├── .github ├── old-workflows │ ├── win-selfinstall-test.yml │ └── win_test.yml └── workflows │ ├── TriggerRemote.yml │ ├── smoke_test.yml │ └── win-gitstrap-selftest.yml ├── .gitignore ├── .readthedocs.yaml ├── GSASII ├── Absorb.py ├── ElementTable.py ├── FormFactors.py ├── G2.py ├── G2compare.py ├── G2shapes.py ├── GSASIIElem.py ├── GSASIIElemGUI.py ├── GSASIIGUI.py ├── GSASIIIntPDFtool.py ├── GSASIIconstrGUI.py ├── GSASIIctrlGUI.py ├── GSASIIdata.py ├── GSASIIdataGUI.py ├── GSASIIddataGUI.py ├── GSASIIexprGUI.py ├── GSASIIfiles.py ├── GSASIIfpaGUI.py ├── GSASIIimage.py ├── GSASIIimgGUI.py ├── GSASIIindex.py ├── GSASIIlattice.py ├── GSASIImapvars.py ├── GSASIImath.py ├── GSASIImiscGUI.py ├── GSASIImpsubs.py ├── GSASIIobj.py ├── GSASIIpath.py ├── GSASIIphsGUI.py ├── GSASIIplot.py ├── GSASIIpwd.py ├── GSASIIpwdGUI.py ├── GSASIIpwdplot.py ├── GSASIIrestrGUI.py ├── GSASIIsasd.py ├── GSASIIscriptable.py ├── GSASIIseqGUI.py ├── GSASIIspc.py ├── GSASIIstrIO.py ├── GSASIIstrMain.py ├── GSASIIstrMath.py ├── GSASIItestplot.py ├── ISODISTORT.py ├── ImageCalibrants.py ├── NIST_profile │ ├── __init__.py │ ├── atan_windowed_FP_profile.py │ ├── meson.build │ └── profile_functions_class.py ├── PlotXNFF.py ├── ReadMarCCDFrame.py ├── SUBGROUPS.py ├── Substances.py ├── __init__.py ├── __main__.py ├── atmdata.py ├── config_example.py ├── defaultIparms.py ├── dmp.py ├── exports │ ├── G2export_Bracket.py │ ├── G2export_CIF.py │ ├── G2export_FIT2D.py │ ├── G2export_JSON.py │ ├── G2export_PDB.py │ ├── G2export_csv.py │ ├── G2export_examples.py │ ├── G2export_image.py │ ├── G2export_map.py │ ├── G2export_pwdr.py │ ├── G2export_shelx.py │ ├── __init__.py │ ├── cif_core.cpickle │ ├── cif_core.dic │ ├── cif_pd.cpickle │ ├── cif_pd.dic │ ├── meson.build │ ├── template_phase.cif │ ├── template_powder.cif │ ├── template_publ.cif │ └── template_single.cif ├── fprime.py ├── git_verinfo.py ├── gltext.py ├── help │ ├── graphbar.jpg │ ├── gsas2logo.png │ ├── gsasII-index.fld │ │ ├── colorschememapping.xml │ │ ├── filelist.xml │ │ ├── item0001.xml │ │ ├── item0006.xml │ │ ├── props002.xml │ │ ├── props007.xml │ │ └── themedata.thmx │ ├── gsasII-index.html │ ├── gsasII-phase.html │ ├── gsasII-phase_files │ │ ├── colorschememapping.xml │ │ ├── filelist.xml │ │ ├── image001.emz │ │ ├── image001.png │ │ ├── image003.emz │ │ ├── image003.png │ │ ├── image005.emz │ │ ├── image005.png │ │ ├── image007.emz │ │ ├── image007.png │ │ ├── image009.emz │ │ ├── image009.png │ │ ├── image010.emz │ │ ├── image010.png │ │ ├── image011.png │ │ ├── image012.emz │ │ ├── image012.png │ │ ├── image013.png │ │ ├── image014.emz │ │ ├── image014.png │ │ ├── image015.png │ │ ├── image016.emz │ │ ├── image016.png │ │ ├── image017.png │ │ ├── image018.emz │ │ ├── image018.png │ │ ├── image019.png │ │ ├── image020.emz │ │ ├── image020.png │ │ ├── image021.png │ │ ├── image022.emz │ │ ├── image022.png │ │ ├── image023.emz │ │ ├── image023.png │ │ ├── image025.emz │ │ ├── image025.png │ │ ├── image027.emz │ │ ├── image027.png │ │ ├── image029.emz │ │ ├── image029.png │ │ ├── image031.emz │ │ ├── image031.png │ │ ├── image033.emz │ │ ├── image033.png │ │ ├── image035.emz │ │ ├── image035.png │ │ ├── image037.emz │ │ ├── image037.png │ │ ├── image039.emz │ │ ├── image039.png │ │ ├── image041.emz │ │ ├── image041.png │ │ ├── image043.emz │ │ ├── image043.png │ │ ├── image044.emz │ │ ├── image044.png │ │ ├── image045.png │ │ ├── image046.emz │ │ ├── image046.png │ │ ├── image047.png │ │ ├── image048.emz │ │ ├── image048.png │ │ ├── image049.png │ │ ├── image050.emz │ │ ├── image050.png │ │ ├── image051.emz │ │ ├── image051.png │ │ ├── image052.png │ │ ├── image053.png │ │ ├── image054.png │ │ ├── image055.emz │ │ ├── image055.png │ │ ├── image056.png │ │ ├── image057.emz │ │ ├── image057.png │ │ ├── image058.png │ │ ├── image059.emz │ │ ├── image059.png │ │ ├── image060.png │ │ ├── image061.emz │ │ ├── image061.png │ │ ├── image062.png │ │ ├── image063.emz │ │ ├── image063.png │ │ ├── image064.emz │ │ ├── image064.png │ │ ├── image065.png │ │ ├── image066.emz │ │ ├── image066.png │ │ ├── image067.png │ │ ├── image068.emz │ │ ├── image068.png │ │ ├── image069.png │ │ ├── image070.emz │ │ ├── image070.png │ │ ├── image071.png │ │ ├── image072.emz │ │ ├── image072.png │ │ ├── image073.png │ │ ├── image074.emz │ │ ├── image075.png │ │ ├── image076.emz │ │ ├── image077.emz │ │ ├── image078.png │ │ ├── image079.emz │ │ ├── image080.png │ │ ├── image081.emz │ │ ├── image082.png │ │ ├── image083.emz │ │ ├── image084.png │ │ ├── image085.emz │ │ ├── image086.png │ │ ├── image087.emz │ │ ├── image088.png │ │ ├── image089.emz │ │ ├── image090.png │ │ ├── image091.emz │ │ ├── image092.png │ │ ├── image093.emz │ │ ├── image094.png │ │ ├── image095.emz │ │ ├── image096.png │ │ ├── image097.emz │ │ ├── image098.emz │ │ ├── image099.png │ │ ├── image100.emz │ │ ├── image101.png │ │ ├── image102.emz │ │ ├── image103.png │ │ ├── image104.emz │ │ ├── image105.emz │ │ ├── image106.png │ │ ├── item0054.xml │ │ ├── item0058.xml │ │ ├── item0060.xml │ │ ├── props055.xml │ │ ├── props059.xml │ │ ├── props061.xml │ │ └── themedata.thmx │ ├── gsasII-pwdr.html │ ├── gsasII-pwdr_files │ │ ├── colorschememapping.xml │ │ ├── filelist.xml │ │ ├── image001.png │ │ ├── image003.png │ │ ├── image055.emz │ │ ├── image056.png │ │ ├── item0008.xml │ │ ├── item0060.xml │ │ ├── props009.xml │ │ ├── props061.xml │ │ └── themedata.thmx │ ├── gsasII.html │ ├── gsasII_files │ │ ├── colorschememapping.xml │ │ ├── filelist.xml │ │ ├── image001.png │ │ ├── image002.png │ │ ├── image004.png │ │ ├── image005.png │ │ ├── image006.png │ │ ├── image007.png │ │ ├── image008.png │ │ ├── image009.png │ │ ├── image010.png │ │ ├── image011.png │ │ ├── image012.png │ │ ├── image013.png │ │ ├── image014.png │ │ ├── image015.png │ │ ├── image016.png │ │ ├── image017.png │ │ ├── image018.png │ │ ├── image019.png │ │ ├── image020.png │ │ ├── image021.png │ │ ├── image022.png │ │ ├── image023.png │ │ ├── image024.png │ │ ├── image025.png │ │ ├── image026.png │ │ ├── image027.png │ │ ├── image028.png │ │ ├── image029.png │ │ ├── image030.png │ │ ├── image031.png │ │ ├── image032.png │ │ ├── image033.png │ │ ├── image034.png │ │ ├── image035.png │ │ ├── image036.png │ │ ├── image037.png │ │ ├── image038.png │ │ ├── image039.png │ │ ├── image040.png │ │ ├── image041.png │ │ ├── image042.png │ │ ├── image043.png │ │ ├── image044.png │ │ ├── image045.png │ │ ├── image046.png │ │ ├── image047.png │ │ ├── image048.png │ │ ├── image049.png │ │ ├── image050.png │ │ ├── image051.png │ │ ├── image052.png │ │ ├── image053.png │ │ ├── image054.png │ │ ├── image055.png │ │ ├── image056.png │ │ ├── image057.png │ │ ├── item0006.xml │ │ ├── item0024.xml │ │ ├── item0054.xml │ │ ├── props007.xml │ │ ├── props025.xml │ │ ├── props055.xml │ │ ├── themedata.thmx │ │ ├── wrong.png │ │ └── xform.png │ └── gsasIIfav.png ├── icons │ ├── darrow.ico │ ├── exarrow.ico │ ├── eyarrow.ico │ ├── gsas2.icns │ ├── gsas2.ico │ ├── gsas2.png │ ├── gsas2mac.ico │ ├── help.ico │ ├── key.ico │ ├── larrow.ico │ ├── meson.build │ ├── publish.ico │ ├── rarrow.ico │ ├── sxarrow.ico │ ├── syarrow.ico │ └── uarrow.ico ├── imports │ ├── G2img_1TIF.py │ ├── G2img_ADSC.py │ ├── G2img_CBF.py │ ├── G2img_CheMin.py │ ├── G2img_EDF.py │ ├── G2img_GE.py │ ├── G2img_HDF5.py │ ├── G2img_MAR.py │ ├── G2img_PILTIF.py │ ├── G2img_Rigaku.py │ ├── G2img_SFRM.py │ ├── G2img_SumG2.py │ ├── G2img_pixirad_1ID_16bit.py │ ├── G2pdf_gr.py │ ├── G2phase.py │ ├── G2phase_CIF.py │ ├── G2phase_GPX.py │ ├── G2phase_INS.py │ ├── G2phase_rmc6f.py │ ├── G2phase_xyz.py │ ├── G2pwd_BrukerBRML.py │ ├── G2pwd_BrukerRAW.py │ ├── G2pwd_CIF.py │ ├── G2pwd_FP.py │ ├── G2pwd_GPX.py │ ├── G2pwd_MIDAS.py │ ├── G2pwd_Panalytical.py │ ├── G2pwd_csv.py │ ├── G2pwd_fxye.py │ ├── G2pwd_rigaku.py │ ├── G2pwd_xye.py │ ├── G2rfd_Panalytical.py │ ├── G2rfd_rigaku.py │ ├── G2rfd_xye.py │ ├── G2sad_xye.py │ ├── G2sfact.py │ ├── G2sfact_CIF.py │ ├── __init__.py │ └── meson.build ├── inputs │ ├── BinariesCache.txt │ ├── DefaultExpressions.txt │ ├── GSASIImacros │ │ ├── angles-resrb.mac │ │ ├── angles.mac │ │ ├── bonds-resrb.mac │ │ ├── bonds.mac │ │ ├── chiral.mac │ │ ├── planes-resrb.mac │ │ ├── planes.mac │ │ ├── ramachandran.mac │ │ ├── residue-rb.mac │ │ └── torsion.mac │ ├── OriginTemplate2.otpu │ ├── Xsect.dat │ ├── meson.build │ └── versioninfo.txt ├── install │ ├── g2app.tar.gz │ ├── git_filters.py.old │ ├── incr-version.py │ ├── macStartScript.py │ ├── makeBat.py │ ├── makeLinux.py │ ├── makeMacApp.py │ ├── makeVarTbl.py │ └── save-versions.py ├── k_vector_search.py ├── meson.build ├── nistlat.py ├── pathHacking.py ├── scanCCD.py ├── testDeriv.py ├── testMagSym.py ├── testSSymbols.py ├── testSytSym.py ├── testXNFF.py └── tutorialIndex.py ├── LICENSE ├── README.md ├── backcompat ├── ElementTable.py ├── GSASIIElem.py ├── GSASIIElemGUI.py ├── GSASIIIntPDFtool.py ├── GSASIIconstrGUI.py ├── GSASIIctrlGUI.py ├── GSASIIdata.py ├── GSASIIdataGUI.py ├── GSASIIddataGUI.py ├── GSASIIexprGUI.py ├── GSASIIfiles.py ├── GSASIIfpaGUI.py ├── GSASIIimage.py ├── GSASIIimgGUI.py ├── GSASIIindex.py ├── GSASIIlattice.py ├── GSASIImapvars.py ├── GSASIImath.py ├── GSASIImiscGUI.py ├── GSASIImpsubs.py ├── GSASIIobj.py ├── GSASIIpath.py ├── GSASIIphsGUI.py ├── GSASIIplot.py ├── GSASIIpwd.py ├── GSASIIpwdGUI.py ├── GSASIIpwdplot.py ├── GSASIIrestrGUI.py ├── GSASIIsasd.py ├── GSASIIscriptable.py ├── GSASIIseqGUI.py ├── GSASIIspc.py ├── GSASIIstrIO.py ├── GSASIIstrMain.py ├── GSASIIstrMath.py ├── GSASIItestplot.py └── meson.build ├── docs ├── Makefile ├── environment.yml ├── find_undoc.py ├── make.bat ├── scripting │ ├── .readthedocs.yaml │ ├── G2_html_logo.png │ ├── GSASIIobj.rst │ ├── GSASIIscriptable.rst │ ├── _static │ ├── conf.py │ ├── favicon.ico │ ├── images │ ├── index.rst │ ├── objvarorg.rst │ ├── packages.rst │ ├── scrpt-constr_ref.rst │ ├── scrpt-import_ref.rst │ └── scrpt-indices.rst └── source │ ├── G2_html_logo.png │ ├── G2tools.rst │ ├── GSASII.rst │ ├── GSASIIGUI.rst │ ├── GSASIIGUIr.rst │ ├── GSASIIdata.rst │ ├── GSASIIimage.rst │ ├── GSASIIindex.rst │ ├── GSASIImapvars.rst │ ├── GSASIImath.rst │ ├── GSASIIobj.rst │ ├── GSASIIpwd.rst │ ├── GSASIIscriptable.rst │ ├── GSASIIscripts.rst │ ├── GSASIIstruc.rst │ ├── GSASIIutil.rst │ ├── GSASIIweb.rst │ ├── SAS.rst │ ├── _static │ └── theme_overrides.css │ ├── conf.py │ ├── exports.rst │ ├── favicon.ico │ ├── graphics.rst │ ├── images │ ├── MakeShortcut.png │ ├── TestShortcut.png │ └── menu.png │ ├── imports.rst │ ├── index.rst │ ├── indices.rst │ ├── objvarorg.rst │ ├── packages.rst │ └── versioning.rst ├── meson.build ├── noxfile.py ├── pixi ├── .gitattributes ├── .gitignore ├── pixi.lock └── pixi.toml ├── pyproject.toml ├── sources ├── .gitignore ├── DIFFaXsubs │ ├── DIFFaX.inc │ ├── DIFFaX.par │ └── DIFFaXsubs.for ├── INCLDS │ └── COPYRIGT.FOR ├── LATTIC.f ├── NISTlatsubs │ ├── BLOCKDATA1.f │ ├── CENTER.f │ ├── CKPT02.f │ ├── DERIV.f │ ├── DETERM.f │ ├── DOT.f │ ├── HEAD0.f │ ├── HEAD2.f │ ├── HEAD3.f │ ├── HEAD4.f │ ├── HEAD5.f │ ├── HEAD6.f │ ├── HMATRX.f │ ├── INVERS.f │ ├── MNCOND.f │ ├── MULTIP.f │ ├── NORMAL.f │ ├── OUTPT1.f │ ├── OUTPT2.f │ ├── QMATRI.f │ ├── RD021.f │ ├── RD051.f │ ├── RD061.f │ ├── REDUCE.f │ ├── SET.f │ ├── SHORTV.f │ ├── SPCON2.f │ ├── SPCOND.f │ ├── TRANS.f │ └── VOLUME.f ├── convcell.f ├── fmask.c ├── histogram2d.for ├── histosigma2d.for ├── install.bat ├── install.sh ├── k_vec_cython │ ├── kvec_general.pyx │ ├── meson.build │ └── setup.py ├── meson.build ├── pack_f.for ├── polymask.for ├── powsubs │ ├── acosd.for │ ├── cosd.for │ ├── epsvoigt.for │ ├── expint.for │ ├── gauleg.for │ ├── gerfc.for │ ├── hfunc.for │ ├── lorentz.for │ ├── psvfcj.f90 │ ├── psvfcjexpo.for │ ├── psvfcjo.for │ ├── psvoigt.for │ ├── sind.for │ └── tand.for ├── pydiffax.for ├── pypowder.for ├── pyspg.for ├── pytexture.for ├── spotmask.for ├── spsubs │ ├── genhkl.for │ ├── sglatc.for │ ├── sglcen.for │ ├── sglpak.for │ ├── sgmtml.for │ ├── sgoprn.for │ ├── sgrmat.for │ ├── sgroupnp.for │ └── sgtrcf.for ├── sysinstall.bat ├── sysinstall.sh ├── tagbinaries.py ├── texturesubs │ ├── aplms.for │ ├── cosd.for │ ├── dgammln.for │ ├── factln.for │ ├── plmpsi.for │ ├── qlmn.for │ ├── qlmninit.for │ └── sind.for └── unpack_cbf.for └── tests ├── debugref.py ├── run_pypowder.py ├── test_diffax.py ├── test_elm.py ├── test_image.py ├── test_kvec.py ├── test_lattice.py ├── test_nistlat.py ├── test_scriptref.py ├── test_spg.py ├── test_tofref.py └── testinp ├── INST_XRY.PRM ├── PBSO4.CWN ├── PBSO4.XRA ├── PbSO4-Wyckoff.cif ├── gencelltests.py ├── genhkltest.py ├── genselftest.py ├── gensgtbx.py ├── inst_d1a.prm ├── nx09_strain_011.imctrl ├── sgtbxlattinp.py ├── sgtbxtestinp.py ├── spctestinp.py └── test.sas /.github/old-workflows/win-selfinstall-test.yml: -------------------------------------------------------------------------------- 1 | name: install self-installer on Windows 2 | 3 | on: 4 | workflow_dispatch: # Allows running this workflow manually 5 | # Runs on pushes targeting the default branch 6 | # push: 7 | # branches-ignore: 8 | # - master 9 | # branches: ['main'] 10 | # pull_request: 11 | # branches: ['main'] 12 | 13 | 14 | jobs: 15 | test-GSAS-II: 16 | #strategy: 17 | # fail-fast: false 18 | runs-on: 'windows-latest' 19 | steps: 20 | - uses: suisei-cn/actions-download-file@818d6b7dc8fe73f2f924b6241f2b1134ca1377d9 # 1.6.0 21 | id: downloadfile 22 | name: Download the file 23 | with: 24 | url: "https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/gsas2new-5804-Windows-x86_64.exe" 25 | #target: download/ 26 | #- name: find it 27 | # shell: bash 28 | # run: | 29 | # ls -R 30 | 31 | - name: GSAS-II install 32 | shell: pwsh 33 | run: Start-Process -FilePath .\gsas2new-5804-Windows-x86_64.exe -ArgumentList "/S /AddToPath=1 " -NoNewWindow -Wait 34 | 35 | #- name: find install 36 | # if: always() 37 | # shell: bash 38 | # run: | 39 | # ls -R 40 | 41 | #- name: GSAS-II find GSAS-II 42 | # if: always() 43 | # shell: bash 44 | # run: | 45 | # cd c:/ProgramData/gsas2new/GSAS-II 46 | # ls 47 | 48 | - name: try all tests 49 | if: always() 50 | shell: cmd 51 | run: | 52 | call c:\ProgramData\gsas2new\Scripts\activate 53 | python -VV 54 | call conda install -y --quiet pytest 55 | call cd c:\ProgramData\gsas2new\GSAS-II 56 | dir 57 | python -m pytest c:/ProgramData/gsas2new/GSAS-II 58 | 59 | # #python -v -c "import sys; print(sys.path)" 60 | # python -c "import pyspg" 61 | 62 | # - name: try ldd 63 | # if: always() 64 | # shell: bash -el {0} 65 | # run: | 66 | # #conda create -n ntldd python=3.12 numpy=2.2 m2w64-ntldd-git 67 | # conda create -n ntldd python=3.11 numpy=1.26 m2w64-ntldd-git 68 | # conda activate ntldd 69 | # cd GSAS-II/GSASII-bin/win_64_p3.11_n1.26 70 | # #cd GSAS-II/GSASII-bin/win_64_p3.12_n2.2 71 | # ls 72 | # ntldd *.pyd 73 | # python -c "import pyspg" 74 | -------------------------------------------------------------------------------- /.github/workflows/TriggerRemote.yml: -------------------------------------------------------------------------------- 1 | # when run, this starts GitHub Actions workflow in another repo (GSAS-II-buildtools) 2 | 3 | # 1) This will trigger all GitHub Actions in workflows that has 4 | # on: repository_dispatch: 5 | # 2) an authorized user (Brian, or perhaps organization) creates a 6 | # personal access token. 