-images/fig3-01 +images/fig3-01

Figure 3.1: Expanding the unit cell using space group information. @@ -1435,7 +1435,7 @@

3.1 Building structure model using crystal symmetry

identical to these described in Creating a simple fit using a preexisting structure file.

-images/fig3-02 +images/fig3-02

Figure 3.2: Setting up symmetry constraints to be used in a refinement. @@ -1472,7 +1472,7 @@

3.2 Calculating PDF from a structure

set is loaded, as shown in Figure 3.3.

-images/fig3-03 +images/fig3-03

Figure 3.3: An example of the calculation configuration panel. @@ -1582,7 +1582,7 @@

3.3.1 Multistage fitting

parameter is not yet refined. An example of this is shown in Figure 3.4.

-images/fig3-04 +images/fig3-04

Figure 3.4: An example of linked fits. The output of a converged fit will be fed into the succeeding fit in the sequence as an input. @@ -1678,7 +1678,7 @@

3.3.2 Sequential fitting of incremental r-series

is done, you can review the results using the plot control.

-images/fig3-05 +images/fig3-05

Figure 3.5: Appearance of the setup panel for specifying an incremental r-series fit conditions. @@ -1741,7 +1741,7 @@

3.3.3 Sequential fitting of temperature series

The data can be ordered by temperature by clicking the “Temperature” header.

-images/fig3-06 +images/fig3-06

Figure 3.6: Setting up a T-series sequential refinement for LaMnO3. Ordering by temperature will ensure that the fits are linked correctly. @@ -1768,7 +1768,7 @@

3.3.3 Sequential fitting of temperature series

the plot of Uiso(20) vs T.

-images/fig3-07 +images/fig3-07

Figure 3.7: Displaying the refinement results as a function of external parameter: T-series refinement of LaMnO3, example of isotropic ADP of @@ -1828,7 +1828,7 @@

3.3.4 Sequential fitting of doping series

previous example.

-images/fig3-08 +images/fig3-08

Figure 3.8: After loading of the Ca-doping data series of LaMnO3 system, proper doping assignment needs to be carried out, as the doping levels introspected @@ -1872,7 +1872,7 @@

3.3.4 Sequential fitting of doping series

sequential refinement of the doping series.

-images/fig3-09 +images/fig3-09

Figure 3.9: Sequence of refined parameters, such as lattice constants, can be plotted vs doping using PDFgui plotting facilities. Figure features lattice @@ -2049,7 +2049,7 @@

3.4 Nanoparticle structure

Quantitative size-dependent structure and strain determination of CdSe nanoparticles using atomic pair distribution function analysis.

-images/fig3-10 +images/fig3-10

Figure 3.10: Fitting the structure of a nanoparticle: 3nm CdSe nanoparticle example. @@ -2141,7 +2141,7 @@

4.1 PDF plotting

-images/fig4-01 +images/fig4-01

Figure 4.1: Plotting window featuring Rw vs refinement step for Ni example. The basic functionality for manipulating the plot is provided through icons @@ -2185,7 +2185,7 @@

4.2 Displaying the structure

An example Ni structure visualization with AtomEye is shown in Figure 4.2.

-images/fig4-02 +images/fig4-02

Figure 4.2: Using AtomEye functionality (if installed on your system) for 3D visualization of the initial and refined PDF structures: example of Ni @@ -2511,7 +2511,7 @@

Renamed variables

(float Å^-1, default 0 Å^-1, qsig in PDFFIT)
PDF Gaussian dampening envelope due to limited Q-resolution. Not applied when equal to zero. The Gaussian envelope is of the form -

images/eq-01.png

+

images/eq-01.png

Dataset: qbroad
@@ -2627,7 +2627,7 @@

5.4 PDF peak width

the motion can be strongly correlated leading to a sharpening of the first peak(s) in the observed PDF. PDFfit2 provides three different correction terms for the PDF peak width. The final width is given by -

images/eq-02.png

+

images/eq-02.png

Here the primed sigma is the peak width without correlation, which is computed from the anisotropic displacement parameters. The first two terms correct for the effects of correlated motion. Within the scope of the users diff --git a/doc/source/conf.py b/doc/source/conf.py index 73026b4a..e4d1788a 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -158,7 +158,7 @@ # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the documentation. -html_extra_path = ["images"] +html_extra_path = ["../manual"] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. diff --git a/doc/source/manual.rst b/doc/source/manual.rst index fa6b1192..158bda6e 100644 --- a/doc/source/manual.rst +++ b/doc/source/manual.rst @@ -13,4 +13,4 @@ Resources used - :download:`Nanoparticle structure ` .. raw:: html - :file: manual_resources/pdfgui.html + :file: ../manual/pdfgui.html diff --git a/news/doc.rst b/news/doc.rst new file mode 100644 index 00000000..176aaf08 --- /dev/null +++ b/news/doc.rst @@ -0,0 +1,23 @@ +**Added:** + +* + +**Changed:** + +* + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* Fixed online manual not showing images. + +**Security:** + +*