diff --git a/.github/workflows/mkdocs_pdf.yml b/.github/workflows/mkdocs_pdf.yml deleted file mode 100644 index 56fe950..0000000 --- a/.github/workflows/mkdocs_pdf.yml +++ /dev/null @@ -1,140 +0,0 @@ -# work on building PDFs from the .md help files - - -name: test MD help to .pdf - -on: [workflow_dispatch] -#on: [push, workflow_dispatch] - -permissions: - contents: write - id-token: write - pages: write - -jobs: - build: # Build web pages - runs-on: ubuntu-latest - steps: - - - name: Python setup - uses: actions/setup-python@v3 -# - name: Sphinx setup -# run: | -# pip install sphinx sphinx_readable_theme -# - name: pandoc setup -# uses: pandoc/actions/setup@v1 - - - name: install debian chrome - run: | - set -ex - wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb - sudo apt install ./google-chrome-stable_current_amd64.deb - -# - name: test newly-installed chrome -# run: | -# which google-chrome-stable -# google-chrome-stable --version -# /usr/bin/google-chrome-stable --headless --disable-gpu --dump-dom https://google.com - - name: mkdocs setup - run: | - pip install mkdocs mkdocs-material python-markdown-math mkdocs-static-i18n - pip install mkdocs-to-pdf pymdown-extensions - - - name: Checkout - uses: actions/checkout@v4 - - - name: convert MDhelp - run: | - cd MDhelp - mv mkdocs.yml_pdf mkdocs.yml - #mkdocs build - ENABLE_PDF_EXPORT=1 mkdocs build - # mv site/GSASII-help.pdf ... - #cp -vr site ../help_test - - - name: Upload help artifact # creates zip file with website contents - uses: actions/upload-pages-artifact@v3 - with: - path: MDhelp/site - name: MDhelp - retention-days: 1 - - # - name: Get tutorials index from source code - # run: | - # curl -L https://github.com/AdvancedPhotonSource/GSAS-II/raw/master/GSASII/tutorialIndex.py -o scripts/tutorialIndex.py - - # - name: convert tutorials - # run: | - # cd MDtutorials - # for path in ./*; do - # [ -d "${path}" ] || continue # skip if not a directory - # dirname="$(basename "${path}")" - # dest="../${dirname}" - # mkdir -pv ${dest} - # [ ! -d "${path}/data" ] || cp -r "${path}/data" ${dest}/ - # [ ! -d "${path}/imgs" ] || cp -r "${path}/imgs" ${dest}/ - # cp tutorial.css ${dest} - # for fil in $dirname/*.md; do - # outfile="${dest}/$(basename "${fil%.md}.html")" - # echo "creating $outfile from $fil" - # pandoc --standalone ${fil} --css tutorial.css -o ${outfile} - # sed -i "s/
/
/g" ${outfile} - # done - # git add ${dest} - # done - # cd .. - - # - name: build tutorials index - # run: | - # cd scripts - # python makeGitTutorial.py .. - -# - name: Note changed files -# run: | -# git add tutorials.html -# git add */data/index.html -# git status -# git commit -m"changes from automated build of tutorials" -# - name: Push changes -# uses: ad-m/github-push-action@master - - # - name: Sphinx build - # run: | - # sphinx-build webdocs . # place output into root dir - # cp webdocs/_static/fix.css _static/fix.css # should be done by sphinx - - # # get the help pages from the GSAS-II sources into the web site - # - name: Get GSAS-II - # run: | - # git clone --depth 1 https://github.com/AdvancedPhotonSource/GSAS-II.git _gsas2 - # - name: move help into site - # run: | - # mv _gsas2/GSASII/help ./help - # - name: Get rid of the rest of the GSAS-II files & other stuff not needed on web - # run: | - # rm -rf _gsas2 webdocs scripts MDtutorials MDhelp - - # - name: Upload artifact # creates zip file with website contents - # uses: actions/upload-pages-artifact@v3 - # with: - # path: . - # name: github-pages - # retention-days: 1 - - # deploy: # Deployment of web pages to GitHub pages - # needs: build - # permissions: - # pages: write - # id-token: write - # environment: - # name: github-pages - # url: ${{ steps.deployment.outputs.page_url }} - # runs-on: ubuntu-latest - - # steps: - # - name: Deploy to GitHub Pages - # id: deployment - # uses: actions/deploy-pages@v4 - # with: - # token: ${{ secrets.GITHUB_TOKEN }} - # artifact_name: github-pages diff --git a/.github/workflows/mkdocs_testbranch.yml b/.github/workflows/mkdocs_testbranch.yml deleted file mode 100644 index c59cabd..0000000 --- a/.github/workflows/mkdocs_testbranch.yml +++ /dev/null @@ -1,147 +0,0 @@ -# work on building PDFs from the .md help files - - -name: test MD help to .pdf - -on: [workflow_dispatch] -#on: [push, workflow_dispatch] - -permissions: - contents: write - id-token: write - pages: write - -jobs: - build: # Build web pages - runs-on: ubuntu-latest - steps: - - - # - name: test installed chrome - # run: | - # which chrome - # chrome --version - - - name: install debian chrome - run: | - set -ex - wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb - sudo apt install ./google-chrome-stable_current_amd64.deb - -# - name: test newly-installed chrome -# run: | -# which google-chrome-stable -# google-chrome-stable --version -# /usr/bin/google-chrome-stable --headless --disable-gpu --dump-dom https://google.com - - - name: Python setup - uses: actions/setup-python@v3 -# - name: Sphinx setup -# run: | -# pip install sphinx sphinx_readable_theme -# - name: pandoc setup -# uses: pandoc/actions/setup@v1 - - name: mkdocs setup - run: | - pip install mkdocs mkdocs-material python-markdown-math mkdocs-static-i18n - pip install pymdown-extensions - #pip install mkdocs-to-pdf - pip install git+https://github.com/domWalters/mkdocs-to-pdf.git@impl-playwright-pdf-engine - - name: Checkout - uses: actions/checkout@v4 - - - name: convert MDhelp - run: | - cd MDhelp - #mkdocs build - mv mkdocs.yml_pdf mkdocs.yml - ENABLE_PDF_EXPORT=1 mkdocs build - # mv site/GSASII-help.pdf ... - #cp -vr site ../help_test - - - name: Upload help artifact # creates zip file with website contents - uses: actions/upload-pages-artifact@v3 - with: - path: MDhelp/site - name: MDhelp - retention-days: 1 - - # - name: Get tutorials index from source code - # run: | - # curl -L https://github.com/AdvancedPhotonSource/GSAS-II/raw/master/GSASII/tutorialIndex.py -o scripts/tutorialIndex.py - - # - name: convert tutorials - # run: | - # cd MDtutorials - # for path in ./*; do - # [ -d "${path}" ] || continue # skip if not a directory - # dirname="$(basename "${path}")" - # dest="../${dirname}" - # mkdir -pv ${dest} - # [ ! -d "${path}/data" ] || cp -r "${path}/data" ${dest}/ - # [ ! -d "${path}/imgs" ] || cp -r "${path}/imgs" ${dest}/ - # cp tutorial.css ${dest} - # for fil in $dirname/*.md; do - # outfile="${dest}/$(basename "${fil%.md}.html")" - # echo "creating $outfile from $fil" - # pandoc --standalone ${fil} --css tutorial.css -o ${outfile} - # sed -i "s/
/