7 | # Do this by clicking on "picture (upper rt) 8 | # then "Settings" in drop-down and 9 | # then select "Developer settings" (at bottom). 10 | # Finally select "Fine-grained tokens" 11 | # Personal access token settings: 12 | # select owner: APS; 13 | # select APS/G2-bld; 14 | # Repo permissions: contents r/w & metadata: r/o. 15 | # 3) Save the created token in this (G2) project. 16 | # Use repo-level settings on 2nd line from top (may be in ... menu). 17 | # Select Actions in Secrets & variables and create a repository secret. 18 | # Name assigned must match ${{ secrets.XXX }} in workflow's curl 19 | # call ("Authorization:" setting) 20 | 21 | name: Test of triggering GSASII-buildtools actions 22 | 23 | on: workflow_dispatch 24 | 25 | jobs: 26 | trigger: 27 | runs-on: ubuntu-latest 28 | 29 | steps: 30 | - name: Trigger Workflow in GSAS-II-buildtools 31 | run: | 32 | # config var follows 33 | repo_owner="AdvancedPhotonSource" 34 | 35 | curl -L \ 36 | -X POST \ 37 | -H "Accept: application/vnd.github+json" \ 38 | -H "Authorization: Bearer ${{ secrets.PAT }}" \ 39 | -H "X-GitHub-Api-Version: 2022-11-28" \ 40 | https://api.github.com/repos/$repo_owner/GSAS-II-buildtools/dispatches \ 41 | -d '{"event_type": "remote build", "client_payload": {"service": "remote build", "unit": false, "integration": true}}' 42 | 43 | -------------------------------------------------------------------------------- /.github/workflows/smoke_test.yml: -------------------------------------------------------------------------------- 1 | name: smoke test 2 | 3 | on: 4 | # Runs on pushes targeting the default branch 5 | push: 6 | branches-ignore: 7 | - master 8 | # branches: ['develop'] 9 | pull_request: 10 | branches: ['main'] 11 | 12 | # Allows you to run this workflow manually from the Actions tab 13 | workflow_dispatch: 14 | 15 | 16 | # Default to bash 17 | defaults: 18 | run: 19 | shell: bash 20 | 21 | 22 | jobs: 23 | build: 24 | strategy: 25 | fail-fast: false 26 | matrix: 27 | os: 28 | - name: 'ubuntu-22.04' 29 | - name: 'macos-latest' 30 | - name: 'windows-latest' 31 | # cmd_extra: '-win' 32 | env: ['py310', 'py311', 'py312', 'py313'] 33 | runs-on: ${{ matrix.os.name }} 34 | steps: 35 | # checkout repo 36 | - uses: actions/checkout@v2 37 | 38 | # set up pixi 39 | - uses: prefix-dev/setup-pixi@v0.8.1 40 | with: 41 | environments: ${{ matrix.env }} 42 | pixi-version: v0.39.5 43 | manifest-path: pixi/pixi.toml 44 | 45 | # run install to see if it works 46 | - name: Build 47 | # run: pixi run --manifest-path pixi/pixi.toml -e ${{ matrix.env }} install${{ matrix.os.cmd_extra }} 48 | run: pixi run --manifest-path pixi/pixi.toml -e ${{ matrix.env }} install 49 | 50 | - name: test 51 | run: pixi run --manifest-path pixi/pixi.toml -e ${{ matrix.env }} test 52 | -------------------------------------------------------------------------------- /.github/workflows/win-gitstrap-selftest.yml: -------------------------------------------------------------------------------- 1 | name: GSAS-II self-tests on Windows via gitstrap 2 | 3 | on: 4 | workflow_dispatch: # Allows running this workflow manually 5 | # Runs on pushes targeting the default branch 6 | # push: 7 | # branches-ignore: 8 | # - master 9 | # branches: ['main'] 10 | # pull_request: 11 | # branches: ['main'] 12 | 13 | 14 | jobs: 15 | test-GSAS-II: 16 | strategy: 17 | fail-fast: false 18 | matrix: 19 | python-version: ["3.12", "3.13"] 20 | # python-version: ["3.11", "3.12", "3.13"] 21 | # python-version: ["3.13"] 22 | runs-on: 'windows-latest' 23 | steps: 24 | - uses: conda-incubator/setup-miniconda@v3 25 | with: 26 | auto-update-conda: true 27 | python-version: ${{ matrix.python-version }} 28 | - name: Conda install 29 | shell: bash -el {0} 30 | run: | 31 | # tailor the numpy version to match the GSAS-II binaries 32 | if [ "${{ matrix.python-version }}" == "3.13" ]; then 33 | npver="2.2 python-gil" 34 | elif [ "${{ matrix.python-version }}" == "3.12" ]; then 35 | npver=2.2 36 | elif [ "${{ matrix.python-version }}" == "3.11" ]; then 37 | npver=1.26 38 | fi 39 | conda install python=${{ matrix.python-version }} numpy=${npver} scipy requests pytest git gitpython pycifrw -c conda-forge --override-channels --quiet 40 | #conda info 41 | #conda list 42 | - name: GSAS-II install 43 | shell: bash -el {0} 44 | run: | 45 | curl -L -O https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/raw/main/install/gitstrap.py 46 | python gitstrap.py --nocheck --noshortcut --branch=main 47 | 48 | - name: GSAS-II all tests 49 | shell: bash -el {0} 50 | run: | 51 | cd GSAS-II 52 | python -m pytest 53 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # obsolete GSAS-II settings file 2 | config.py 3 | 4 | # local code for debugging 5 | debug_setup.py.example 6 | debug_setup.py 7 | 8 | # created by install/saved-versions.py 9 | GSASII/saved_version.py 10 | 11 | # created on MacOS by makeMacApp.py 12 | GSAS-II.app/ 13 | GSAS-II.py 14 | 15 | # created by gitstrap.py 16 | GSASII-bin 17 | 18 | # created by docs/build/conf.py 19 | version.rst 20 | vars.rst 21 | docs/build/ 22 | 23 | # cruft from Python 24 | __pycache__ 25 | 26 | # cruft from MacOS 27 | .DS_Store 28 | 29 | # from Spyder 30 | .spyproject 31 | 32 | # GSAS binaries 33 | GSASII/bindist 34 | GSASII/bin 35 | 36 | # Local dev env files 37 | .vscode 38 | 39 | 40 | dist 41 | build 42 | 43 | # 44 | *.gpx 45 | *.lst 46 | 47 | *~ 48 | -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- 1 | # .readthedocs.yaml 2 | # Read the Docs configuration file 3 | # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details 4 | 5 | version: 2 6 | 7 | build: 8 | os: "ubuntu-20.04" 9 | tools: 10 | python: "mambaforge-4.10" 11 | 12 | conda: 13 | environment: docs/environment.yml 14 | 15 | formats: 16 | - epub 17 | - pdf 18 | 19 | sphinx: 20 | # Path to Sphinx configuration file. 21 | configuration: docs/source/conf.py 22 | -------------------------------------------------------------------------------- /GSASII/G2.py: -------------------------------------------------------------------------------- 1 | # Starts GSAS-II from clone of GitHub repo when contents is not 2 | # installed into current Python. 3 | # 4 | # This can be used when GSAS-II is installed, but why bother as the command: 5 | # python -c "from GSASII.GSASIIGUI import main; main()" 6 | # will do just as well. 7 | # Even better: 8 | # GSASII_NOPATHHACKING="true" python -c "from GSASII.GSASIIGUI import main; main()" 9 | 10 | import os 11 | import sys 12 | # patch 4/25: cleanup old GSASII.py script if still around (replaced by this file) 13 | oldg2script = os.path.join(os.path.dirname(__file__),'GSASII.py') 14 | if os.path.exists(oldg2script): 15 | os.remove(oldg2script) 16 | print(f'Cleanup: removing old {oldg2script!r} file') 17 | # end patch 18 | import importlib.util 19 | try: 20 | pkginfo = importlib.util.find_spec('GSASII.GSASIIGUI') 21 | except ModuleNotFoundError: 22 | pkginfo = None 23 | 24 | if __name__ == '__main__': 25 | if pkginfo is None: # hack path if GSASII not installed into Python 26 | print('Adding GSAS-II location to Python system path') 27 | sys.path.insert(0,os.path.dirname(os.path.dirname(__file__))) 28 | from GSASII.GSASIIGUI import main 29 | main() 30 | -------------------------------------------------------------------------------- /GSASII/NIST_profile/__init__.py: -------------------------------------------------------------------------------- 1 | from __future__ import absolute_import 2 | from .profile_functions_class import FP_profile, best_irfft, best_rfft 3 | from .atan_windowed_FP_profile import FP_atan_windowed_convolver 4 | 5 | class FP_windowed(FP_atan_windowed_convolver, FP_profile): 6 | pass 7 | 8 | 9 | -------------------------------------------------------------------------------- /GSASII/NIST_profile/meson.build: -------------------------------------------------------------------------------- 1 | py.install_sources([ 2 | '__init__.py', 3 | 'profile_functions_class.py', 4 | 'atan_windowed_FP_profile.py', 5 | ], 6 | pure: false, # Will be installed next to binaries 7 | subdir: 'GSASII/NIST_profile' # Folder relative to site-packages to install to 8 | ) 9 | -------------------------------------------------------------------------------- /GSASII/__init__.py: -------------------------------------------------------------------------------- 1 | import os 2 | import sys 3 | 4 | sys.path.append('.') 5 | 6 | class PathHackingException(Exception): pass 7 | 8 | def make_path_watcher(): 9 | import sys 10 | import traceback 11 | 12 | init_path = tuple(sys.path) 13 | def no_path_hacking(event_name, args): 14 | if event_name != 'import': 15 | return 16 | module, filename, path, meta_path, path_hooks = args 17 | if path is not None and tuple(path) != init_path: 18 | lines = list(traceback.format_stack()) 19 | for line in lines: 20 | print(line.strip()) 21 | print(set(path) - set(init_path)) 22 | #sys.exit(1) 23 | raise PathHackingException(lines[-2].strip()) 24 | return no_path_hacking 25 | 26 | if os.environ.get("GSASII_NOPATHHACKING", ''): 27 | sys.addaudithook(make_path_watcher()) 28 | 29 | del sys, make_path_watcher, os 30 | 31 | 32 | from .GSASIIGUI import main # noqa: E402 33 | 34 | __all__ = ['main'] 35 | -------------------------------------------------------------------------------- /GSASII/__main__.py: -------------------------------------------------------------------------------- 1 | from . import main 2 | 3 | main() 4 | -------------------------------------------------------------------------------- /GSASII/exports/G2export_image.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | '''Classes in :mod:`~GSASII.exports.G2export_image` follow: 3 | ''' 4 | from __future__ import division, print_function 5 | import os.path 6 | try: 7 | import matplotlib.pyplot as plt 8 | except ImportError: 9 | plt = None 10 | from .. import GSASIIfiles as G2fil 11 | 12 | class ExportImagePNG(G2fil.ExportBaseclass): 13 | '''Used to create a PNG file for a GSAS-II image 14 | 15 | :param wx.Frame G2frame: reference to main GSAS-II frame 16 | ''' 17 | def __init__(self,G2frame): 18 | super(self.__class__,self).__init__( # fancy way to say .__init__ 19 | G2frame=G2frame, 20 | formatName = 'PNG image file', 21 | extension='.png', 22 | longFormatName = 'Export image in PNG format' 23 | ) 24 | if plt is None: 25 | self.exporttype = [] 26 | else: 27 | self.exporttype = ['image'] 28 | #self.multiple = True 29 | def Exporter(self,event=None): 30 | '''Export an image 31 | ''' 32 | # the export process starts here 33 | self.InitExport(event) 34 | # load all of the tree into a set of dicts 35 | self.loadTree() 36 | if self.ExportSelect(): return # select one image; ask for a file name 37 | # process the selected image(s) (at present only one image) 38 | for i in sorted(self.histnam): 39 | filename = os.path.join( 40 | self.dirname, 41 | os.path.splitext(self.filename)[0] + self.extension 42 | ) 43 | imgFile = self.Histograms[i].get('Data',(None,None)) 44 | Image = G2fil.GetImageData(self.G2frame,imgFile,imageOnly=True) 45 | plt.imsave(filename,Image) 46 | print('Image '+imgFile+' written to file '+filename) 47 | -------------------------------------------------------------------------------- /GSASII/exports/__init__.py: -------------------------------------------------------------------------------- 1 | from . import G2export_Bracket 2 | from . import G2export_CIF 3 | from . import G2export_FIT2D 4 | from . import G2export_JSON 5 | from . import G2export_PDB 6 | from . import G2export_csv 7 | from . import G2export_examples 8 | from . import G2export_image 9 | from . import G2export_map 10 | from . import G2export_pwdr 11 | from . import G2export_shelx 12 | 13 | __all__ = [ 14 | "G2export_Bracket", 15 | "G2export_CIF", 16 | "G2export_FIT2D", 17 | "G2export_JSON", 18 | "G2export_PDB", 19 | "G2export_csv", 20 | "G2export_examples", 21 | "G2export_image", 22 | "G2export_map", 23 | "G2export_pwdr", 24 | "G2export_shelx", 25 | ] 26 | -------------------------------------------------------------------------------- /GSASII/exports/meson.build: -------------------------------------------------------------------------------- 1 | py.install_sources([ 2 | 'G2export_Bracket.py', 3 | 'G2export_CIF.py', 4 | 'G2export_FIT2D.py', 5 | 'G2export_JSON.py', 6 | 'G2export_PDB.py', 7 | 'G2export_csv.py', 8 | 'G2export_examples.py', 9 | 'G2export_image.py', 10 | 'G2export_map.py', 11 | 'G2export_pwdr.py', 12 | 'G2export_shelx.py', 13 | '__init__.py', 14 | 'cif_core.cpickle', 15 | 'cif_core.dic', 16 | 'cif_pd.cpickle', 17 | 'cif_pd.dic', 18 | 'template_phase.cif', 19 | 'template_powder.cif', 20 | 'template_publ.cif', 21 | 'template_single.cif', 22 | ], 23 | pure: false, # Will be installed next to binaries 24 | subdir: 'GSASII/exports' # Folder relative to site-packages to install to 25 | ) 26 | 27 | -------------------------------------------------------------------------------- /GSASII/exports/template_phase.cif: -------------------------------------------------------------------------------- 1 | # GSAS-II phase information template file 2 | 3 | data_Phase_Template 4 | #============================================================================== 5 | # 7. CHEMICAL, STRUCTURAL AND CRYSTAL DATA 6 | 7 | _pd_char_particle_morphology ? 8 | 9 | _chemical_name_systematic 10 | ; ? 11 | ; 12 | _chemical_name_common ? 13 | _chemical_formula_moiety ? 14 | _chemical_formula_structural ? 15 | _chemical_formula_analytical ? 16 | _chemical_melting_point ? 17 | _chemical_compound_source ? # for minerals and 18 | # natural products 19 | _symmetry_space_group_name_Hall ? 20 | 21 | _exptl_crystal_F_000 ? 22 | _exptl_crystal_density_meas ? 23 | _exptl_crystal_density_method ? 24 | 25 | _cell_special_details 26 | ; ? 27 | ; 28 | 29 | _geom_special_details ? 30 | 31 | # The following item identifies the program(s) used (if appropriate). 32 | _computing_structure_solution ? 33 | 34 | #============================================================================== 35 | 36 | # 8. Phase information from GSAS-II 37 | 38 | -------------------------------------------------------------------------------- /GSASII/exports/template_single.cif: -------------------------------------------------------------------------------- 1 | # GSAS-II single-crystal instrument template file 2 | 3 | data_Instrument_Template 4 | #============================================================================== 5 | # 9. INSTRUMENT CHARACTERIZATION 6 | 7 | _exptl_special_details 8 | ; ? 9 | ; 10 | 11 | _diffrn_ambient_temperature ? 12 | _diffrn_source ? 13 | _diffrn_source_target ? 14 | _diffrn_source_type ? 15 | _diffrn_measurement_device_type ? 16 | _diffrn_detector ? 17 | _diffrn_detector_type ? # make or model of detector 18 | 19 | # The following two items identify the data collection program(s) used 20 | _computing_data_collection ? 21 | _computing_data_reduction ? 22 | 23 | _diffrn_radiation_monochromator ? 24 | 25 | -------------------------------------------------------------------------------- /GSASII/git_verinfo.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # git_verinfo.py - GSAS-II version info from git 3 | # Do not edit, generated by 'GSASII/install/incr-version.py' script 4 | # Created 2025-05-26 14:08:11.331511-05:00 5 | 6 | git_version = 'c37c8ba4cdc73a97e0a8ccf9d9f3c95758502e5b' 7 | git_tags = ['5813'] 8 | git_prevtaggedversion = '144bf1bd2a45ebb481af31fce19a1345cde48512' 9 | git_prevtags = ['5812'] 10 | git_versiontag = 'v5.4.6' 11 | -------------------------------------------------------------------------------- /GSASII/help/graphbar.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AdvancedPhotonSource/GSAS-II/4725770466eda23171ee532c2cf745fbe0634fdd/GSASII/help/graphbar.jpg -------------------------------------------------------------------------------- /GSASII/help/gsas2logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AdvancedPhotonSource/GSAS-II/4725770466eda23171ee532c2cf745fbe0634fdd/GSASII/help/gsas2logo.png -------------------------------------------------------------------------------- /GSASII/help/gsasII-index.fld/colorschememapping.xml: -------------------------------------------------------------------------------- 1 | 2 | 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None 13 | class png_ReaderClass(G2obj.ImportImage): 14 | '''Reads standard PNG images; parameters are set to those of the 15 | Mars Rover (CheMin) diffractometer. 16 | ''' 17 | def __init__(self): 18 | if imageio is None: 19 | self.UseReader = False 20 | msg = 'CheMin Reader skipped because imageio library is not installed' 21 | if GSASIIpath.condaTest(): 22 | msg += ' To fix this use command:\n\tconda install imageio' 23 | G2fil.ImportErrorMsg(msg,{'CheMin image importer':['imageio']}) 24 | super(self.__class__,self).__init__( # fancy way to self-reference 25 | extensionlist=('.png',), 26 | strictExtension=True, 27 | formatName = 'CheMin PNG image', 28 | longFormatName = 'PNG image from CheMin' 29 | ) 30 | 31 | def ContentsValidator(self, filename): 32 | '''no test at this time 33 | ''' 34 | return True 35 | 36 | def Reader(self,filename, ParentFrame=None, **unused): 37 | '''Reads using standard scipy PNG reader 38 | ''' 39 | self.Image = imageio.imread(filename,flatten=True) 40 | self.Npix = self.Image.size 41 | if self.Npix == 0: 42 | return False 43 | if ParentFrame: 44 | self.SciPy = True 45 | self.Comments = ['no metadata'] 46 | pixy = list(self.Image.shape) 47 | sizexy = [40.,40.] 48 | self.Data = {'wavelength': 1.78892, 'pixelSize': sizexy, 'distance': 18.0,'size':pixy,'det2theta':0.0} 49 | self.Data['center'] = [pixy[0]*sizexy[0]/1000.,pixy[1]*sizexy[1]/2000.] 50 | self.LoadImage(ParentFrame,filename) 51 | return True 52 | -------------------------------------------------------------------------------- /GSASII/imports/G2img_SumG2.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | ''' 3 | ''' 4 | 5 | from __future__ import division, print_function 6 | import pickle 7 | from .. import GSASIIobj as G2obj 8 | class G2_ReaderClass(G2obj.ImportImage): 9 | '''Routine to read an image that has been pickled in Python. Images 10 | in this format are created by the "Sum image data" command. At least for 11 | now, only one image is permitted per file. 12 | ''' 13 | def __init__(self): 14 | super(self.__class__,self).__init__( # fancy way to self-reference 15 | extensionlist=('.G2img',), 16 | strictExtension=True, 17 | formatName = 'GSAS-II image', 18 | longFormatName = 'pickled image from GSAS-II' 19 | ) 20 | 21 | def ContentsValidator(self, filename): 22 | '''test by trying to unpickle (should be quick) 23 | ''' 24 | try: 25 | fp = open(filename,'rb') 26 | pickle.load(fp) 27 | fp.close() 28 | except: 29 | return False 30 | return True 31 | 32 | def Reader(self,filename, ParentFrame=None, **unused): 33 | '''Read using pickle 34 | ''' 35 | Fp = open(filename,'rb') 36 | self.Comments,self.Data,self.Npix,self.Image = pickle.load(Fp) 37 | Fp.close() 38 | self.LoadImage(ParentFrame,filename) 39 | return True 40 | -------------------------------------------------------------------------------- /GSASII/imports/__init__.py: -------------------------------------------------------------------------------- 1 | from . import G2img_1TIF 2 | from . import G2img_ADSC 3 | from . import G2img_CBF 4 | from . import G2img_CheMin 5 | from . import G2img_EDF 6 | from . import G2img_GE 7 | from . import G2img_HDF5 8 | from . import G2img_MAR 9 | from . import G2img_PILTIF 10 | from . import G2img_Rigaku 11 | from . import G2img_SFRM 12 | from . import G2img_SumG2 13 | from . import G2img_pixirad_1ID_16bit 14 | from . import G2pdf_gr 15 | from . import G2phase 16 | from . import G2phase_CIF 17 | from . import G2phase_GPX 18 | from . import G2phase_INS 19 | from . import G2phase_rmc6f 20 | from . import G2phase_xyz 21 | from . import G2pwd_BrukerBRML 22 | from . import G2pwd_BrukerRAW 23 | from . import G2pwd_CIF 24 | from . import G2pwd_FP 25 | from . import G2pwd_GPX 26 | from . import G2pwd_MIDAS 27 | from . import G2pwd_Panalytical 28 | from . import G2pwd_csv 29 | from . import G2pwd_fxye 30 | from . import G2pwd_rigaku 31 | from . import G2pwd_xye 32 | from . import G2rfd_Panalytical 33 | from . import G2rfd_rigaku 34 | from . import G2rfd_xye 35 | from . import G2sad_xye 36 | from . import G2sfact 37 | from . import G2sfact_CIF 38 | 39 | __all__ = [ 40 | "G2img_1TIF", 41 | "G2img_ADSC", 42 | "G2img_CBF", 43 | "G2img_CheMin", 44 | "G2img_EDF", 45 | "G2img_GE", 46 | "G2img_HDF5", 47 | "G2img_MAR", 48 | "G2img_PILTIF", 49 | "G2img_Rigaku", 50 | "G2img_SFRM", 51 | "G2img_SumG2", 52 | "G2img_pixirad_1ID_16bit", 53 | "G2pdf_gr", 54 | "G2phase", 55 | "G2phase_CIF", 56 | "G2phase_GPX", 57 | "G2phase_INS", 58 | "G2phase_rmc6f", 59 | "G2phase_xyz", 60 | "G2pwd_BrukerBRML", 61 | "G2pwd_BrukerRAW", 62 | "G2pwd_CIF", 63 | "G2pwd_FP", 64 | "G2pwd_GPX", 65 | "G2pwd_MIDAS", 66 | "G2pwd_Panalytical", 67 | "G2pwd_csv", 68 | "G2pwd_fxye", 69 | "G2pwd_rigaku", 70 | "G2pwd_xye", 71 | "G2rfd_Panalytical", 72 | "G2rfd_rigaku", 73 | "G2rfd_xye", 74 | "G2sad_xye", 75 | "G2sfact", 76 | "G2sfact_CIF", 77 | ] 78 | -------------------------------------------------------------------------------- /GSASII/imports/meson.build: -------------------------------------------------------------------------------- 1 | py.install_sources([ 2 | '__init__.py', 3 | 'G2img_1TIF.py', 4 | 'G2img_ADSC.py', 5 | 'G2img_CBF.py', 6 | 'G2img_CheMin.py', 7 | 'G2img_EDF.py', 8 | 'G2img_GE.py', 9 | 'G2img_HDF5.py', 10 | 'G2img_MAR.py', 11 | 'G2img_PILTIF.py', 12 | 'G2img_Rigaku.py', 13 | 'G2img_SFRM.py', 14 | 'G2img_SumG2.py', 15 | 'G2img_pixirad_1ID_16bit.py', 16 | 'G2pdf_gr.py', 17 | 'G2phase.py', 18 | 'G2phase_CIF.py', 19 | 'G2phase_GPX.py', 20 | 'G2phase_INS.py', 21 | 'G2phase_rmc6f.py', 22 | 'G2phase_xyz.py', 23 | 'G2pwd_BrukerBRML.py', 24 | 'G2pwd_BrukerRAW.py', 25 | 'G2pwd_CIF.py', 26 | 'G2pwd_FP.py', 27 | 'G2pwd_GPX.py', 28 | 'G2pwd_MIDAS.py', 29 | 'G2pwd_Panalytical.py', 30 | 'G2pwd_csv.py', 31 | 'G2pwd_fxye.py', 32 | 'G2pwd_rigaku.py', 33 | 'G2pwd_xye.py', 34 | 'G2rfd_Panalytical.py', 35 | 'G2rfd_rigaku.py', 36 | 'G2rfd_xye.py', 37 | 'G2sad_xye.py', 38 | 'G2sfact.py', 39 | 'G2sfact_CIF.py', 40 | ], 41 | pure: false, # Will be installed next to binaries 42 | subdir: 'GSASII/imports' # Folder relative to site-packages to install to 43 | ) 44 | -------------------------------------------------------------------------------- /GSASII/inputs/BinariesCache.txt: -------------------------------------------------------------------------------- 1 | linux_64_p3.11_n1.26 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/linux_64_p3.11_n1.26.tgz 2 | linux_64_p3.12_n2.2 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/linux_64_p3.12_n2.2.tgz 3 | linux_64_p3.13_n2.2 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/linux_64_p3.13_n2.2.tgz 4 | linux_arm32_p3.11_n1.24 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/linux_arm32_p3.11_n1.24.tgz 5 | linux_arm64_p3.11_n1.26 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/linux_arm64_p3.11_n1.26.tgz 6 | mac_64_p3.11_n1.26 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/mac_64_p3.11_n1.26.tgz 7 | mac_64_p3.12_n2.2 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/mac_64_p3.12_n2.2.tgz 8 | mac_64_p3.13_n2.2 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/mac_64_p3.13_n2.2.tgz 9 | mac_arm_p3.11_n1.26 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/mac_arm_p3.11_n1.26.tgz 10 | mac_arm_p3.12_n2.2 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/mac_arm_p3.12_n2.2.tgz 11 | mac_arm_p3.13_n2.2 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/mac_arm_p3.13_n2.2.tgz 12 | win_64_p3.11_n1.26 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/win_64_p3.11_n1.26.tgz 13 | win_64_p3.12_n2.2 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/win_64_p3.12_n2.2.tgz 14 | win_64_p3.13_n2.2 : https://github.com/AdvancedPhotonSource/GSAS-II-buildtools/releases/download/v1.0.1/win_64_p3.13_n2.2.tgz 15 | -------------------------------------------------------------------------------- /GSASII/inputs/DefaultExpressions.txt: -------------------------------------------------------------------------------- 1 | # GSAS-II Configuration File 2 | # This contains expressions to be used as default options for the expression editor 3 | m*x+b # fit a straight line 4 | a*x**2 + b*x + c # fit a quadradic 5 | -------------------------------------------------------------------------------- /GSASII/inputs/GSASIImacros/angles-resrb.mac: -------------------------------------------------------------------------------- 1 | !standard angle restraints for amino acids using flexible rigid bodies - Engh & Huber 2 | F 1.5 3 | S * 116.20 2.00 CA C N+ 4 | S * 123.00 1.60 O C N+ 5 | S * 121.70 1.80 C N+ CA+ 6 | S PRO 104.53 2.00 CA CB CG 7 | S PRO 106.07 2.00 CB CG CD 8 | -------------------------------------------------------------------------------- /GSASII/inputs/GSASIImacros/bonds-resrb.mac: -------------------------------------------------------------------------------- 1 | !standard bond restraints for amino acids using flexible rigid bodies - Engh & Huber 2 | F 0.3 3 | !peptide chain 4 | S * 1.329 .01 C N 5 | S * 1.249 .01 C OXT 6 | S * 3.80 .1 CA CA 7 | !disulfides 8 | S CYS 2.031 .01 SG SG 9 | -------------------------------------------------------------------------------- /GSASII/inputs/GSASIImacros/chiral.mac: -------------------------------------------------------------------------------- 1 | !standard chiral volume restraints for amino acids 2 | F 0.5 3 | S ALA 2.478 .1 CA C CB N 4 | S ARG 2.503 .1 CA C CB N 5 | S ASN 2.503 .1 CA C CB N 6 | S ASP 2.503 .1 CA C CB N 7 | S CYS 2.503 .1 CA C CB N 8 | S GLN 2.503 .1 CA C CB N 9 | S GLU 2.503 .1 CA C CB N 10 | S HIS 2.503 .1 CA C CB N 11 | S ILE 2.519 .1 CA C CB N 12 | S LEU 2.503 .1 CA C CB N 13 | S LYS 2.503 .1 CA C CB N 14 | S MET 2.503 .1 CA C CB N 15 | S PHE 2.503 .1 CA C CB N 16 | S PRO 2.728 .1 CA C CB N 17 | S SER 2.503 .1 CA C CB N 18 | S THR 2.519 .1 CA C CB N 19 | S TRP 2.503 .1 CA C CB N 20 | S TYR 2.503 .1 CA C CB N 21 | S VAL 2.519 .1 CA C CB N 22 | S ILE 2.5 .5 CB CA CG1 CG2 23 | S THR 2.5 .5 CB CA OG1 CG2 24 | -------------------------------------------------------------------------------- /GSASII/inputs/GSASIImacros/planes-resrb.mac: -------------------------------------------------------------------------------- 1 | !standard plane restraints for amino acids using flexible rigid bodies 2 | F 0.5 3 | S * .01 CA C O N+ -------------------------------------------------------------------------------- /GSASII/inputs/GSASIImacros/planes.mac: -------------------------------------------------------------------------------- 1 | !standard plane restraints for amino acids using flexible rigid bodies 2 | F 0.5 3 | S ARG .01 NE CZ NH1 NH2 4 | S ARG .01 CD NE CZ NH1 NH2 5 | S ASN .01 CB CG OD1 ND2 6 | S ASP .01 CB CG OD1 OD2 7 | S GLN .01 CG CD OE1 NE2 8 | S GLU .01 CG CD OE1 OE2 9 | S HIS .01 CB CG ND1 CD2 CE1 NE2 10 | S PHE .01 CB CG CD1 CD2 CE1 CE2 CZ 11 | S TRP .01 CB CG CD1 NE1 CD2 CE2 CE3 CZ2 CZ3 CH2 12 | S TYR .01 CB CG CD1 CD2 CE1 CE2 CZ OH 13 | S * .01 CA C O N+ -------------------------------------------------------------------------------- /GSASII/inputs/OriginTemplate2.otpu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AdvancedPhotonSource/GSAS-II/4725770466eda23171ee532c2cf745fbe0634fdd/GSASII/inputs/OriginTemplate2.otpu -------------------------------------------------------------------------------- /GSASII/inputs/meson.build: -------------------------------------------------------------------------------- 1 | foreach file: ['DefaultExpressions.txt', 'OriginTemplate2.otpu', 'versioninfo.txt', 'Xsect.dat'] 2 | 3 | install_data( 4 | file, 5 | install_tag: 'data', 6 | install_dir: py.get_install_dir(subdir: 'GSASII/inputs') 7 | ) 8 | 9 | endforeach 10 | 11 | install_subdir( 12 | 'GSASIImacros', 13 | install_tag: 'data', 14 | install_dir: py.get_install_dir(subdir: 'GSASII/inputs') 15 | ) 16 | -------------------------------------------------------------------------------- /GSASII/inputs/versioninfo.txt: -------------------------------------------------------------------------------- 1 | # information to be shown to users about new GSAS-II versions (also 2 | # update GSASIIctrlGUI.updateNoticeDict). Lines starting with "#" are 3 | # comments. 4 | # Each version should be tagged with a version number and a colon. All subsequent text 5 | # will be part of the the notice for that version. Separate versions 6 | # with one or more blank lines between. Note that line breaks and 7 | # indentation are ignored. Use && to insert a single "&" 8 | # character. Use %% to insert a new line. 9 | 10 | 4919: With this version of GSAS-II, the profile functions have been changed to account for possible variation in the powder 11 | pattern step size across the scan. This will likely change the histogram scale factor (see Sample Parameters), peak 12 | intensities (see Peak List) and background peak intensities (see 13 | Background). %%%%If you choose to repeat the refinement for 14 | this project, you may need to turn off the parameters affecting 15 | peak shape for an initial refinement. It should converge quickly to the new scale factor. 16 | %%%%For Constant Wavelength data, the scale factor, etc. will change 17 | by a factor related to the pattern step size, e.g. for 11-BM data with a step size of 0.001 deg. 2-theta the new scale factor will be 18 | ~0.1 times the old one. 19 | For TOF data there may be similar changes to the scale factor && 20 | peak intensities, as noted above. 21 | Significant improvement in profile residuals have been observed in some cases with these new functions. 22 | This change is of no consequence for single crystal, small angle or 23 | reflectometry data in GSAS-II. 24 | 25 | 5038: With this version a major revision to the constraints module is 26 | released. This provides better diagnostics, works better with 27 | sequential fits and treats cases not 28 | previously allowed, such as where both refined and unrefined 29 | parameters appear in a constraint. %%%%Please contact Brian if you find a 30 | case where a set of constraints that used to work, but now fails. 31 | -------------------------------------------------------------------------------- /GSASII/install/g2app.