/g" ${outfile} - # done - # git add ${dest} - # done - # cd .. - - # - name: build tutorials index - # run: | - # cd scripts - # python makeGitTutorial.py .. - -# - name: Note changed files -# run: | -# git add tutorials.html -# git add */data/index.html -# git status -# git commit -m"changes from automated build of tutorials" -# - name: Push changes -# uses: ad-m/github-push-action@master - - # - name: Sphinx build - # run: | - # sphinx-build webdocs . # place output into root dir - # cp webdocs/_static/fix.css _static/fix.css # should be done by sphinx - - # # get the help pages from the GSAS-II sources into the web site - # - name: Get GSAS-II - # run: | - # git clone --depth 1 https://github.com/AdvancedPhotonSource/GSAS-II.git _gsas2 - # - name: move help into site - # run: | - # mv _gsas2/GSASII/help ./help - # - name: Get rid of the rest of the GSAS-II files & other stuff not needed on web - # run: | - # rm -rf _gsas2 webdocs scripts MDtutorials MDhelp - - # - name: Upload artifact # creates zip file with website contents - # uses: actions/upload-pages-artifact@v3 - # with: - # path: . - # name: github-pages - # retention-days: 1 - - # deploy: # Deployment of web pages to GitHub pages - # needs: build - # permissions: - # pages: write - # id-token: write - # environment: - # name: github-pages - # url: ${{ steps.deployment.outputs.page_url }} - # runs-on: ubuntu-latest - - # steps: - # - name: Deploy to GitHub Pages - # id: deployment - # uses: actions/deploy-pages@v4 - # with: - # token: ${{ secrets.GITHUB_TOKEN }} - # artifact_name: github-pages diff --git a/.github/workflows/test_pushhelp.yml b/.github/workflows/test_pushhelp.yml new file mode 100644 index 0000000..3d18876 --- /dev/null +++ b/.github/workflows/test_pushhelp.yml @@ -0,0 +1,190 @@ +# create a documentation web site for GSAS-II from four sources +# * HTML tutorials are simply copied +# * markdown tutorials (in ./MDtutorials) are formatted with pandoc and are copied over +# * sphinx is used to generate HTML from files in ./webdocs + +# Also the tutorials.html file and the */data/index.html files are +# created by running scripts/makeGitTutorial + +# this is a development version that creates draft help pages from the MDhelp directory +# For now +# * HTML help files are copied over from the GSAS-II sources +# Eventually, the help files generated here need to get into the GSASII/help +# directory + +name: build GSAS-II web site w/test MD Help + +on: + workflow_dispatch: + + push: + branches: + - newhelp + +permissions: + contents: write + pull-requests: write + id-token: write + pages: write + +jobs: + build: # Build web pages + runs-on: ubuntu-latest + steps: + + - name: Python setup + uses: actions/setup-python@v3 +# Code below removed for more rapid testing + # - name: Sphinx setup + # run: | + # pip install sphinx sphinx_readable_theme + # - name: pandoc setup + # uses: pandoc/actions/setup@v1 + +# Code below removed for more rapid testing + # # MD help tools + # - name: install debian chrome + # run: | + # set -ex + # wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb + # sudo apt install ./google-chrome-stable_current_amd64.deb + +# - name: test newly-installed chrome +# run: | +# which google-chrome-stable +# google-chrome-stable --version +# /usr/bin/google-chrome-stable --headless --disable-gpu --dump-dom https://google.com + - name: mkdocs setup + run: | + pip install mkdocs mkdocs-material python-markdown-math mkdocs-static-i18n + pip install mkdocs-to-pdf pymdown-extensions + + - name: Checkout + uses: actions/checkout@v4 + + # MD help conversion + - name: convert MDhelp + run: | + cd MDhelp + mkdocs build + #ENABLE_PDF_EXPORT=1 mkdocs build + #mv site/GSASII-help.pdf ../docs/ + # create an anchor index + python findMDanchors.py + cp -vr site ../help + + # - name: Upload help artifact # debug: creates zip file with website contents + # uses: actions/upload-pages-artifact@v3 + # with: + # path: MDhelp/site + # name: MDhelp + # retention-days: 1 + +# Code below removed for more rapid testing + # - name: Get tutorials index from source code + # run: | + # curl -L https://github.com/AdvancedPhotonSource/GSAS-II/raw/master/GSASII/tutorialIndex.py -o scripts/tutorialIndex.py + +# Code below removed for more rapid testing + # - name: convert tutorials + # run: | + # cd MDtutorials + # for path in ./*; do + # [ -d "${path}" ] || continue # skip if not a directory + # dirname="$(basename "${path}")" + # dest="../${dirname}" + # mkdir -pv ${dest} + # [ ! -d "${path}/data" ] || cp -r "${path}/data" ${dest}/ + # [ ! -d "${path}/imgs" ] || cp -r "${path}/imgs" ${dest}/ + # cp tutorial.css ${dest} + # for fil in $dirname/*.md; do + # outfile="${dest}/$(basename "${fil%.md}.html")" + # echo "creating $outfile from $fil" + # pandoc --standalone ${fil} --css tutorial.css -o ${outfile} + # sed -i "s/
/
/g" ${outfile} + # done + # git add ${dest} + # done + # cd .. + +# Code below removed for more rapid testing + # - name: build tutorials index + # run: | + # cd scripts + # python makeGitTutorial.py .. + +# - name: Note changed files # unused development code +# run: | +# git add tutorials.html +# git add */data/index.html +# git status +# git commit -m"changes from automated build of tutorials" +# - name: Push changes +# uses: ad-m/github-push-action@master + +# Code below removed for more rapid testing + # - name: Sphinx build + # run: | + # sphinx-build webdocs . # place output into root dir + # cp webdocs/_static/fix.css _static/fix.css # should be done by sphinx + + # get the new help pages into the GSAS-II sources + - name: Checkout + uses: actions/checkout@v4 + with: + repository: AdvancedPhotonSource/GSAS-II.git + path: _gsas2 + ref: newhelp +# token: '' + - name: move help into site + run: | + #rm -rf _gsas2/GSASII/help/assets/javascripts/ + rm -rf _gsas2/GSASII/help/assets/stylesheets/ + cp -rpv MDhelp/site/* _gsas2/GSASII/help + cd _gsas2 + git status + git diff + git add GSASII/help + echo "After add" + git status + - name: commit changes + run: | + cd _gsas2 + git config user.name "github-actions[bot]" + git config user.email "github-actions[bot]@users.noreply.github.com" + git commit -m"update help files" + - name: push help into site + run: | + cd _gsas2 + git push + + # before uploading, clean up + - name: Get rid of the rest of the GSAS-II files & other stuff not needed on web + run: | + rm -rf _gsas2 webdocs scripts MDtutorials MDhelp + +# Code below removed for more rapid testing + # - name: Upload artifact # creates zip file with website contents + # uses: actions/upload-pages-artifact@v3 + # with: + # path: . + # name: github-pages + # retention-days: 1 + + # deploy: # Deployment of web pages to GitHub pages + # needs: build + # permissions: + # pages: write + # id-token: write + # environment: + # name: github-pages + # url: ${{ steps.deployment.outputs.page_url }} + # runs-on: ubuntu-latest + + # steps: + # - name: Deploy to GitHub Pages + # id: deployment + # uses: actions/deploy-pages@v4 + # with: + # token: ${{ secrets.GITHUB_TOKEN }} + # artifact_name: github-pages diff --git a/MDhelp/docs/phasedrawatoms.md b/MDhelp/docs/phasedrawatoms.md index 8eca237..1b9a747 100644 --- a/MDhelp/docs/phasedrawatoms.md +++ b/MDhelp/docs/phasedrawatoms.md @@ -14,45 +14,65 @@ The contents of this tab is a list of the atoms that are displayed. These may be

What can I do here?