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AdvancedPhotonSource/GSAS-II/4725770466eda23171ee532c2cf745fbe0634fdd/GSASII/install/g2app.tar.gz -------------------------------------------------------------------------------- /GSASII/meson.build: -------------------------------------------------------------------------------- 1 | py.install_sources([ 2 | '__init__.py', 3 | '__main__.py', 4 | 'Absorb.py', 5 | 'ElementTable.py', 6 | 'FormFactors.py', 7 | 'G2compare.py', 8 | 'G2shapes.py', 9 | 'GSASIIGUI.py', 10 | 'GSASIIElem.py', 11 | 'GSASIIElemGUI.py', 12 | # 'GSASIIIO.py', 13 | 'GSASIImiscGUI.py', 14 | 'GSASIIIntPDFtool.py', 15 | 'GSASIIconstrGUI.py', 16 | 'GSASIIctrlGUI.py', 17 | 'GSASIIdata.py', 18 | 'GSASIIdataGUI.py', 19 | 'GSASIIddataGUI.py', 20 | 'GSASIIexprGUI.py', 21 | 'GSASIIfiles.py', 22 | 'GSASIIfpaGUI.py', 23 | 'GSASIIimage.py', 24 | 'GSASIIimgGUI.py', 25 | 'GSASIIindex.py', 26 | 'GSASIIlattice.py', 27 | # 'GSASIIlog.py', 28 | 'GSASIImapvars.py', 29 | 'GSASIImath.py', 30 | 'GSASIImpsubs.py', 31 | 'GSASIIobj.py', 32 | 'GSASIIpath.py', 33 | 'GSASIIphsGUI.py', 34 | 'GSASIIplot.py', 35 | 'GSASIIpwd.py', 36 | 'GSASIIpwdGUI.py', 37 | 'GSASIIpwdplot.py', 38 | 'GSASIIrestrGUI.py', 39 | 'GSASIIsasd.py', 40 | 'GSASIIscriptable.py', 41 | 'GSASIIseqGUI.py', 42 | 'GSASIIspc.py', 43 | 'GSASIIstrIO.py', 44 | 'GSASIIstrMain.py', 45 | 'GSASIIstrMath.py', 46 | 'GSASIItestplot.py', 47 | 'ISODISTORT.py', 48 | 'ImageCalibrants.py', 49 | 'PlotXNFF.py', 50 | 'ReadMarCCDFrame.py', 51 | 'SUBGROUPS.py', 52 | 'Substances.py', 53 | 'atmdata.py', 54 | 'config_example.py', 55 | 'defaultIparms.py', 56 | 'dmp.py', 57 | 'fprime.py', 58 | 'git_verinfo.py', 59 | 'gltext.py', 60 | 'k_vector_search.py', 61 | 'nistlat.py', 62 | 'scanCCD.py', 63 | 'testDeriv.py', 64 | 'testSSymbols.py', 65 | 'testSytSym.py', 66 | 'testXNFF.py', 67 | 'tutorialIndex.py', 68 | ], 69 | pure: false, # Will be installed next to binaries 70 | subdir: 'GSASII' # Folder relative to site-packages to install to 71 | ) 72 | 73 | subdir('NIST_profile') 74 | subdir('imports') 75 | subdir('exports') 76 | subdir('icons') 77 | subdir('inputs') 78 | -------------------------------------------------------------------------------- /backcompat/ElementTable.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.ElementTable import * 4 | 5 | warn( 6 | "Importing GSASIIElem as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIElem.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIElem import * 4 | 5 | warn( 6 | "Importing GSASIIElem as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIElemGUI.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIElemGUI import * 4 | 5 | warn( 6 | "Importing GSASIIElemGUI as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIIntPDFtool.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIIntPDFtool import * 4 | 5 | warn( 6 | "Importing GSASIIIntPDFtool as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIconstrGUI.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIconstrGUI import * 4 | 5 | warn( 6 | "Importing GSASIIconstrGUI as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIctrlGUI.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIctrlGUI import * 4 | 5 | warn( 6 | "Importing GSASIIctrlGUI as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIdata.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIdata import * 4 | 5 | warn( 6 | "Importing GSASIIdata as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIdataGUI.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIdataGUI import * 4 | 5 | warn( 6 | "Importing GSASIIdataGUI as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIddataGUI.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIddataGUI import * 4 | 5 | warn( 6 | "Importing GSASIIddataGUI as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIexprGUI.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIexprGUI import * 4 | 5 | warn( 6 | "Importing GSASIIexprGUI as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIfiles.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIfiles import * 4 | 5 | warn( 6 | "Importing GSASIIfiles as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIfpaGUI.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIfpaGUI import * 4 | 5 | warn( 6 | "Importing GSASIIfpaGUI as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIimage.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIimage import * 4 | 5 | warn( 6 | "Importing GSASIIimage as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIimgGUI.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIimgGUI import * 4 | 5 | warn( 6 | "Importing GSASIIimgGUI as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIindex.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIindex import * 4 | 5 | warn( 6 | "Importing GSASIIindex as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIlattice.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIlattice import * 4 | 5 | warn( 6 | "Importing GSASIIlattice as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIImapvars.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIImapvars import * 4 | 5 | warn( 6 | "Importing GSASIImapvars as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIImath.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIImath import * 4 | 5 | warn( 6 | "Importing GSASIImath as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIImiscGUI.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIImiscGUI import * 4 | 5 | warn( 6 | "Importing GSASIImiscGUI as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIImpsubs.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIImpsubs import * 4 | 5 | warn( 6 | "Importing GSASIImpsubs as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIobj.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIobj import * 4 | 5 | warn( 6 | "Importing GSASIIobj as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIpath.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIpath import * 4 | 5 | warn( 6 | "Importing GSASIIpath as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIphsGUI.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIphsGUI import * 4 | 5 | warn( 6 | "Importing GSASIIphsGUI as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIplot.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIplot import * 4 | 5 | warn( 6 | "Importing GSASIIplot as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIpwd.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIpwd import * 4 | 5 | warn( 6 | "Importing GSASIIpwd as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIpwdGUI.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIpwdGUI import * 4 | 5 | warn( 6 | "Importing GSASIIpwdGUI as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIpwdplot.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIpwdplot import * 4 | 5 | warn( 6 | "Importing GSASIIpwdplot as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIrestrGUI.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIrestrGUI import * 4 | 5 | warn( 6 | "Importing GSASIIrestrGUI as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIsasd.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIsasd import * 4 | 5 | warn( 6 | "Importing GSASIIsasd as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIscriptable.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIscriptable import * 4 | 5 | warn( 6 | "Importing GSASIIscriptable as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIseqGUI.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIseqGUI import * 4 | 5 | warn( 6 | "Importing GSASIIseqGUI as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIspc.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIspc import * 4 | 5 | warn( 6 | "Importing GSASIIspc as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIstrIO.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIstrIO import * 4 | 5 | warn( 6 | "Importing GSASIIstrIO as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIstrMain.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIstrMain import * 4 | 5 | warn( 6 | "Importing GSASIIstrMain as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIIstrMath.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIIstrMath import * 4 | 5 | warn( 6 | "Importing GSASIIstrMath as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/GSASIItestplot.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | from GSASII.GSASIItestplot import * 4 | 5 | warn( 6 | "Importing GSASIItestplot as a top level module is deprecated, please import " 7 | + "it as a sub-module of GSASII", 8 | stacklevel=2, 9 | ) 10 | -------------------------------------------------------------------------------- /backcompat/meson.build: -------------------------------------------------------------------------------- 1 | py.install_sources([ 2 | 'GSASIIElem.py', 3 | 'GSASIIElemGUI.py', 4 | 'GSASIImiscGUI.py', 5 | 'GSASIIIntPDFtool.py', 6 | 'GSASIIconstrGUI.py', 7 | 'GSASIIctrlGUI.py', 8 | 'GSASIIdata.py', 9 | 'GSASIIdataGUI.py', 10 | 'GSASIIddataGUI.py', 11 | 'GSASIIexprGUI.py', 12 | 'GSASIIfiles.py', 13 | 'GSASIIfpaGUI.py', 14 | 'GSASIIimage.py', 15 | 'GSASIIimgGUI.py', 16 | 'GSASIIindex.py', 17 | 'GSASIIlattice.py', 18 | 'GSASIImapvars.py', 19 | 'GSASIImath.py', 20 | 'GSASIImpsubs.py', 21 | 'GSASIIobj.py', 22 | 'GSASIIpath.py', 23 | 'GSASIIphsGUI.py', 24 | 'GSASIIplot.py', 25 | 'GSASIIpwd.py', 26 | 'GSASIIpwdGUI.py', 27 | 'GSASIIpwdplot.py', 28 | 'GSASIIrestrGUI.py', 29 | 'GSASIIsasd.py', 30 | 'GSASIIscriptable.py', 31 | 'GSASIIseqGUI.py', 32 | 'GSASIIspc.py', 33 | 'GSASIIstrIO.py', 34 | 'GSASIIstrMain.py', 35 | 'GSASIIstrMath.py', 36 | 'GSASIItestplot.py', 37 | 'ElementTable.py' 38 | ], 39 | pure: false, # Will be installed next to binaries 40 | subdir: '' # Folder relative to site-packages to install to 41 | ) 42 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line, and also 5 | # from the environment for the first two. 6 | SPHINXOPTS ?= 7 | SPHINXBUILD ?= sphinx-build 8 | SOURCEDIR = source 9 | BUILDDIR = build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 21 | -------------------------------------------------------------------------------- /docs/environment.yml: -------------------------------------------------------------------------------- 1 | channels: 2 | - conda-forge 3 | - nodefaults 4 | dependencies: 5 | - python=3.11 6 | - scipy 7 | - pyopengl 8 | - imageio 9 | - h5py 10 | - numpy 11 | - sphinx-rtd-theme 12 | # - sphinx # included by RTD 13 | # - pillow # included by RTD 14 | - pip 15 | - matplotlib 16 | - wxpython 17 | - gitpython 18 | - pytest 19 | -------------------------------------------------------------------------------- /docs/find_undoc.py: -------------------------------------------------------------------------------- 1 | '''Find Python files in GSASII that are not referenced in the sphinx 2 | documentation. Git-reorg version. 3 | ''' 4 | import glob 5 | import os.path 6 | import git 7 | 8 | # get list of documented files (misses out on data files -- with no functions or classes) 9 | import glob 10 | loc = os.path.dirname(os.path.realpath(__file__)) # where is the documentation? 11 | G2loc = os.path.join(loc,'..') 12 | 13 | # prepare a list of the files that show up in the documentation already 14 | # look for a reference in the .rst files 15 | documented = [] 16 | for fil in glob.glob(os.path.join(loc,'source/*.rst')): 17 | for line in open(fil,'r').readlines(): 18 | if line.strip().startswith('.. automodule::'): 19 | documented.append(line.strip().split('::')[1].strip()) 20 | 21 | undoc = [] 22 | G2repo = git.Repo(G2loc) 23 | for entry in G2repo.commit().tree.traverse(): 24 | fil = entry.path 25 | if not fil.endswith('.py'): continue 26 | if os.path.dirname(fil) not in ( 27 | 'GSASII','GSASII/imports','GSASII/exports','GSASII/install'): 28 | continue 29 | if os.path.splitext(os.path.split(fil)[1])[0] in documented: 30 | #print(fil+' doc') 31 | continue 32 | else: 33 | print(fil+' undocumented') 34 | undoc.append(fil) 35 | # generate code to place in a .rst file 36 | if undoc: 37 | print("\n# place this code somewhere in the .rst files\n#") 38 | for fil in undoc: 39 | print(".. automodule:: "+os.path.splitext(os.path.split(fil)[1])[0]) 40 | print(" :members: ") 41 | print("") 42 | -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=source 11 | set BUILDDIR=build 12 | 13 | if "%1" == "" goto help 14 | 15 | %SPHINXBUILD% >NUL 2>NUL 16 | if errorlevel 9009 ( 17 | echo. 18 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 19 | echo.installed, then set the SPHINXBUILD environment variable to point 20 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 21 | echo.may add the Sphinx directory to PATH. 22 | echo. 23 | echo.If you don't have Sphinx installed, grab it from 24 | echo.http://sphinx-doc.org/ 25 | exit /b 1 26 | ) 27 | 28 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 29 | goto end 30 | 31 | :help 32 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 33 | 34 | :end 35 | popd 36 | -------------------------------------------------------------------------------- /docs/scripting/.readthedocs.yaml: -------------------------------------------------------------------------------- 1 | # .readthedocs.yaml 2 | # Read the Docs configuration file 3 | # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details 4 | 5 | version: 2 6 | 7 | build: 8 | os: "ubuntu-20.04" 9 | tools: 10 | python: "mambaforge-4.10" 11 | 12 | conda: 13 | environment: docs/environment.yml 14 | 15 | sphinx: 16 | configuration: docs/scripting/conf.py 17 | 18 | formats: 19 | - epub 20 | - pdf 21 | -------------------------------------------------------------------------------- /docs/scripting/G2_html_logo.png: -------------------------------------------------------------------------------- 1 | ../source/G2_html_logo.png -------------------------------------------------------------------------------- /docs/scripting/GSASIIobj.rst: -------------------------------------------------------------------------------- 1 | ../source/GSASIIobj.rst -------------------------------------------------------------------------------- /docs/scripting/GSASIIscriptable.rst: -------------------------------------------------------------------------------- 1 | ../source/GSASIIscriptable.rst -------------------------------------------------------------------------------- /docs/scripting/_static: -------------------------------------------------------------------------------- 1 | ../source/_static -------------------------------------------------------------------------------- /docs/scripting/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AdvancedPhotonSource/GSAS-II/4725770466eda23171ee532c2cf745fbe0634fdd/docs/scripting/favicon.ico -------------------------------------------------------------------------------- /docs/scripting/images: -------------------------------------------------------------------------------- 1 | ../source/images -------------------------------------------------------------------------------- /docs/scripting/index.rst: -------------------------------------------------------------------------------- 1 | GSAS-II Scripting Manual 2 | ================================= 3 | 4 | This is a subset of the 5 | `Developer's Documentation `_ 6 | covering the :mod:`GSASIIscriptable` package, used to 7 | create Python scripts for running GSAS-II. 8 | Note that most 9 | data structures used in GSAS-II are defined in module :mod:`GSASIIobj`, also 10 | included here. 11 | 12 | .. only:: html 13 | 14 | *Documentation Version:* 15 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 16 | 17 | .. include:: version.rst 18 | 19 | *Contents:* 20 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 21 | 22 | .. toctree:: 23 | :maxdepth: 2 24 | :numbered: 4 25 | 26 | GSASIIscriptable.rst 27 | objvarorg.rst 28 | GSASIIobj.rst 29 | packages.rst 30 | scrpt-indices.rst 31 | 32 | .. toctree:: 33 | :hidden: 34 | 35 | scrpt-constr_ref.rst 36 | scrpt-import_ref.rst 37 | -------------------------------------------------------------------------------- /docs/scripting/objvarorg.rst: -------------------------------------------------------------------------------- 1 | ../source/objvarorg.rst -------------------------------------------------------------------------------- /docs/scripting/packages.rst: -------------------------------------------------------------------------------- 1 | ../source/packages.rst -------------------------------------------------------------------------------- /docs/scripting/scrpt-constr_ref.rst: -------------------------------------------------------------------------------- 1 | References to the GSAS-II `Developer's Documentation `_ 2 | ============================================================================================================= 3 | 4 | .. _Constraints_processing: 5 | 6 | Constraints_processing: 7 | See the `Constraints Processing `_ from :mod:`GSASIImapvars`. 8 | -------------------------------------------------------------------------------- /docs/scripting/scrpt-import_ref.rst: -------------------------------------------------------------------------------- 1 | References to the GSAS-II `Developer's Documentation `_ 2 | ============================================================================================================= 3 | 4 | .. _import_routines: 5 | 6 | Imports: 7 | See the `Import models documentation 8 | `_ 9 | for information on reading data files. 10 | -------------------------------------------------------------------------------- /docs/scripting/scrpt-indices.rst: -------------------------------------------------------------------------------- 1 | .. only:: html 2 | 3 | *Indices* 4 | ================================ 5 | 6 | `General Index <./genindex.html>`_ 7 | -------------------------------------------- 8 | -------------------------------------------------------------------------------- /docs/source/G2_html_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AdvancedPhotonSource/GSAS-II/4725770466eda23171ee532c2cf745fbe0634fdd/docs/source/G2_html_logo.png -------------------------------------------------------------------------------- /docs/source/G2tools.rst: -------------------------------------------------------------------------------- 1 | *GSAS-II Independent Tools* 2 | ================================ 3 | 4 | The modules here are used for independent programs to be used as 5 | tools within the GSAS-II package and run 6 | independently of the main GSAS-II program. 7 | 8 | * :ref:`GSASIIIntPDFtool`: Parallelized auto-integration/PDF program 9 | * :ref:`G2compare`: Project Comparison program 10 | 11 | Both are under development. 12 | 13 | .. _GSASIIautoint: 14 | 15 | *GSASIIIntPDFtool: autointegration routines* 16 | --------------------------------------------- 17 | 18 | An auto-integration program based on GSAS-II but with 19 | a minimal GUI and no visualization that runs independently from 20 | the main GSAS-II program . This is intended to implement 21 | significant levels of parallelization and require less of a memory footprint. 22 | 23 | .. automodule:: GSASII.GSASIIIntPDFtool 24 | :members: 25 | 26 | .. _G2compare: 27 | 28 | *G2compare: Tool for project comparison* 29 | --------------------------------------------- 30 | 31 | This is intended to read in multiple GSAS-II projects and provide 32 | graphics, tables of information and so on. Not much of this has been 33 | written at present. 34 | 35 | .. automodule:: GSASII.G2compare 36 | :members: 37 | 38 | -------------------------------------------------------------------------------- /docs/source/GSASIIdata.rst: -------------------------------------------------------------------------------- 1 | *GSAS-II Data Storage Modules* 2 | =============================== 3 | 4 | These modules are used to provide a place to find constants that are 5 | used in various locations. 6 | 7 | ----------------------------------------- 8 | *GSASIIdata: Ramachandran Parameters* 9 | ----------------------------------------- 10 | 11 | .. automodule:: GSASII.GSASIIdata 12 | :members: 13 | 14 | ----------------------------------------- 15 | *ElementTable: Periodic Table Data* 16 | ----------------------------------------- 17 | 18 | .. automodule:: GSASII.ElementTable 19 | :members: 20 | 21 | ----------------------------------------- 22 | *FormFactors: Scattering Data* 23 | ----------------------------------------- 24 | 25 | .. automodule:: GSASII.FormFactors 26 | :members: 27 | 28 | ----------------------------------------- 29 | *ImageCalibrants: Calibration Standards* 30 | ----------------------------------------- 31 | 32 | .. automodule:: GSASII.ImageCalibrants 33 | :members: 34 | 35 | ----------------------------------------- 36 | *atmdata: Table of atomic data* 37 | ----------------------------------------- 38 | 39 | .. automodule:: GSASII.atmdata 40 | :members: 41 | 42 | ------------------------------------------------- 43 | *defaultIparms: Table of instrument parameters* 44 | ------------------------------------------------- 45 | 46 | .. automodule:: GSASII.defaultIparms 47 | :members: 48 | -------------------------------------------------------------------------------- /docs/source/GSASIIimage.rst: -------------------------------------------------------------------------------- 1 | *GSASIIimage: Image calc module* 2 | ================================ 3 | 4 | *Summary/Contents* 5 | ---------------------------- 6 | 7 | Image calibration, masking & image integration routines. 8 | 9 | Note that the GSAS-II image coordinate system is defined as follows: 10 | standing facing the x-ray source (e.g. behind the beamstop), 11 | the synchrotron ring will be to the left (for a left handed 12 | synchrotron – almost all are left handed). That left-right direction 13 | defines X. Y is up and thus Z is toward the source/sample. 14 | The resulting 2D image is then viewed from the sample position 15 | (e.g. between the x-ray source and the detector). 16 | The detector is addressed in units of pixels (or distances using the 17 | pixel size) with the origin as the lower left corner. 18 | The beam center is measured from this point; usually somewhere near 19 | the center of the image, thus both Xc & Yc will be greater than zero 20 | unless the beam center is not on the image. Note that when images are 21 | displayed in image viewers, most software puts the origin in the upper 22 | left corner. 23 | 24 | .. contents:: Section Contents 25 | 26 | *GSASIIimage Routines* 27 | ------------------------------------ 28 | 29 | 30 | .. automodule:: GSASII.GSASIIimage 31 | :members: 32 | :private-members: 33 | :special-members: 34 | -------------------------------------------------------------------------------- /docs/source/GSASIIindex.rst: -------------------------------------------------------------------------------- 1 | *GSASIIindex: Cell Indexing Module* 2 | =================================== 3 | 4 | *Summary/Contents* 5 | ---------------------------- 6 | 7 | Unit cell indexing routines (based on work of A. Coehlo) and 8 | cell refinement from peak positions 9 | 10 | .. contents:: Section Contents 11 | 12 | *GSASIIindex routines* 13 | ------------------------------------ 14 | 15 | .. automodule:: GSASII.GSASIIindex 16 | :members: 17 | :private-members: 18 | :special-members: 19 | -------------------------------------------------------------------------------- /docs/source/GSASIImath.rst: -------------------------------------------------------------------------------- 1 | *GSASIImath: computation module* 2 | ================================ 3 | 4 | *Summary/Contents* 5 | ---------------------------- 6 | 7 | Least-squares minimization and misc. computation routines. 8 | 9 | .. contents:: Section Contents 10 | 11 | *GSASIImath Classes and routines* 12 | ------------------------------------ 13 | 14 | .. automodule:: GSASII.GSASIImath 15 | :members: 16 | :private-members: 17 | :special-members: 18 | -------------------------------------------------------------------------------- /docs/source/GSASIIobj.rst: -------------------------------------------------------------------------------- 1 | *GSASIIobj: Data objects & Docs* 2 | ================================================= 3 | 4 | This module defines many data structures used in GSAS-II, as well 5 | as provides misc. support routines for accessing them. 6 | 7 | *GSASIIobj Classes and routines* 8 | ------------------------------------ 9 | 10 | .. automodule:: GSASIIobj 11 | :members: 12 | :private-members: 13 | :special-members: 14 | -------------------------------------------------------------------------------- /docs/source/GSASIIpwd.rst: -------------------------------------------------------------------------------- 1 | *GSASIIpwd: Powder calculations* 2 | ============================================== 3 | 4 | *Summary/Contents* 5 | ---------------------------- 6 | 7 | Routines for powder pattern computations, includes 8 | peak fitting, creation of PDF fitting scripts, 9 | interfaces to DIFFaX & Dysnomia. 10 | 11 | .. contents:: Section Contents 12 | 13 | *GSASIIpwd Classes and routines* 14 | ------------------------------------ 15 | 16 | 17 | .. automodule:: GSASII.GSASIIpwd 18 | :members: 19 | :private-members: 20 | :special-members: 21 | -------------------------------------------------------------------------------- /docs/source/GSASIIstruc.rst: -------------------------------------------------------------------------------- 1 | *GSAS-II Structure Submodules* 2 | =============================== 3 | 4 | These modules are used to perform structure-related (mostly intensity) 5 | computations that are needed for refinement and related computations. 6 | 7 | --------------------------------------- 8 | *GSASIIstrMain: main structure routine* 9 | --------------------------------------- 10 | 11 | GSASIIstrMain Classes & Routines 12 | --------------------------------------- 13 | 14 | 15 | .. automodule:: GSASII.GSASIIstrMain 16 | :members: 17 | 18 | ------------------------------------------ 19 | *GSASIIstrMath - structure math routines* 20 | ------------------------------------------ 21 | 22 | GSASIIstrMath Classes & Routines 23 | --------------------------------------- 24 | 25 | 26 | .. automodule:: GSASII.GSASIIstrMath 27 | :members: 28 | 29 | --------------------------------------- 30 | *GSASIIstrIO: structure I/O routines* 31 | --------------------------------------- 32 | 33 | GSASIIstrIO Classes & Routines 34 | --------------------------------------- 35 | 36 | .. automodule:: GSASII.GSASIIstrIO 37 | :members: 38 | -------------------------------------------------------------------------------- /docs/source/GSASIIweb.rst: -------------------------------------------------------------------------------- 1 | *GSAS-II Web Modules* 2 | ========================= 3 | 4 | These modules are used to access external web sites. 5 | 6 | --------------------------------------------------------------------- 7 | *SUBGROUPS: Interface Bilbao SUBGROUPS & k-SUBGROUPSMAG web pages* 8 | --------------------------------------------------------------------- 9 | 10 | Extraction of space subgroups for a given space group and a propagation vector 11 | from the GSAS version of SUBGROUPS & k-SUBGROUPSMAG web page on the Bilbao Crystallographic server. Note that the web pages are special to GSAS-II. 12 | This uses the :func:`GSASIIpath.postURL` function for web access. 13 | 14 | .. automodule:: GSASII.SUBGROUPS 15 | :members: 16 | 17 | 18 | ------------------------------------------------------ 19 | *ISODISTORT: Interface to BYU ISODISTORT web pages* 20 | ------------------------------------------------------ 21 | 22 | Uses the BYU ISODISTORT web site to search over all k-points for a structure or to relate a parent and child structure by irreps. 23 | This uses the mod:`requests` package. 24 | 25 | .. automodule:: GSASII.ISODISTORT 26 | :members: 27 | -------------------------------------------------------------------------------- /docs/source/SAS.rst: -------------------------------------------------------------------------------- 1 | *GSAS-II Small Angle Scattering* 2 | ============================================= 3 | 4 | *GSASII small angle calculation module* 5 | -------------------------------------------- 6 | 7 | .. automodule:: GSASII.GSASIIsasd 8 | :members: 9 | 10 | *Substances: Define Materials* 11 | --------------------------------------------------------------------------------- 12 | 13 | .. automodule:: GSASII.Substances 14 | :members: 15 | 16 | 17 | -------------------------------------------------------------------------------- /docs/source/_static/theme_overrides.css: -------------------------------------------------------------------------------- 1 | /* override table width restrictions */ 2 | @media screen and (min-width: 767px) { 3 | 4 | .wy-table-responsive table td { 5 | /* !important prevents the common CSS stylesheets from overriding 6 | this as on RTD they are loaded after this stylesheet */ 7 | white-space: normal !important; 8 | } 9 | 10 | .wy-table-responsive { 11 | overflow: visible !important; 12 | } 13 | } 14 | -------------------------------------------------------------------------------- /docs/source/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AdvancedPhotonSource/GSAS-II/4725770466eda23171ee532c2cf745fbe0634fdd/docs/source/favicon.ico -------------------------------------------------------------------------------- /docs/source/images/MakeShortcut.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AdvancedPhotonSource/GSAS-II/4725770466eda23171ee532c2cf745fbe0634fdd/docs/source/images/MakeShortcut.png -------------------------------------------------------------------------------- /docs/source/images/TestShortcut.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AdvancedPhotonSource/GSAS-II/4725770466eda23171ee532c2cf745fbe0634fdd/docs/source/images/TestShortcut.png -------------------------------------------------------------------------------- /docs/source/images/menu.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AdvancedPhotonSource/GSAS-II/4725770466eda23171ee532c2cf745fbe0634fdd/docs/source/images/menu.png -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- 1 | .. This lists all the sections of the documentation. Some of the below 2 | .. reference a single file. Others reference multiple files. 3 | 4 | GSAS-II Developer's Documentation 5 | ================================= 6 | 7 | The documentation here is intended for those wishing to extend the 8 | capabilities within the GSAS-II framework, for scientists/students 9 | working to understand how 10 | GSAS-II works, or for people wishing to develop scripting applications 11 | using the GSAS-II Python API (module :mod:`GSASIIscriptable`). Note that most 12 | data structures used in GSAS-II are defined in module :mod:`GSASIIobj`. 