-Note that on a Mac with a one-button mouse, [some alternate actions must be used](./others.md#MacOS). +The commands and operations here determine what atoms are included in the structure drawing and how those atoms are displayed. Note that options for display type are by atom, so van der Waals, ball & stick and polyhedral display, for example, can all be mixed in a single display. Note that when atoms are added to the list, the anisotropic thermal displacement parameters (Uij) for atoms created by symmetry operations will be transformed as appropriate. Note that any atom positions that duplicate atoms already in the list are not retained. + +There are two convenient ways to use the capabilities here. Select atoms and then select a menu item, typically from the **Edit Figure** menu. Alternately, right-click on the table and you will be offered a list of commands that can be performed on the selected atoms. + +### Atom Selection +Atoms may be selected by a number of methods: 1. **Atom Selection from table**: select individual atoms by a left click of the mouse when pointed at the left most column (atom numbers) of the atom display; hold down the Ctrl key to add to your selection; a previously selected atom will be deselected; hold down Shift key to select from last in list selected to current selection. A selected atom will be highlighted (in grey) and the atoms will be shown in green on the plot. Selection without the Ctrl key will clear previous selections. A double left click in the (empty) upper left box will select or deselect all atoms. 2. **Atom Selection from drawing**: select an atom by a left click of the mouse while holding down the Shift key and pointed at the center of the displayed atom, it will turn green if successful and the corresponding entry in the table will be highlighted (in grey); any previous selections will be cleared. To add to your selection, use the right mouse button (Shift down); if a previously selection is reselected it is removed from the selection list. NB: beware of atoms that are hiding behind the one you are trying to select they may be selected inadvertently. You can rotate the structure anytime during the selection process. 3. **Double left click a Name, Type and Sym Op column heading**: a dialog box is shown that allows you to select all atoms with that characteristic. For example, selecting the Type column will show all the atom types; your choice will then cause all those atoms to be selected. 4. **Double left click a Style, Label or Color column**: a dialog box is shown that allows you to select a rendering option for all the atoms. For Color a color choice dialog is displayed that covers the entire color spectrum. Choose a color by any of the means available, press the "Add to Custom Colors", select that color in the Custom colors display and then press OK. NB: selecting Color will make all atoms have the same color and for Style "blank" means the atoms aren't rendered and thus the drawing will not show any atoms or bonds! -5. Menu '**Edit Figure**' - The edit menu shows operations that can be performed on your selected atoms. You must select one or more atoms before using any of the menu items. Most of these items can also be accessed by selecting one or more atoms and right-clicking the mouse. - * **Atom style** – select the rendering style for the selected atoms - * **Atom label** – select the item to be shown as a label for each atom in selection. The choices are: none, type, name or number. (NB: atom labelling slows drawing response time). - * **Atom color** – select the color for the atom; a color choice dialog is displayed that covers the entire color spectrum. Choose a color by any of the means available, press the "Add to Custom Colors", select that color in the Custom colors display and then press OK. - * **Reset atom colors** – return the atom color back to their defaults for the selected atoms. - * **Edit atom radii** – modify atom radii used in the bond assignment algorithm. - * **View point** – position the plot view point to the first atom in the selection. - * **Select from list** – select atoms from a popup list of names. - * **Add atoms** – using the selected atoms, new ones are added to the bottom of the list after applying your choice of symmetry operator and unit cell translation selected via a dialog display. Duplicate atom positions are not retained. Any anisotropic thermal displacement parameters (Uij) will be transformed as appropriate. - * **Add sphere of atoms** – fill in all equivalent atoms that fall within a sphere of selected radius about selected atoms. - * **Transform draw atoms** – apply a symmetry operator and unit cell translation to the set of selected atoms; they will be changed in place. Any anisotropic thermal displacement parameters (Uij) will be transformed as appropriate. - * **Fill CN-sphere** – using the atoms currently in the draw atom table, find all atoms that belong in the coordination sphere around the selected atoms via unit cell