13 | 14 | For information on downloading/installing GSAS-II, please see 15 | the GSAS-II home page: 16 | https://advancedphotonsource.github.io/GSAS-II-tutorials. 17 | To learn how to 18 | use GSAS-II, please see the tutorials, which can be accessed from the 19 | GSAS-II Help menu or from this web page: 20 | https://advancedphotonsource.github.io/GSAS-II-tutorials/tutorials.html. 21 | 22 | 23 | For scripting use of GSAS-II, see :ref:`GSASIIscriptable`. 24 | 25 | **Invention Information:** Argonne has assigned Software Invention #SF-22-147 to GSAS-II. 26 | 27 | .. only:: html 28 | 29 | *Documentation Version:* 30 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | 32 | .. include:: version.rst 33 | 34 | *Contents:* 35 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 36 | 37 | .. toctree:: 38 | :maxdepth: 2 39 | :numbered: 4 40 | 41 | packages.rst 42 | versioning.rst 43 | objvarorg.rst 44 | GSASII.rst 45 | GSASIIobj.rst 46 | GSASIIutil.rst 47 | GSASIIGUIr.rst 48 | GSASIIGUI.rst 49 | GSASIIdata.rst 50 | GSASIIstruc.rst 51 | GSASIImapvars.rst 52 | GSASIIimage.rst 53 | GSASIImath.rst 54 | GSASIIindex.rst 55 | graphics.rst 56 | GSASIIpwd.rst 57 | SAS.rst 58 | GSASIIscriptable.rst 59 | GSASIIscripts.rst 60 | GSASIIweb.rst 61 | imports.rst 62 | exports.rst 63 | G2tools.rst 64 | indices.rst 65 | -------------------------------------------------------------------------------- /docs/source/indices.rst: -------------------------------------------------------------------------------- 1 | .. only:: html 2 | 3 | *Indices* 4 | ================================ 5 | 6 | `General Index <./genindex.html>`_ 7 | -------------------------------------------- 8 | 9 | `Module Index <./py-modindex.html>`_ 10 | -------------------------------------------- 11 | -------------------------------------------------------------------------------- /pixi/.gitattributes: -------------------------------------------------------------------------------- 1 | # SCM syntax highlighting 2 | pixi.lock linguist-language=YAML linguist-generated=true 3 | -------------------------------------------------------------------------------- /pixi/.gitignore: -------------------------------------------------------------------------------- 1 | 2 | # pixi environments 3 | .pixi 4 | *.egg-info 5 | -------------------------------------------------------------------------------- /sources/.gitignore: -------------------------------------------------------------------------------- 1 | *module.c 2 | *-f2pywrappers.f 3 | GSASIIversion.txt -------------------------------------------------------------------------------- /sources/INCLDS/COPYRIGT.FOR: -------------------------------------------------------------------------------- 1 | 2 | !Written by: Allen C. Larson and Robert B. Von Dreele 3 | ! MS-H805 4 | ! Los Alamos National Laboratory 5 | ! Los Alamos, NM 87545 6 | 7 | ! Copyright, 1984-2000, The Regents of the University of California. 8 | 9 | ! This software was produced under a U.S. Government contract (W-7405-ENG-36) by the Los Alamos 10 | ! National Laboratory, which is operated by the University of California for the U.S. Department of 11 | ! Energy. The U.S. Government is licensed to use, reproduce, and distribute this software. Permission 12 | ! is granted to the public to copy and use this software without charge, provided that this notice 13 | ! and any statement of authorship are reproduced on all copies. Neither the Government nor the 14 | ! University makes any warranty, express or implied, or assumes any liability or responsibility for 15 | ! the use of this software. 16 | 17 | -------------------------------------------------------------------------------- /sources/NISTlatsubs/BLOCKDATA1.f: -------------------------------------------------------------------------------- 1 | BLOCKDATA 2 | C SUB-PROGRAM 'BLOCKDATA' ... 3 | C INITIALIZES VARIABLES 4 | C 5 | C 6 | COMMON /UNIT1/ IUNITA 7 | COMMON /UNIT2/ IUNITB 8 | COMMON /UNIT4/ IUNITD 9 | C 10 | C 11 | DATA IUNITA/5/, IUNITB/6/, IUNITD/10/ 12 | C 13 | END 14 | -------------------------------------------------------------------------------- /sources/NISTlatsubs/DETERM.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE DETERM 2 | COMMON /ERR2/ IERR2 3 | COMMON /FCN1/ IFCN 4 | COMMON /MATR1/ U1,V1,W1,U2,V2,W2,U3,V3,W3 5 | COMMON /UNIT2/ IUNITB 6 | C 7 | C 8 | C SUBROUTINE 'DETERM' ... 9 | C CALCULATE THE DETERMINANT OF A 3 BY 3 MATRIX 10 | C TO CHECK FOR VALID INPUT MATRIX 11 | C 12 | C 13 | C 14 | C --- INITIALIZE VARIABLES 15 | DET = 0 16 | IERR2 = 0 17 | C 18 | C --- CALCULATE DETERMINANT 19 | DET = U1*V2*W3 + V1*W2*U3 + W1*U2*V3 - U3*V2*W1 - V3*W2*U1 - 20 | $ W3*U2*V1 21 | C 22 | C --- CHECK VALUE OF DETERMINANT FOR ERROR OR WARNING 23 | C SITUATIONS (DIFFERENT ACTIONS ARE REQUIRED FOR 24 | C DIFFERENT PROGRAM FUNCTIONS) 25 | IF(.NOT.(IFCN.EQ.2.OR.IFCN.EQ.6)) GO TO 100 26 | C 27 | C --- RSS, SYM (R,R1 OPTION) PROGRAM FUNCTIONS ARE 28 | C BEING EXECUTED 29 | C 30 | C --- FOR ZERO OR NEGATIVE DETERMINANT, STOP PROGRAM 31 | C EXECUTION (SHOULD NOT OCCUR) 32 | IF(DET.LE.0.01) STOP 33 | $ '*DETERM* ERROR ... Determinant is zero or negative.' 34 | C 35 | C --- FOR DETERMINANTS GREATER THAN 9, STOP PROGRAM 36 | C EXECUTION (SHOULD NOT OCCUR) 37 | IF(DET.GE.9.01) STOP 38 | $ '*DETERM* ERROR ... Determinant is greater than nine.' 39 | GO TO 400 40 | 100 CONTINUE 41 | IF(.NOT.(IFCN.EQ.3.OR.IFCN.EQ.4)) GO TO 200 42 | C 43 | C --- TRANS,INV PROGRAM FUNCTIONS ARE BEING EXECUTED 44 | C 45 | C --- FOR NEGATIVE DETERMINANT, WRITE WARNING AND CONTINUE 46 | IF(DET.LT.-0.01) WRITE(IUNITB,6000) 47 | C 48 | C --- FOR ZERO DETERMINANT, SET ERROR FLAG 49 | C (DO NOT HAVE A VALID MATRIX) 50 | IF(DET.GE.-0.01.AND.DET.LE.0.01) IERR2 = 1 51 | C 52 | C --- FOR DETERMINANTS >= 100 OR <= -100, SET ERROR FLAG 53 | C (DO NOT HAVE A VALID MATRIX) 54 | IF(ABS(DET).GE.100.0) IERR2 = 1 55 | GO TO 400 56 | 200 CONTINUE 57 | C 58 | C --- STOP PROGRAM EXECUTION SINCE A VALID PROGRAM FUNCTION 59 | C HAS NOT BEEN ENCOUNTERED (SHOULD NOT OCCUR) 60 | STOP '*DETERM* ERROR ... Invalid progam function.' 61 | 400 CONTINUE 62 | RETURN 63 | 6000 FORMAT(/1X,'*DETERM* WARNING ... Determinant of matrix is negative 64 | $.'/) 65 | END 66 | -------------------------------------------------------------------------------- /sources/NISTlatsubs/DOT.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE DOT (UX,VX,WX,UY,VY,WY,AI,BI,CI,AR,BR,GR,DOTXY) 2 | C 3 | C 4 | C SUBROUTINE 'DOT' ... 5 | C CALCULATE DOT PRODUCT OF VECTORS X AND Y 6 | C 7 | C 8 | C --- VECTOR X = (UX A + VX B + WX C) 9 | C VECTOR Y = (UY A + VY B + WY C) 10 | C 11 | DOTXY = UX*UY*(AI**2) + VX*VY*(BI**2) + WX*WY*(CI**2) + 12 | $ (VX*WY + WX*VY)*BI*CI*COS(AR) + 13 | $ (UX*WY + WX*UY)*AI*CI*COS(BR) + 14 | $ (UX*VY + VX*UY)*AI*BI*COS(GR) 15 | RETURN 16 | END 17 | -------------------------------------------------------------------------------- /sources/NISTlatsubs/HEAD0.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE HEAD0 2 | COMMON /UNIT2/ IUNITB 3 | C 4 | C 5 | C SUBROUTINE 'HEAD0' ... 6 | C WRITE SHORT DESCRIPTION OF PROGRAM OUTPUT 7 | C 8 | C 9 | C --- WRITE HEADING FOR OUTPUT 10 | WRITE(IUNITB,6100) 11 | WRITE(IUNITB,6110) 12 | WRITE(IUNITB,6120) 13 | WRITE(IUNITB,6122) 14 | WRITE(IUNITB,6130) 15 | WRITE(IUNITB,6140) 16 | WRITE(IUNITB,6150) 17 | WRITE(IUNITB,6160) 18 | WRITE(IUNITB,9020) 19 | WRITE(IUNITB,6170) 20 | WRITE(IUNITB,6180) 21 | WRITE(IUNITB,6190) 22 | WRITE(IUNITB,9040) 23 | RETURN 24 | 6100 FORMAT(1H1,////T45,'*** NIST*LATTICE ***'/) 25 | 6110 FORMAT(1X,T34,'A PROGRAM TO ANALYZE LATTICE RELATIONSHIPS') 26 | 6120 FORMAT(1X,T44,'Version of Spring, 1991'/) 27 | 6122 FORMAT(1X,/T54,'by'//) 28 | 6130 FORMAT(1X,T36,'Vicky Lynn Karen and Alan D. Mighell'/) 29 | 6140 FORMAT(1X,T32,'National Institute of Standards and Technology') 30 | 6150 FORMAT(1X,T33,'Materials Science and Engineering Laboratory') 31 | 6160 FORMAT(1X,T41,'Gaithersburg, Maryland 20899') 32 | 6170 FORMAT(1X,T22,'*** Patent Pending on certain algorithms used in th 33 | $is program ***') 34 | 6180 FORMAT(1X,T17,'Copyright by the U.S. Secretary of Commerce on beha 35 | $lf of the United States') 36 | 6190 FORMAT(1X,T45,'All Rights Reserved.') 37 | 9020 FORMAT(//) 38 | 9040 FORMAT(////) 39 | END 40 | -------------------------------------------------------------------------------- /sources/NISTlatsubs/HEAD3.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE HEAD3 2 | COMMON /UNIT2/ IUNITB 3 | C 4 | C 5 | C SUBROUTINE 'HEAD3' ... 6 | C WRITE SHORT DESCRIPTION OF PROGRAM OUTPUT 7 | C TRANS FUNCTION (CELL TRANSFORMATION) 8 | C 9 | C 10 | C --- WRITE HEADING FOR OUTPUT 11 | WRITE(IUNITB,6100) 12 | WRITE(IUNITB,6110) 13 | WRITE(IUNITB,6120) 14 | WRITE(IUNITB,6130) 15 | WRITE(IUNITB,6140) 16 | WRITE(IUNITB,6150) 17 | WRITE(IUNITB,6160) 18 | WRITE(IUNITB,6170) 19 | WRITE(IUNITB,6180) 20 | WRITE(IUNITB,6190) 21 | WRITE(IUNITB,9020) 22 | RETURN 23 | 6100 FORMAT(19X,'** CELL TRANSFORMATION **'/) 24 | 6110 FORMAT(5X,' CELL 1 = Input cell.') 25 | 6120 FORMAT(5X,' CELL 2 = Transformed cell.') 26 | 6130 FORMAT(5X,' T 2 = Input transformation matrix.') 27 | 6140 FORMAT(5X,' T 2 INV = Inverse matrix for T 2.'/) 28 | 6150 FORMAT(5X,'For CELL 1 and CELL 2, the output parameters given are: 29 | $') 30 | 6160 FORMAT(5X,' a, b, c, alpha, beta, gamma and volume. Cell edges 31 | $') 32 | 6170 FORMAT(5X,' are in angstroms and angles in degrees.'/) 33 | 6180 FORMAT(5X,'The cell matrix is of the form: a.a b.b c.c') 34 | 6190 FORMAT(34X,' b.c a.c a.b .') 35 | 9020 FORMAT(//) 36 | END 37 | -------------------------------------------------------------------------------- /sources/NISTlatsubs/HEAD4.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE HEAD4 2 | COMMON /UNIT2/ IUNITB 3 | C 4 | C 5 | C SUBROUTINE 'HEAD4' ... 6 | C WRITE SHORT DESCRIPTION OF PROGRAM OUTPUT 7 | C INV FUNCTION (MATRIX INVERSION) 8 | C 9 | C 10 | C --- WRITE HEADING FOR OUTPUT 11 | WRITE(IUNITB,6100) 12 | WRITE(IUNITB,6110) 13 | WRITE(IUNITB,6120) 14 | WRITE(IUNITB,9020) 15 | RETURN 16 | 6100 FORMAT(21X,'** MATRIX INVERSION **'/) 17 | 6110 FORMAT(7X,' T 2 = Input transformation matrix.') 18 | 6120 FORMAT(7X,' T 2 INV = Inverse matrix for T 2.') 19 | 9020 FORMAT(//) 20 | END 21 | -------------------------------------------------------------------------------- /sources/NISTlatsubs/INVERS.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE INVERS(IPRINV) 2 | COMMON /INVER1/ UI1,VI1,WI1,UI2,VI2,WI2,UI3,VI3,WI3 3 | COMMON /MATR1/ U1,V1,W1,U2,V2,W2,U3,V3,W3 4 | C 5 | C 6 | C SUBROUTINE 'INVERS' ... 7 | C CALCULATE THE INVERSE OF A 3 BY 3 MATRIX 8 | C 9 | C 10 | C 11 | C --- CALCULATE DETERMINANT 12 | DET = U1*V2*W3 + V1*W2*U3 + W1*U2*V3 - U3*V2*W1 - V3*W2*U1 - 13 | $ W3*U2*V1 14 | C 15 | C --- CALCULATE INVERSE 16 | UI1 = (V2*W3 - V3*W2)/DET 17 | VI1 = -(V1*W3 - V3*W1)/DET 18 | WI1 = (V1*W2 - V2*W1)/DET 19 | UI2 = -(U2*W3 - U3*W2)/DET 20 | VI2 = (U1*W3 - U3*W1)/DET 21 | WI2 = -(U1*W2 - U2*W1)/DET 22 | UI3 = (U2*V3 - U3*V2)/DET 23 | VI3 = -(U1*V3 - U3*V1)/DET 24 | WI3 = (U1*V2 - U2*V1)/DET 25 | C 26 | C --- PRINT OUT FOR INVERSE MATRIX 27 | IF(IPRINV.EQ.1) CALL OUTPT1(12) 28 | RETURN 29 | END 30 | -------------------------------------------------------------------------------- /sources/NISTlatsubs/MULTIP.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE MULTIP 2 | COMMON /MATR1/ U1,V1,W1,U2,V2,W2,U3,V3,W3 3 | COMMON /MATR2/ U(9),T(9) 4 | C 5 | C 6 | C SUBROUTINE 'MULTIP' ... 7 | C MULTIPLY TWO 3X3 MATRICES 8 | C WHEN THIS SUBROUTINE IS CALLED (RSS FUNCTION), 9 | C THE TOTAL TRANSFORMATION MATRIX IS UPDATED 10 | C 11 | C 12 | C 13 | C --- (PRODUCT MATRIX) = (U-MATRIX) (T-MATRIX) 14 | U1 = T(1)*U(1) + T(4)*U(2) + T(7)*U(3) 15 | V1 = T(2)*U(1) + T(5)*U(2) + T(8)*U(3) 16 | W1 = T(3)*U(1) + T(6)*U(2) + T(9)*U(3) 17 | U2 = T(1)*U(4) + T(4)*U(5) + T(7)*U(6) 18 | V2 = T(2)*U(4) + T(5)*U(5) + T(8)*U(6) 19 | W2 = T(3)*U(4) + T(6)*U(5) + T(9)*U(6) 20 | U3 = T(1)*U(7) + T(4)*U(8) + T(7)*U(9) 21 | V3 = T(2)*U(7) + T(5)*U(8) + T(8)*U(9) 22 | W3 = T(3)*U(7) + T(6)*U(8) + T(9)*U(9) 23 | RETURN 24 | END 25 | -------------------------------------------------------------------------------- /sources/NISTlatsubs/SET.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE SET 2 | COMMON /MATR1/ U1,V1,W1,U2,V2,W2,U3,V3,W3 3 | COMMON /MATR2/ U(9),T(9) 4 | C 5 | C 6 | C SUBROUTINE 'SET' ... 7 | C PREPARE TO UPDATE THE TOTAL TRANSFORMATION MATRIX 8 | C (U1,V1,W1,U2,V2,W2,U3,V3,W3) BY MATRIX MULTIPLICATION 9 | C 10 | C 11 | C --- SAVE THE CURRENT VALUES OF THE ELEMENTS FOR THE TOTAL 12 | C TRANSFORMATION MATRIX IN THE ARRAY T AND SET THE MATRIX 13 | C ELEMENTS IN THE UPDATE MATRIX U TO ZERO 14 | T(1) = U1 15 | T(2) = V1 16 | T(3) = W1 17 | T(4) = U2 18 | T(5) = V2 19 | T(6) = W2 20 | T(7) = U3 21 | T(8) = V3 22 | T(9) = W3 23 | DO 100 I = 1,9 24 | U(I) = 0.0 25 | 100 CONTINUE 26 | RETURN 27 | END 28 | -------------------------------------------------------------------------------- /sources/NISTlatsubs/SHORTV.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE SHORTV(SXX,SXY,ELEM1,ELEM5,ELEM9,ELEMX) 2 | C** 3 | COMMON /CK02/ ICK021,ICK022,ICK023,ICK024,ICK025,ICK026,ICK027, 4 | $ ICK028,ICK029 5 | C* 6 | C 7 | C 8 | C SUBROUTINE 'SHORTV' ... 9 | C FOR TWO VECTORS X AND Y, FIND THE SHORTEST Y' RELATIVE TO X 10 | C 11 | C 12 | C** 13 | C --- FOR CHECKING, WRITE EXECUTION POINT AND INTERMEDIATE VARIABLES 14 | IF(ICK026.EQ.1) CALL CKPT02(8) 15 | C* 16 | C 17 | C --- INITIALIZE VARIABLES 18 | AXY = ABS(SXY) 19 | XN = 0.0 20 | IF(SXY.LE.0.0) XN = 1.0 21 | IF(SXY.GT.0.0) XN = -1.0 22 | XN1 = 0.0 23 | C 24 | C --- DETERMINE THE NUMBER OF VECTOR ADDITIONS OR SUBTRACTIONS 25 | C REQUIRED TO OBTAIN THE SHORTEST Y' RELATIVE TO X. IF THE 26 | C INITIAL ANGLE IS < 90 DEGREES, VECTOR X IS SUBTRACTED XN1 27 | C TIMES, IF THE INITIAL ANGLE IS >= 90 DEGREES, VECTOR X IS 28 | C ADDED XN1 TIMES. 29 | 100 CONTINUE 30 | RXY = ABS(SXY + XN*SXX) 31 | IF((RXY-AXY).GT.0.0) GO TO 160 32 | IF(SXY.GE.0.0) GO TO 120 33 | XN = XN + 1.0 34 | XN1 = XN1 + 1.0 35 | GO TO 140 36 | 120 CONTINUE 37 | XN = XN - 1.0 38 | XN1 = XN1 - 1.0 39 | 140 CONTINUE 40 | AXY = RXY 41 | GO TO 100 42 | 160 CONTINUE 43 | C 44 | C --- SET THE MATRIX ELEMENTS FOR THE MATRIX USED TO UPDATE 45 | C THE TOTAL TRANSFORMATION MATRIX (U) 46 | CALL SET 47 | ELEM1 = 1.0 48 | ELEM5 = 1.0 49 | ELEM9 = 1.0 50 | ELEMX = XN1 51 | C 52 | RETURN 53 | END 54 | -------------------------------------------------------------------------------- /sources/NISTlatsubs/SPCON2.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE SPCON2(ICOND,EXP1,EXP2,EXP3,ISPFIX,ELE1,ELE2,ELE3,ELE4, 2 | $ ELE5,ELE6) 3 | C** 4 | COMMON /CK02/ ICK021,ICK022,ICK023,ICK024,ICK025,ICK026,ICK027, 5 | $ ICK028,ICK029 6 | C* 7 | DATA PC2/0.0005/ 8 | C 9 | C 10 | C SUBROUTINE 'SPCON2' ... 