translations. NB: symmetry operations are not used in this search; do Fill unit cell first. - * **Fill unit cell** - using the atoms currently selected from the draw atom table, find all atoms that fall inside or on the edge/surface/corners of the unit cell. This operation is frequently performed before Fill CN-sphere. - * **Complete molecule** – beginning with a selected atom, transform other atoms to equivalent positions that form a contiguous molecule. Not appropriate for continuous structures (a warning will appear) - * **Create void map** – by using a grid of probe positions, locate points outside of normal contact distances within a structure. Result is a mesh of small blue points in structural voids (e.g. possible locations of missing water molecules). - * **Delete atoms** – clear the entire draw atom table; it is then refilled from the Atoms table. You should do this operation after any changes in the Atoms table, e.g. by a structure refinement. - * **Update draw atoms** – refresh the drawn atom positions from the Atoms list. - * **Load selected atoms** - refresh the selected drawn atom positions from the Atoms list. - -6. Menu '**Compute**' - The compute menu gives a choice of geometric calculations to be performed with the selected atoms. You must select the appropriate number of atoms for these to work and the computation is done for the atoms in selection order. - - * **View pt. dist.** - this calculates distance from view-point to all selected draw atoms; result is given on the console window. - * **Dist. Ang. Tors.** – when 2-4 atoms are selected, a distance, angle or torsion angle will be found for them. The angles are computed for the atoms in their selection order. The torsion angle is a right-hand angle about the A2-A3 vector for the sequence of atoms A1-A2-A3-A4. An estimated standard deviation is given for the calculated value if a current variance-covariance matrix is available. The result is shown on the console window; it may be cut & pasted to another application (e.g. Microsoft Word). - * **Best plane** – when 4 or more atoms are selected, a best plane is determined for them. The result is shown on the console window; it may be cut & pasted to another application (e.g. Microsoft Word). Shown are the atom coordinates transformed to Cartesian best plane coordinates where the largest range is over the X-axis and the smallest is over the Z-axis with the origin at the unweighted center of the selection. Root mean square displacements along each axis for the best plane are also listed. The Z-axis RMS value indicates the flatness of the proposed plane. NB: if you select (e.g. all) atoms then Best plane will give Cartesian coordinates for these atoms with respect to a coordinate system where the X-axis is along the longest axis of the atom grouping and the Z-axis is along the shortest distance. The origin is at the unweighted center of the selected atoms. - -7. Menu '**Restraints**' – Individual restraints may be generated by selecting atoms and the corresponding restraint type from the menu - - * **Add bond restraint** – for selected atom pair (A-B). - * **Add angle restraint** – for selected atom triple (A-B-C) - * **Add plane restraint** – for selected 4 or more atoms - * **Add chiral restraint** – for selected 4 atoms; chiral atom first followed by 3 other atoms; if selected in righthand sequence, chiral volume will be > 0. - -8. Menu '**Rigid body**'/'**Define rigid body**' – assign a previously defined rigid body to selected atoms. +5. **Select from list** menu command (see below). A list of atoms is displayed and one can select using checkmark buttons. This will be offered automatically when a menu command requires selected atoms and none have been selected. + +Note that on a Mac with a one-button mouse, [some alternate actions must be used](./others.md#MacOS) for selection. + +### Menu '**Edit Figure**' Contents +The edit menu shows operations that can be performed on your selected atoms. If you have not selected any atoms using any of the menu items, you will be presented with a window where you can select atoms. + +Many of the options below can also be accessed after selecting one or more atoms by right-clicking the mouse on the table. + + * **Atom style** – select the rendering style for the selected atoms + * **Atom label** – select the item to be shown as a label for each atom in selection. The choices are: none, type, name or number. (NB: atom labelling slows drawing response time). + * **Atom color** – select the color for the atom; a color choice dialog is displayed that covers the entire color spectrum. Choose a color by any of the means available, press the "Add to Custom Colors", select that color in the Custom colors display and then press OK. + * **Reset atom colors** – return the atom color back to their defaults for the selected atoms. + * **Edit atom radii** – modify atom radii used in the bond assignment algorithm. + * **View point** – position the plot view point to the first atom in