11 | C CHECK AND, IF NECESSARY, SATISFY SPECIAL CONDITIONS 12 | C FOR REDUCTION 13 | C 14 | C 15 | C 16 | C --- WHEN A SPECIAL RELATIONSHIP IN THE CELL MATRIX OCCURS, 17 | C CHECK, AND IF NECESSARY SATISFY, THE SPECIAL CONDITION 18 | IF(EXP1.GT.PC2) GO TO 100 19 | C** 20 | C --- FOR CHECKING, WRITE EXECUTION POINT, SPECIAL CONDITION 21 | C NUMBER, INTERMEDIATE VARIABLES 22 | IF(ICK027.EQ.1) CALL CKPT02(30+ICOND) 23 | C* 24 | C 25 | IF(EXP2.GE.ABS(EXP3)) GO TO 100 26 | C 27 | C --- FAILED ... NOW SATISFY SPECIAL CONDITION 28 | ELE1 = -1.0 29 | ELE2 = -1.0 30 | ELE3 = -1.0 31 | ELE4 = 1.0 32 | ELE5 = 1.0 33 | ELE6 = 1.0 34 | C 35 | C --- UPDATE THE TOTAL TRANSFORMATION MATRIX AND 36 | C APPLY THE RESULTING MATRIX TO THE INPUT CELL 37 | CALL MULTIP 38 | CALL TRANS(0) 39 | C** 40 | C --- FOR CHECKING, WRITE EXECUTION POINT AND INTERMEDIATE 41 | C VARIABLES 42 | IF(ICK028.EQ.1) CALL CKPT02(11) 43 | C* 44 | C 45 | CALL NORMAL 46 | ISPFIX = 1 47 | 100 CONTINUE 48 | RETURN 49 | END 50 | -------------------------------------------------------------------------------- /sources/NISTlatsubs/VOLUME.f: -------------------------------------------------------------------------------- 1 | SUBROUTINE VOLUME(AX,BX,CX,ALPX,BETX,GAMX,VOLX) 2 | COMMON /CONST1/ RADIAN 3 | COMMON /ERR1/ IERR1 4 | COMMON /UNIT2/ IUNITB 5 | C 6 | C 7 | C SUBROUTINE 'VOLUME' ... 8 | C CALCULATE CELL VOLUME - THESE CALCULATIONS 9 | C ARE ALSO USED TO CHECK FOR VALID INPUT DATA 10 | C 11 | C 12 | C 13 | C --- INITIALIZE VARIABLES 14 | VOLX = 0.0 15 | IERR1 = 0 16 | C 17 | C --- WHEN ONE OR MORE CELL EDGES ARE <= 0.01, 18 | C SET ERROR FLAG AND DO NOT CALCULATE VOLUME 19 | IF(AX.GT.0.01.AND.BX.GT.0.01.AND.CX.GT.0.01) GO TO 100 20 | IERR1 = 1 21 | GO TO 400 22 | 100 CONTINUE 23 | C 24 | C --- WHEN ONE OR MORE CELL ANGLES ARE <= 0.1 OR >=180.0, 25 | C SET ERROR FLAG AND DO NOT CALCULATE VOLUME 26 | IF(ALPX.GT.0.1.AND.ALPX.LT.180.0.AND.BETX.GT.0.1.AND.BETX.LT. 27 | $ 180.0.AND.GAMX.GT.0.1.AND.GAMX.LT.180.0) GO TO 200 28 | IERR1 = 1 29 | GO TO 400 30 | 200 CONTINUE 31 | C 32 | C --- CALCULATE THE COSINES OF THE CELL ANGLES 33 | COS1 = COS(ALPX/RADIAN) 34 | COS2 = COS(BETX/RADIAN) 35 | COS3 = COS(GAMX/RADIAN) 36 | C 37 | C --- IF THE INTERMEDIATE EXPRESSION (TEM) IS GREATER THAN ZERO, 38 | C CALCULATE THE CELL VOLUME ... OTHERWISE, SET ERROR FLAG 39 | C SINCE DO NOT HAVE A LEGAL CELL 40 | TEM = (1.0 - COS1**2 - COS2**2 - COS3**2 + 2.0*COS1*COS2*COS3) 41 | IF(TEM.GT.0.0) GO TO 300 42 | IERR1 = 1 43 | GO TO 400 44 | 300 CONTINUE 45 | VOLX = AX*BX*CX*SQRT(TEM) 46 | C 47 | C --- WRITE WARNING MESSAGE IF CALCULATED CELL VOLUME IS 48 | C EITHER VERY SMALL OR VERY LARGE 49 | IF(VOLX.LT.8.0.OR.VOLX.GT.50000.0) WRITE(IUNITB,6000) 50 | 400 CONTINUE 51 | RETURN 52 | 6000 FORMAT(/1X,'*VOLUME* WARNING ... Unusual cell volume has been calc 53 | $ulated.'/) 54 | END 55 | -------------------------------------------------------------------------------- /sources/histogram2d.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE HISTOGRAM2D(N,X,Y,Z,NXBINS,NYBINS,XLIM,YLIM,DX,DY, 2 | 1 NST,HST) 3 | 4 | Cf2py intent(in) n 5 | Cf2py intent(in) x 6 | Cf2py depend(n) x 7 | Cf2py intent(in) y 8 | Cf2py depend(n) y 9 | Cf2py intent(in) z 10 | Cf2py depend(n) z 11 | Cf2py intent(in) nxbins 12 | Cf2py intent(in) nybins 13 | Cf2py intent(in) xlim 14 | Cf2py intent(in) ylim 15 | Cf2py intent(in) dx 16 | Cf2py intent(in) dy 17 | Cf2py intent(in,out) nst 18 | Cf2py depend(nxbins,nybins) nst 19 | Cf2py intent(in,out) hst 20 | Cf2py depend(nxbins,nybins) hst 21 | 22 | IMPLICIT NONE 23 | INTEGER*8 N 24 | REAL*4 X(0:N-1),Y(0:N-1),Z(0:N-1) 25 | INTEGER*8 NXBINS,NYBINS 26 | REAL*8 XLIM(0:1),YLIM(0:1) 27 | REAL*4 NST(0:NXBINS-1,0:NYBINS-1) 28 | REAL*4 HST(0:NXBINS-1,0:NYBINS-1) 29 | 30 | INTEGER*4 I,J,K 31 | REAL*8 DX,DY 32 | REAL*4 DDX,DDY 33 | DO K=0,N-1 34 | C if ( mod(k,8000) .eq. 0 ) 35 | C 1 print *,k,x(k),xlim,y(k),ylim 36 | IF ( ( X(K).GE.XLIM(0) .AND. X(K).LT.XLIM(1) ) .AND. 37 | 1 ( Y(K).GE.YLIM(0) .AND. Y(K).LT.YLIM(1) )) THEN 38 | DDX = (X(K)-XLIM(0))/DX 39 | I = MIN(MAX(0,INT(DDX)),NXBINS-1) 40 | DDY = (Y(K)-YLIM(0))/DY 41 | J = MIN(MAX(0,INT(DDY)),NYBINS-1) 42 | NST(I,J) = NST(I,J)+1.0 43 | HST(I,J) = HST(I,J)+Z(K) 44 | C if ( mod(k,8000) .eq. 0 ) 45 | C 1 print *,i,j,nst(i,j),hst(i,j) 46 | END IF 47 | END DO 48 | RETURN 49 | END 50 | -------------------------------------------------------------------------------- /sources/histosigma2d.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE HISTOSIGMA2D(N,X,Y,Z,NXBINS,NYBINS,XLIM,YLIM,DX,DY, 2 | 1 NST,HST,AMAT,QMAT) 3 | 4 | Cf2py intent(in) n 5 | Cf2py intent(in) x 6 | Cf2py depend(n) x 7 | Cf2py intent(in) y 8 | Cf2py depend(n) y 9 | Cf2py intent(in) z 10 | Cf2py depend(n) z 11 | Cf2py intent(in) nxbins 12 | Cf2py intent(in) nybins 13 | Cf2py intent(in) xlim 14 | Cf2py intent(in) ylim 15 | Cf2py intent(in) dx 16 | Cf2py intent(in) dy 17 | Cf2py intent(in,out) nst 18 | Cf2py depend(nxbins,nybins) nst 19 | Cf2py intent(in,out) hst 20 | Cf2py depend(nxbins,nybins) hst 21 | Cf2py intent(in,out) amat 22 | Cf2py depend(nxbins,nybins) amat 23 | Cf2py intent(in,out) qmat 24 | Cf2py depend(nxbins,nybins) qmat 25 | 26 | IMPLICIT NONE 27 | INTEGER*8 N 28 | REAL*4 X(0:N-1),Y(0:N-1),Z(0:N-1) 29 | INTEGER*8 NXBINS,NYBINS 30 | REAL*8 XLIM(0:1),YLIM(0:1) 31 | REAL*4 NST(0:NXBINS-1,0:NYBINS-1) 32 | REAL*4 HST(0:NXBINS-1,0:NYBINS-1) 33 | REAL*4 AMAT(0:NXBINS-1,0:NYBINS-1) 34 | REAL*4 QMAT(0:NXBINS-1,0:NYBINS-1) 35 | 36 | INTEGER*4 I,J,K 37 | REAL*8 DX,DY 38 | REAL*4 DDX,DDY,AOLD 39 | DO K=0,N-1 40 | IF ( ( X(K).GE.XLIM(0) .AND. X(K).LT.XLIM(1) ) .AND. 41 | 1 ( Y(K).GE.YLIM(0) .AND. Y(K).LT.YLIM(1) )) THEN 42 | DDX = (X(K)-XLIM(0))/DX 43 | I = INT(DDX) 44 | DDY = (Y(K)-YLIM(0))/DY 45 | J = INT(DDY) 46 | NST(I,J) = NST(I,J)+1.0 47 | HST(I,J) = HST(I,J)+Z(K) 48 | AOLD = AMAT(I,J) 49 | AMAT(I,J) = AOLD+(Z(K)-AOLD)/NST(I,J) 50 | QMAT(I,J) = QMAT(I,J)+(Z(K)-AOLD)*(Z(K)-AMAT(I,J)) 51 | END IF 52 | END DO 53 | RETURN 54 | END 55 | -------------------------------------------------------------------------------- /sources/install.bat: -------------------------------------------------------------------------------- 1 | mkdir %USERPROFILE%\.GSASII 2 | mkdir %USERPROFILE%\.GSASII\bin 3 | set OUTDIR=%USERPROFILE%\.GSASII\bin 4 | copy /y "%MESON_BUILD_ROOT%\sources\"*.pyd %OUTDIR%\ 5 | copy /y "%MESON_BUILD_ROOT%\sources\k_vec_cython\"*.pyd %OUTDIR%\ 6 | copy /y "%MESON_BUILD_ROOT%\sources\"LATTIC.exe %OUTDIR%\ 7 | copy /y "%MESON_BUILD_ROOT%\sources\"convcell.exe %OUTDIR%\ 8 | copy /y "%MESON_BUILD_ROOT%\sources\"GSAS*.txt %OUTDIR%\ 9 | copy /y %CONDA_PREFIX%\Library\bin\libgfortran*.dll %OUTDIR%\ 10 | copy /y %CONDA_PREFIX%\Library\bin\libquadmath*.dll %OUTDIR%\ 11 | copy /y %CONDA_PREFIX%\Library\bin\libgcc*.dll %OUTDIR%\ 12 | REM copy /y %CONDA_PREFIX%\Library\bin\libwinthread*.dll %OUTDIR%\ 13 | -------------------------------------------------------------------------------- /sources/install.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | OUTDIR=~/.GSASII/bin 3 | mkdir -p ${OUTDIR} 4 | cp -v "${MESON_BUILD_ROOT}/sources/"*.so ${OUTDIR}/ 5 | cp -v "${MESON_BUILD_ROOT}/sources/"*/*.so ${OUTDIR}/ 6 | cp -v "${MESON_BUILD_ROOT}/sources/"LATTIC ${OUTDIR}/ 7 | cp -v "${MESON_BUILD_ROOT}/sources/"convcell ${OUTDIR}/ 8 | cp -v "${MESON_BUILD_ROOT}/sources/"GSAS*.txt ${OUTDIR}/ 9 | -------------------------------------------------------------------------------- /sources/k_vec_cython/meson.build: -------------------------------------------------------------------------------- 1 | py.extension_module('kvec_general', 2 | 'kvec_general.pyx', 3 | dependencies : [py_dep, numpy_dep], 4 | # include_directories : ['include'], 5 | install: true, 6 | subdir: 'GSASII', 7 | ) 8 | -------------------------------------------------------------------------------- /sources/k_vec_cython/setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup 2 | from Cython.Build import cythonize 3 | import numpy as np 4 | 5 | setup( 6 | ext_modules=cythonize("kvec_general.pyx"), 7 | include_dirs=[np.get_include()] 8 | ) 9 | -------------------------------------------------------------------------------- /sources/polymask.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE POLYMASK(N,X,Y,M,POLY,MASK) 2 | 3 | Cf2py intent(in) N 4 | Cf2py intent(in) X 5 | Cf2py depend(N) X 6 | Cf2py intent(in) Y 7 | Cf2py depend(N) Y 8 | Cf2py intent(in) M 9 | Cf2py intent(in) POLY 10 | Cf2py depend(M) POLY 11 | Cf2py intent(in,out) MASK 12 | 13 | IMPLICIT NONE 14 | INTEGER*4 N,M 15 | REAL*4 X(0:N-1),Y(0:N-1) 16 | REAL*8 POLY(0:M-1,0:1) 17 | LOGICAL*1 MASK(0:1024*1024-1) 18 | 19 | INTEGER*4 I,K 20 | REAL*4 P1X,P1Y,P2X,P2Y,XINTERS 21 | 22 | DO K=0,N-1 23 | MASK(K) = .FALSE. 24 | DO I=0,M-1 25 | P2X = POLY(I,0) 26 | P2Y = POLY(I,1) 27 | IF (Y(K) .GT. MIN(P1Y,P2Y)) THEN 28 | IF (Y(K) .LE. MAX(P1Y,P2Y)) THEN 29 | IF (X(K) .LE. MAX(P1X,P2X)) THEN 30 | IF (P1Y .NE.P2Y) THEN 31 | XINTERS = (Y(K)-P1Y)*(P2X-P1X)/(P2Y-P1Y)+P1X 32 | END IF 33 | IF ( (P1X .EQ. P2X) .OR. (X(K) .LE. XINTERS) ) THEN 34 | MASK(K) = .NOT.MASK(K) 35 | END IF 36 | END IF 37 | END IF 38 | END IF 39 | P1X = P2X 40 | P1Y = P2Y 41 | END DO 42 | END DO 43 | 44 | RETURN 45 | END 46 | 47 | -------------------------------------------------------------------------------- /sources/powsubs/acosd.for: -------------------------------------------------------------------------------- 1 | REAL*4 FUNCTION ACOSD(ARG) 2 | 3 | !PURPOSE: 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | !CALLING ARGUMENTS: 8 | 9 | REAL*4 ARG 10 | 11 | !INCLUDE STATEMENTS: 12 | 13 | !LOCAL VARIABLES: 14 | 15 | !FUNCTION DEFINITIONS: 16 | 17 | !DATA STATEMENTS: 18 | 19 | DATA RPD/0.017453292519943/ 20 | 21 | !CODE: 22 | 23 | ARG1 = MIN(1.0,MAX(-1.0,ARG)) 24 | ACOSD = ACOS(ARG1)/RPD 25 | RETURN 26 | END 27 | -------------------------------------------------------------------------------- /sources/powsubs/cosd.for: -------------------------------------------------------------------------------- 1 | REAL*4 FUNCTION COSD(ARG) 2 | 3 | !PURPOSE: Calculate cosine from angle in deg. 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | !CALLING ARGUMENTS: 8 | 9 | REAL*4 ARG !Cosine argument in degrees 10 | 11 | !INCLUDE STATEMENTS: 12 | 13 | !LOCAL VARIABLES: 14 | 15 | !FUNCTION DEFINITIONS: 16 | 17 | !DATA STATEMENTS: 18 | 19 | DATA RPD/0.017453292519943/ 20 | 21 | !CODE: 22 | 23 | COSD = COS(ARG*RPD) 24 | RETURN 25 | END 26 | -------------------------------------------------------------------------------- /sources/powsubs/gauleg.for: -------------------------------------------------------------------------------- 1 | subroutine gauleg(x1,x2,x,w,n) 2 | c Routine from Numerical Recipes (Press, Flannery, Teukolsky and Vetterling, 3 | c 1986, Cambridge University Press, ISBN 0 521 30811 9) 4 | c 5 | c Given the lower and upper limits of integration (X1, X2) and the number 6 | c of intervals (N), this routine returns arrays X and W of length N, 7 | c containing the abscissas and weights of the Gauss-Legendre N-point 8 | c quadrature formula. 9 | c 10 | implicit real*4 (a-h,o-z) 11 | REAL*4 X1,X2,X(N),W(N) 12 | parameter (eps=3.e-7) 13 | C 14 | m=(n+1)/2 15 | xm=0.5*(x2+x1) 16 | xl=0.5*(x2-x1) 17 | do i=1,m 18 | z=cos(3.141592654*(i-.25)/(n+.5)) 19 | z1 = 0.0 20 | do while (abs(z-z1).gt.eps) 21 | p1=1.0 22 | p2=0.0 23 | do j=1,n 24 | p3=p2 25 | p2=p1 26 | p1=((2.0*j-1.0)*z*p2-(j-1.0)*p3)/j 27 | end do 28 | pp=n*(z*p1-p2)/(z*z-1.0) 29 | z1=z 30 | z=z1-p1/pp 31 | end do 32 | x(i)=xm-xl*z 33 | x(n+1-i)=xm+xl*z 34 | w(i)=2.0*xl/((1.0-z*z)*pp*pp) 35 | w(n+1-i)=w(i) 36 | end do 37 | return 38 | end 39 | 40 | -------------------------------------------------------------------------------- /sources/powsubs/hfunc.for: -------------------------------------------------------------------------------- 1 | FUNCTION HFUNC(X,Y,IFLAG,DHDY) 2 | 3 | !PURPOSE: Compute exp(x)exp(y**2)erfc(y) and partial derivatives 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | !PSEUDOCODE: 8 | 9 | !CALLING ARGUMENTS: 10 | 11 | REAL*4 X,Y !Arguments 12 | INTEGER*4 IFLAG !Control for calculation method 13 | REAL*4 DHDY !Partial derivative wrt y 14 | REAL*4 HFUNC !Value of function 15 | 16 | !INCLUDE STATEMENTS: 17 | 18 | !LOCAL VARIABLES: 19 | 20 | !SUBROUTINES CALLED: 21 | 22 | !FUNCTION DEFINITIONS: 23 | 24 | REAL*4 GERFC !Complementary error function 25 | 26 | !DATA STATEMENTS: 27 | 28 | DATA CONST/1.128379167/,CONS2/1.273239545/ !2/SQRT(PI),4/PI 29 | 30 | !CODE: 31 | 32 | T = Y**2+X 33 | HFUNC = 0.0 34 | DHDY = 0.0 35 | IF ( Y.GE.6.000 .OR. IFLAG.EQ.1 ) THEN !Compute function - protect against underflows 36 | T1 = SQRT(Y**2+CONS2) 37 | IF ( X.GT.-75.0 ) HFUNC = EXP(X) !Upper inequality 38 | HFUNC = HFUNC*CONST/(Y+T1) 39 | DHDY = -HFUNC/T1 40 | ELSE IF ( Y.LE.-6.375 ) THEN 41 | IF ( T.GT.-75.0 ) HFUNC = 2.0*EXP(T) !Upper inequality 42 | DHDY = 2.0*Y*HFUNC 43 | ELSE 44 | IF ( T.GT.-75.0 ) HFUNC = EXP(T) 45 | HFUNC = HFUNC*GERFC(Y) 46 | IF ( X.GT.-75.0 ) DHDY = EXP(X) 47 | DHDY = 2.0*Y*HFUNC-CONST*DHDY 48 | END IF 49 | RETURN 50 | END 51 | -------------------------------------------------------------------------------- /sources/powsubs/lorentz.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE LORENTZ(DT,GAM,FUNC,DLDT,DLDG) 2 | 3 | !PURPOSE:Calculate Lorentzian function & derivatives 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | !PSEUDOCODE: 8 | 9 | !CALLING ARGUMENTS: 10 | 11 | REAL*4 DT !Delta 12 | REAL*4 GAM !Coefficient 13 | REAL*4 FUNC !Function 14 | REAL*4 DLDT !df/dt 15 | REAL*4 DLDG !df/dg 16 | 17 | !INCLUDE STATEMENTS: 18 | 19 | !LOCAL VARIABLES: 20 | 21 | !SUBROUTINES CALLED: 22 | 23 | !FUNCTION DEFINITIONS: 24 | 25 | !DATA STATEMENTS: 26 | 27 | DATA PI/3.1415292654/ 28 | !CODE: 29 | 30 | FNORM = 2.0*GAM/PI 31 | DENOM = GAM**2+4.0*DT**2 32 | IF ( ABS(GAM).GT.5.0E-6 ) THEN 33 | FUNC = FNORM/DENOM 34 | DLDT = -8.0*DT*FUNC/DENOM 35 | DLDG = (8.0*DT**2-2.0*GAM**2)/(PI*DENOM**2) 36 | ELSE 37 | FUNC = 0.0 38 | DLDT = 0.0 39 | IF ( ABS(DT).LT.1.0E-5 ) THEN 40 | DLDG = 0.0 41 | ELSE 42 | DLDG = 2.0/(PI*DT**2) 43 | END IF 44 | END IF 45 | RETURN 46 | END 47 | -------------------------------------------------------------------------------- /sources/powsubs/sind.for: -------------------------------------------------------------------------------- 1 | REAL*4 FUNCTION SIND(ARG) 2 | 3 | !PURPOSE: Calculate sine from angle in deg. 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | !CALLING ARGUMENTS: 8 | 9 | REAL*4 ARG !Sine argument in degrees 10 | 11 | !INCLUDE STATEMENTS: 12 | 13 | !LOCAL VARIABLES: 14 | 15 | !FUNCTION DEFINITIONS: 16 | 17 | !DATA STATEMENTS: 18 | 19 | DATA RPD/0.017453292519943/ 20 | 21 | !CODE: 22 | 23 | SIND = SIN(ARG*RPD) 24 | RETURN 25 | END 26 | -------------------------------------------------------------------------------- /sources/powsubs/tand.for: -------------------------------------------------------------------------------- 1 | REAL*4 FUNCTION TAND(ARG) 2 | 3 | !PURPOSE: Calculate tangent from angle in deg. 