the selection. The view point is shown as crossing red, blue and green lines and this is placed at the center of the plot diagram in all three dimensions. + * **Select from list** – select atoms from a popup list of names. + * **Add atoms** – using the selected atoms, additional atoms are added to the bottom of the list after applying your choice of symmetry operator and unit cell translation to the *selected atom* coordinates. Through use of this command, usually after the **Fill unit cell** and/or **Complete molecule** commands, makes it possible to display multiple unit cells. + * **Add sphere of atoms** – fill in all atoms that fall within a sphere of selected radius about selected atom(s). + * **Add box of atoms** – Not yet implemented + * **Transform draw atoms** – apply a symmetry operator and unit cell translation to the set of selected atoms; they transformed atoms will replace the original atoms in the draw atoms list. + * **Fill CN-sphere** – using the atoms currently in the draw atom table, find all atoms that belong in the coordination sphere around the selected atoms via unit cell translations. NB: symmetry operations are not used in this search; do **Fill unit cell** first. + * **Fill unit cell** - using the atoms currently selected from the draw atom table, find all atoms that fall inside or on the edge/surface/corners of the unit cell. This operation is frequently performed before Fill CN-sphere. + * **Complete molecule** – beginning with a selected atom, transform other atoms to equivalent positions that form a contiguous molecule. Not appropriate for continuous structures (a warning will appear if the command is not completing) + * **Create void map** – by using a grid of probe positions, locate points outside of normal contact distances within a structure. Result is a mesh of small blue points in structural voids. These could indicate possible locations of missing solvent molecules or voids in porous materials. + * **Delete atoms** – Remove selected atoms from the draw atom table. If you remove all atoms, the table is then refilled from the Atoms table. You should do this operation after any changes to the contents of the Atoms table, e.g. if atoms are added or deleted. + * **Update draw atoms** – refresh the drawn atom positions from the Atoms list, You should do this operation after any changes to the contents of the Atoms table, e.g. by a structure refinement. This operates on all atoms and ignores any previous atom selection. + * **Load selected atoms** - refresh the selected atom positions in the draw atoms list from the Atoms list. + +### Menu '**Compute**' Contents + +The compute menu gives a choice of geometric calculations to be performed with the selected atoms. You must select the appropriate number of atoms for these to work and the computation is done for the atoms in selection order. + + * **View pt. dist.** - this calculates distance from view-point to all selected draw atoms; result is given on the console window. + * **Dist. Ang. Tors.** – when 2-4 atoms are selected, a distance, angle or torsion angle will be found for them. The angles are computed for the atoms in their selection order. The torsion angle is a right-hand angle about the A2-A3 vector for the sequence of atoms A1-A2-A3-A4. An estimated standard deviation is given for the calculated value if a current variance-covariance matrix is available. The result is shown on the console window; it may be cut & pasted to another application (e.g. Microsoft Word). + * **Best plane** – when 4 or more atoms are selected, a best plane is determined for them. The result is shown on the console window; it may be cut & pasted to another application (e.g. Microsoft Word). Shown are the atom coordinates transformed to Cartesian best plane coordinates where the largest range is over the X-axis and the smallest is over the Z-axis with the origin at the unweighted center of the selection. Root mean square displacements along each axis for the best plane are also listed. The Z-axis RMS value indicates the flatness of the proposed plane. NB: if you select (e.g. all) atoms then Best plane will give Cartesian coordinates for these atoms with respect to a coordinate system where the X-axis is along the longest axis of the atom grouping and the Z-axis is along the shortest distance. The origin is at the unweighted center of the selected atoms. + +### Menu '**Restraints**' Contents + +Individual restraints may be generated by selecting atoms and the corresponding restraint type from the menu. + + * **Add bond restraint** – for selected atom pair (A-B). + * **Add angle restraint** – for selected atom triple (A-B-C) + * **Add plane restraint** – for selected 4 or more atoms + * **Add chiral restraint** – for selected 4 atoms; chiral atom first followed by 3 other atoms; if selected in righthand sequence, chiral volume will be > 0. + +### Menu '**Rigid body**' Contents + + * **Define rigid body**' - Assign a previously defined rigid body to selected atoms.

What is plotted here?

diff --git a/MDhelp/mkdocs.yml b/MDhelp/mkdocs.yml index bd87e6e..59cbf92 100644 --- a/MDhelp/mkdocs.yml +++ b/MDhelp/mkdocs.yml @@ -45,10 +45,6 @@ nav: - Small Angle (SASD): smallanglescattering.md - Reflectometry (REFD): reflectometry.md - Powder Peaks (PKS): peaks.md - -# - Powder peaks (PKS): powderpeak.md - - - Other info: others.md diff --git a/MDhelp/mkdocs.yml_html b/MDhelp/mkdocs.yml_html index 0b0c44a..b41a4df 100644 --- a/MDhelp/mkdocs.yml_html +++ b/MDhelp/mkdocs.yml_html @@ -45,10 +45,6 @@ nav: - Small Angle (SASD): smallanglescattering.md - Reflectometry (REFD): reflectometry.md - Powder Peaks (PKS): peaks.md - -# - Powder peaks (PKS): powderpeak.md - - - Other info: others.md diff --git a/README.md b/README.md index cc8f826..7686946 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,11 @@ This repository contains files used to create GSAS-II web content, which include * **Tutorials**: When the tutorials will be run, It is best to access them from within GSAS-II using the Help->Tutorials menu (this will simplifies downloading the files needed to run the tutorials), but tutorials can also be accessed [from this link](https://advancedphotonsource.github.io/GSAS-II-tutorials/tutorials.html). The HTML, images and data files for the tutorials are found in this repo. Note that when new functionality is added to GSAS-II, it is customary to create a new tutorial. -* **Help Pages**: There are three HTML web pages used within GSAS-II (plus a table of contents page) for context-sensitive help. These files are maintained in the [GSAS-II source code repo](https://github.com/AdvancedPhotonSource/GSAS-II/tree/master/GSASII/help), but for convenience, [they can also be accessed from the web pages](https://advancedphotonsource.github.io/GSAS-II-tutorials/help/gsasII-index.html). +* **Help Pages**: There are a set of web files that are +distributed with GSAS-II, or can be [viewed here](help/index.html). These +help pages provide information on how different sections of the program +work. The help information can also be viewed [as a PDF document](https://advancedphotonsource.github.io/GSAS-II-tutorials/docs/GSASII-help.pdf). +Comments, corrections, additions and issue reports on Help are most welcome. ## Repo Organization Each tutorial is placed here in its own subdirectory. In that subdirectory, there will be a web page for that tutorial (extension .html or .htm) and two additional subdirectories, one named `data`, with the input file(s) needed for that tutorial and another with a name generated from the web page file name that contains images for the web page. diff --git a/fullrmc-SF6/fullrmc-SF6.html b/fullrmc-SF6/fullrmc-SF6.html index e24e772..459304b 100644 --- a/fullrmc-SF6/fullrmc-SF6.html +++ b/fullrmc-SF6/fullrmc-SF6.html @@ -1615,7 +1615,7 @@

Installing fullrmc

mso-bidi-theme-font:major-bidi'>When fullrmc is selected on the Phase RMC tab (as will be done below), GSAS-II will look for a fullrmc program in a number of locations (documented +href="https://advancedphotonsource.github.io/GSAS-II-tutorials/help/phaseRMC.html#fullrmc">documented here). If this is not found, the program will offer to install it for you, as below.

@@ -1720,9 +1720,9 @@

Installing fullrmc

href="https://github.com/bachiraoun/fullrmc/tree/master/standalones">https://github.com/bachiraoun/fullrmc/tree/master/standalones. If this is done manually, either install it into the search path described in the GSAS-II +href="https://advancedphotonsource.github.io/GSAS-II-tutorials/help/phaseRMC.html#fullrmc">GSAS-II help or define the GSAS-II configuration +href="https://advancedphotonsource.github.io/GSAS-II-tutorials/help/others.html#Preferences">configuration variable