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | !CALLING ARGUMENTS: 8 | 9 | REAL*4 ARG !Tangent argument in degrees 10 | 11 | !INCLUDE STATEMENTS: 12 | 13 | !LOCAL VARIABLES: 14 | 15 | !FUNCTION DEFINITIONS: 16 | 17 | !DATA STATEMENTS: 18 | 19 | DATA RPD/0.017453292519943/ 20 | 21 | !CODE: 22 | 23 | TAND = TAN(ARG*RPD) 24 | RETURN 25 | END 26 | -------------------------------------------------------------------------------- /sources/pyspg.for: -------------------------------------------------------------------------------- 1 | C Space group access routines for python 2 | 3 | SUBROUTINE SGFORPY(SPG,LAUE,SGINV,SGLATT,SGUNIQ,SGPOL, 4 | 1 SGNOPS,SGMTRX,SGTRNS,SGGEN,IERR) 5 | Cf2py intent(in) SPG 6 | Cf2py intent(out) LAUE 7 | Cf2py intent(out) SGINV 8 | Cf2py intent(out) SGLATT 9 | Cf2py intent(out) SGUNIQ 10 | Cf2py intent(out) SGPOL 11 | Cf2py intent(out) SGNOPS 12 | Cf2py intent(out) SGMTRX 13 | Cf2py intent(out) SGTRNS 14 | Cf2py intent(out) SGGEN 15 | Cf2py intent(out) IERR 16 | 17 | CHARACTER*(20) SPG 18 | INTEGER*4 LAUE,SGINV,SGLATT,SGUNIQ,SGNOPS,IERR,SGNCEN 19 | REAL*4 SGMTRX(24,3,3),SGTRNS(24,3),SGGEN(24) 20 | REAL*4 RT(5,4,25),CEN(3,4) 21 | INTEGER*4 JRT(3,5,24) 22 | 23 | 24 | CALL SGROUPNP(SPG,LAUE,SGUNIQ,SGINV,SGLATT,SGNOPS,SGPOL,JRT, 25 | 1 CEN,SGNCEN,RT,IERR) 26 | DO K=1,SGNOPS 27 | DO I=1,3 28 | DO J=1,3 29 | SGMTRX(K,I,J) = JRT(I,J,K) 30 | SGTRNS(K,I) = JRT(I,4,K)/12. 31 | END DO 32 | END DO 33 | SGGEN(K) = JRT(3,5,K) 34 | END DO 35 | RETURN 36 | END 37 | 38 | SUBROUTINE GENHKLPY(XH,NSYM,SGMTRX,SGTRNS,ICEN,NCV,SGCEN,JHK, 39 | 1 HKL,IABSNT,MULP) 40 | Cf2py intent(in) XH 41 | Cf2py intent(in) NSYM 42 | Cf2py intent(in) SGMTRX 43 | Cf2py intent(in) SGTRNS 44 | Cf2py depend(NSYM) SGMTRX,SGTRNS 45 | Cf2py intent(in) ICEN 46 | Cf2py intent(in) NCV 47 | Cf2py intent(in) SGCEN 48 | Cf2py depend(NCV) SGCEN 49 | Cf2py intent(out) JHK 50 | Cf2py intent(out) HKL 51 | Cf2py intent(out) IABSNT 52 | Cf2py intent(out) MULP 53 | 54 | INTEGER*4 ICEN,NSYM 55 | REAL*4 SGMTRX(NSYM,3,3),SGTRNS(NSYM,3),SGCEN(NCV,3) 56 | REAL*4 CEN(3,NCV),HKL(4,24),XH(4) 57 | INTEGER*4 JRT(3,5,24),JHK,NCV 58 | 59 | DO J=1,NCV 60 | DO I=1,3 61 | CEN(I,J) = SGCEN(J,I) 62 | END DO 63 | END DO 64 | DO K=1,NSYM 65 | DO I=1,3 66 | DO J=1,3 67 | JRT(I,J,K) = SGMTRX(K,I,J)*1. 68 | JRT(I,4,K) = SGTRNS(K,I)*12. 69 | END DO 70 | END DO 71 | END DO 72 | CALL GENHKL(XH,NSYM,JRT,ICEN,NCV,CEN,JHK,HKL,IABSNT,MULP) 73 | RETURN 74 | END -------------------------------------------------------------------------------- /sources/pytexture.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE PYPLMPSI(L,I,NPHI,PHI,PCRS,DPDPS) 2 | Cf2py intent(in) L 3 | Cf2Py intent(in) I 4 | Cf2py intent(in) NPHI 5 | Cf2py intent(in) PHI 6 | Cf2py intent(out) PCRS 7 | Cf2py intent(out) DPDPS 8 | Cf2py depend(NPHI) PHI,PCRS,DPDPS 9 | 10 | INTEGER*4 L 11 | INTEGER*4 I 12 | REAL*4 PHI(0:NPHI-1) 13 | REAL*4 PCRS(0:NPHI-1) 14 | REAL*4 DPDPS(0:NPHI-1) 15 | 16 | DO K = 0,NPHI-1 17 | CALL PLMPSI(L,I,PHI(K),PCRS(K),DPDPS(K)) 18 | END DO 19 | RETURN 20 | END 21 | 22 | SUBROUTINE PYQLMNINIT() 23 | CALL QLMNINIT 24 | RETURN 25 | END 26 | 27 | 28 | -------------------------------------------------------------------------------- /sources/spotmask.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE SPOTMASK(N,X,Y,M,SPOTS,MASK) 2 | 3 | Cf2py intent(in) N 4 | Cf2py intent(in) X 5 | Cf2py depend(N) X 6 | Cf2py intent(in) Y 7 | Cf2py depend(N) Y 8 | Cf2py intent(in) M 9 | Cf2py intent(in) SPOTS 10 | Cf2py depend(M) SPOTS 11 | Cf2py intent(in,out) MASK 12 | 13 | IMPLICIT NONE 14 | INTEGER*4 N,M 15 | REAL*4 X(0:N-1),Y(0:N-1) 16 | REAL*8 SPOTS(0:M-1,0:2) 17 | LOGICAL*1 MASK(0:1024*1024-1) 18 | 19 | INTEGER*4 I,K 20 | REAL*4 XYRAD2,XINTERS 21 | 22 | DO K=0,N-1 23 | MASK(K) = .FALSE. 24 | DO I=0,M-1 25 | XYRAD2 = (X(K)-SPOTS(I,0))**2+(Y(K)-SPOTS(I,1))**2 26 | IF ( XYRAD2 .LE. SPOTS(I,2) ) THEN 27 | MASK(K) = .NOT.MASK(K) 28 | END IF 29 | END DO 30 | END DO 31 | 32 | RETURN 33 | END 34 | -------------------------------------------------------------------------------- /sources/spsubs/sglcen.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE SGLCEN(LCENT,CEN,NCV) 2 | 3 | INCLUDE '../INCLDS/COPYRIGT.FOR' 4 | 5 | C This program was developed for 6 | C The Division of Chemistry 7 | C of 8 | C The National Research Council of Canada 9 | C by 10 | C Allen C. Larson, 14 Cerrado Loop, Santa Fe, NM 87505, USA 11 | 12 | INTEGER*4 LCENT !Lattice centering type flag 13 | REAL*4 CEN(3,4) !List of lattice centering vectors 14 | INTEGER*4 NCV !Number of lattcie centering vectors 15 | 16 | REAL*4 CENV(3,6) 17 | INTEGER*4 NCVT(7) 18 | 19 | DATA NCVT/1,2,2,2,2,4,3/ 20 | DATA CENV/ 0,0.5,0.5, 0.5,0,0.5, 0.5,0.5,0, 0.5,0.5,0.5, 21 | 1 0.3333333,0.6666667,0.6666667, 0.6666667,0.3333333,0.3333333/ 22 | 23 | NCV = NCVT(LCENT) 24 | CEN(1,1) = 0.0 25 | CEN(2,1) = 0.0 26 | CEN(3,1) = 0.0 27 | IF ( NCV.GT.1 ) THEN 28 | J = LCENT-1 29 | IF ( LCENT.EQ.6 ) J=1 30 | IF ( LCENT.EQ.7 ) J=5 31 | DO I=2,NCV !Copy the lattice centering vectors 32 | CEN(1,I) = CENV(1,J) 33 | CEN(2,I) = CENV(2,J) 34 | CEN(3,I) = CENV(3,J) 35 | J = J+1 36 | END DO 37 | END IF 38 | RETURN 39 | END 40 | -------------------------------------------------------------------------------- /sources/spsubs/sglpak.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE SGLPAK(L,IER) 2 | 3 | INCLUDE '../INCLDS/COPYRIGT.FOR' 4 | 5 | C THIS PROGRAM WAS DEVELOPED FOR 6 | C THE DIVISION OF CHEMISTRY 7 | C OF 8 | C THE NATIONAL RESEARCH COUNCIL OF CANADA 9 | C BY 10 | C ALLEN C. LARSON, P.O.BOX 5898, SANTA FE, NM 87502,USA 11 | 12 | DIMENSION L(4) 13 | 14 | IF ( L(2).LT.12 ) IER=4 15 | IF ( L(2).GT.17 ) IER=4 16 | L(1) = L(2) 17 | L(2) = 18 18 | RETURN 19 | END 20 | -------------------------------------------------------------------------------- /sources/spsubs/sgmtml.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE SGMTML(X,I,J,K) 2 | 3 | !Purpose: Form product of operators to generate the full group 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | C This program was developed for 8 | C The Division of Chemistry 9 | C of 10 | C The National Research Council of Canada 11 | C by 12 | C Allen C. Larson, 14 Cerrado Loop, Santa Fe, NM 87505, USA 13 | 14 | REAL*4 X(5,4,25) 15 | INTEGER*4 I !Input matrix number 16 | INTEGER*4 J !Input matrix number 17 | INTEGER*4 K !Output matrix number 18 | 19 | DO L=1,4 20 | DO M=1,4 21 | X(L,M,K) = 0.0 22 | DO N=1,4 23 | X(L,M,K) = X(L,M,K)+X(L,N,J)*X(N,M,I) 24 | END DO 25 | END DO 26 | END DO 27 | 28 | X(1,4,K) = MOD(NINT((7.0+X(1,4,K))*12)/12.0,1.0) !Force the translations to be in the cell 29 | X(2,4,K) = MOD(NINT((7.0+X(2,4,K))*12)/12.0,1.0) !Also reset them to the value nearest to n/12 30 | X(3,4,K) = MOD(NINT((7.0+X(3,4,K))*12)/12.0,1.0) 31 | 32 | X(5,1,K) = 81*(2*X(1,1,K)+3*X(1,2,K)+4*X(1,3,K)) !Calculate a matrix flag 33 | 1 +9*(2*X(2,1,K)+3*X(2,2,K)+4*X(2,3,K)) 34 | 1 +2*X(3,1,K)+3*X(3,2,K)+4*X(3,3,K) 35 | X(5,2,K) = 1728*X(1,4,K)+144*X(2,4,K)+12*X(3,4,K) !Calculate the translation flag 36 | X(5,2,K) = NINT(X(5,2,K)) !These should be whole numbers 37 | X(5,3,K) = IEOR(NINT(X(5,3,J)),NINT(X(5,3,I))) !Note the generator matrix number 38 | X(5,4,K) = 0.0 39 | 40 | RETURN 41 | END 42 | -------------------------------------------------------------------------------- /sources/spsubs/sgrmat.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE SGRMAT(IOP,RT,N,A,B,C,D,E,F,G,H,O) 2 | 3 | !Purpose: S.R. to create a 3,3 matrix from 9 scalers 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | C THIS PROGRAM WAS DEVELOPED FOR 8 | C THE DIVISION OF CHEMISTRY 9 | C OF 10 | C THE NATIONAL RESEARCH COUNCIL OF CANADA 11 | C BY 12 | C ALLEN C. LARSON, 14 CERRADO LOOP, SANTA FE, NM 87505, USA 13 | 14 | !Calling sequence parameters: 15 | 16 | INTEGER*4 IOP !Matrix generator count 17 | REAL*4 RT(5,4,25) !Matrix to be generated 18 | INTEGER*4 N !Number of the matrix to be generated 19 | REAL*4 A,B,C,D,E,F,G,H,O !Matrix terms 20 | 21 | !Local varaibles: 22 | 23 | !Code: 24 | 25 | RT(1,1,N) = A 26 | RT(1,2,N) = B 27 | RT(1,3,N) = C 28 | RT(1,4,N) = 0.0 29 | RT(2,1,N) = D 30 | RT(2,2,N) = E 31 | RT(2,3,N) = F 32 | RT(2,4,N) = 0.0 33 | RT(3,1,N) = G 34 | RT(3,2,N) = H 35 | RT(3,3,N) = O 36 | RT(3,4,N) = 0.0 37 | RT(4,1,N) = 0.0 38 | RT(4,2,N) = 0.0 39 | RT(4,3,N) = 0.0 40 | RT(4,4,N) = 1.0 41 | RT(5,1,N) = 81*(2*RT(1,1,N)+3*RT(1,2,N)+4*RT(1,3,N)) 42 | 1 +9*(2*RT(2,1,N)+3*RT(2,2,N)+4*RT(2,3,N)) 43 | 1 +2*RT(3,1,N)+3*RT(3,2,N)+4*RT(3,3,N) 44 | RT(5,2,N) = 0.0 !Clear the translation info 45 | RT(5,3,N) = IOP 46 | RT(5,4,N) = 20. 47 | 48 | RETURN 49 | END 50 | -------------------------------------------------------------------------------- /sources/sysinstall.bat: -------------------------------------------------------------------------------- 1 | set OUTDIR=%MESON_SOURCE_ROOT%\GSASII\bin 2 | mkdir %OUTDIR% 3 | copy /y "%MESON_BUILD_ROOT%\sources\"*.pyd %OUTDIR%\ 4 | copy /y "%MESON_BUILD_ROOT%\sources\k_vec_cython\"*.pyd %OUTDIR%\ 5 | copy /y "%MESON_BUILD_ROOT%\sources\"LATTIC.exe %OUTDIR%\ 6 | copy /y "%MESON_BUILD_ROOT%\sources\"convcell.exe %OUTDIR%\ 7 | copy /y "%MESON_BUILD_ROOT%\sources\"GSAS*.txt %OUTDIR%\ 8 | copy /y %CONDA_PREFIX%\Library\bin\libgfortran*.dll %OUTDIR%\ 9 | copy /y %CONDA_PREFIX%\Library\bin\libquadmath*.dll %OUTDIR%\ 10 | copy /y %CONDA_PREFIX%\Library\bin\libgcc*.dll %OUTDIR%\ 11 | REM copy /y %CONDA_PREFIX%\Library\bin\libwinthread*.dll %OUTDIR%\ 12 | -------------------------------------------------------------------------------- /sources/sysinstall.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | OUTDIR=${MESON_SOURCE_ROOT}/GSASII/bin 3 | mkdir -p ${OUTDIR} 4 | cp -v "${MESON_BUILD_ROOT}/sources/"*.so ${OUTDIR}/ 5 | cp -v "${MESON_BUILD_ROOT}/sources/"*/*.so ${OUTDIR}/ 6 | cp -v "${MESON_BUILD_ROOT}/sources/"LATTIC ${OUTDIR}/ 7 | cp -v "${MESON_BUILD_ROOT}/sources/"convcell ${OUTDIR}/ 8 | cp -v "${MESON_BUILD_ROOT}/sources/"GSAS*.txt ${OUTDIR}/ 9 | -------------------------------------------------------------------------------- /sources/tagbinaries.py: -------------------------------------------------------------------------------- 1 | # this routine is intended to be run from inside meson and creates a 2 | # file named GSASIIversion.txt with that information 3 | import sys 4 | import os 5 | import shutil 6 | import subprocess 7 | import datetime 8 | source = os.environ.get('MESON_SOURCE_ROOT', 9 | os.path.dirname(os.path.dirname(__file__))) 10 | build = os.environ.get('MESON_BUILD_ROOT', 11 | os.path.dirname(os.path.dirname(__file__))) 12 | 13 | if shutil.which('git'): 14 | out = subprocess.run(['git','tag','-l','--sort=-authordate','v*'], 15 | stdout=subprocess.PIPE,cwd=source) 16 | version = out.stdout.decode('latin-1').split('\n')[0].strip() 17 | out = subprocess.run(['git','tag','-l','--sort=-authordate','[0-9]*'], 18 | stdout=subprocess.PIPE,cwd=source) 19 | number = out.stdout.decode('latin-1').split('\n')[0].strip() 20 | out = subprocess.run(['git','log','HEAD','-1'], 21 | stdout=subprocess.PIPE,cwd=source) 22 | githash = out.stdout.decode('latin-1').split('commit')[1].split('\n')[0].strip() 23 | how = 'git' 24 | else: 25 | how = 'git_verinfo' 26 | try: 27 | sys.path.insert(0,source) 28 | from GSASII import git_verinfo 29 | number = '?' 30 | githash = git_verinfo.git_version 31 | version = git_verinfo.git_versiontag 32 | for item in git_verinfo.git_tags+git_verinfo.git_prevtags: 33 | if item.isnumeric(): 34 | number = item 35 | break 36 | except: 37 | sys.exit() 38 | outfile = os.path.join(build,'sources','GSASIIversion.txt') 39 | with open(outfile,'w') as fp: 40 | fp.write(f"{version}\n{number}\ncommit {githash}\n") 41 | fp.write(f"#created by {__file__} on {datetime.datetime.now()} from {how}\n") 42 | fp.close() 43 | print(outfile) 44 | -------------------------------------------------------------------------------- /sources/texturesubs/aplms.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE APLMS(L,M,S,AP) 2 | 3 | !PURPOSE: Compute A'(l,m,s) 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | !CALLING ARGUMENTS: 8 | 9 | INTEGER*4 L,M,S !Order & subindices 10 | REAL*4 AP !Output value 11 | 12 | !INCLUDE STATEMENTS: 13 | 14 | !LOCAL VARIABLES: 15 | 16 | REAL*4 LNORM,ALM0S,A1,A2 17 | 18 | !FUNCTION DEFINITIONS: 19 | 20 | !DATA STATEMENTS: 21 | 22 | !CODE: 23 | 24 | LNORM = SQRT((2.0*L+1.0)/2.0) 25 | CALL QLMN(L,M,S,A1) 26 | CALL QLMN(L,0,S,A2) 27 | ALM0S = A1*A2 28 | IF ( MOD(ABS(M),2).EQ.0 ) THEN 29 | IF ( S.EQ.0 ) THEN 30 | AP = ALM0S*LNORM 31 | ELSE 32 | AP = 2.0*ALM0S*LNORM 33 | END IF 34 | IF ( MOD(ABS(M),4).EQ.2 ) AP = -AP 35 | ELSE 36 | IF ( S.EQ.0 ) THEN 37 | AP = 0.0 38 | ELSE 39 | AP = 2.0*ALM0S*LNORM 40 | END IF 41 | IF ( MOD(ABS(M),4).EQ.1 ) AP = -AP 42 | END IF 43 | IF ( ABS(AP).LT.1.0E-6 ) AP = 0.0 44 | RETURN 45 | END 46 | 47 | -------------------------------------------------------------------------------- /sources/texturesubs/cosd.for: -------------------------------------------------------------------------------- 1 | REAL*4 FUNCTION COSD(ARG) 2 | 3 | !PURPOSE: Calculate cosine from angle in deg. 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | !CALLING ARGUMENTS: 8 | 9 | REAL*4 ARG !Cosine argument in degrees 10 | 11 | !INCLUDE STATEMENTS: 12 | 13 | !LOCAL VARIABLES: 14 | 15 | !FUNCTION DEFINITIONS: 16 | 17 | !DATA STATEMENTS: 18 | 19 | DATA RPD/0.017453292519943/ 20 | 21 | !CODE: 22 | 23 | COSD = COS(ARG*RPD) 24 | RETURN 25 | END 26 | -------------------------------------------------------------------------------- /sources/texturesubs/dgammln.for: -------------------------------------------------------------------------------- 1 | FUNCTION DGAMMLN(XX) 2 | 3 | !PURPOSE: ln(gamma(xx)), taken from Numerical Recipes, p156-157 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | !PSEUDOCODE: 8 | 9 | !CALLING ARGUMENTS: 10 | 11 | REAL*8 DGAMMLN !ln(gamma(xx)) with xx>0 12 | REAL*4 XX !argument must be >0 13 | 14 | !INCLUDE STATEMENTS: 15 | 16 | !LOCAL VARIABLES: 17 | 18 | REAL*8 COF(6),STP,HALF,ONE,FPF,X,TMP,SER 19 | 20 | !SUBROUTINES CALLED: 21 | 22 | !FUNCTION DEFINITIONS: 23 | 24 | !DATA STATEMENTS: 25 | 26 | DATA COF,STP/76.18009172947146D0,-86.50532032941677D0, 27 | 1 24.01409824083091D0,-1.231739572450155D0,0.1208650973866D-2, 28 | 1 -0.5395239384953D-5,2.5066282746310005D0/ 29 | DATA HALF,ONE,FPF/0.5D0,1.000000000190015D0,5.5D0/ 30 | 31 | !CODE: 32 | 33 | X = XX-ONE 34 | TMP = X+FPF 35 | TMP = (X+HALF)*DLOG(TMP)-TMP 36 | SER = ONE 37 | DO J=1,6 38 | X = X+ONE 39 | SER = SER+COF(J)/X 40 | END DO 41 | DGAMMLN = TMP+DLOG(STP*SER) 42 | RETURN 43 | END 44 | -------------------------------------------------------------------------------- /sources/texturesubs/factln.for: -------------------------------------------------------------------------------- 1 | FUNCTION FACTLN(N) 2 | 3 | !PURPOSE: Compute ln(factorial) - adapted from Numerical Recipes 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | !CALLING ARGUMENTS: 8 | 9 | INTEGER*4 N !Order of factorial 10 | REAL*8 FACTLN !ln(N!) returned 11 | 12 | !INCLUDE STATEMENTS: 13 | 14 | !LOCAL VARIABLES: 15 | 16 | REAL*8 A(100) 17 | INTEGER*4 IA(100) 18 | 19 | !FUNCTION DEFINITIONS: 20 | 21 | REAL*8 DGAMMLN 22 | 23 | !DATA STATEMENTS: 24 | 25 | DATA A/100*-1.0D0/,IA/100*0/ 26 | 27 | !CODE: 28 | 29 | IF ( N.LE.99 ) THEN 30 | IF ( IA(N+1).EQ.0 ) THEN 31 | IA(N+1) = 1 32 | A(N+1) = DGAMMLN(N+1.0) 33 | END IF 34 | FACTLN = A(N+1) 35 | ELSE 36 | FACTLN = DGAMMLN(N+1.0) 37 | END IF 38 | RETURN 39 | END 40 | 41 | -------------------------------------------------------------------------------- /sources/texturesubs/plmpsi.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE PLMPSI(L,M,PSI,P,DPDPS) 2 | 3 | !PURPOSE: Compute P(l,m,psi) 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | !CALLING ARGUMENTS: 8 | 9 | INTEGER*4 L,M !Order & index 10 | REAL*4 PSI !Angle (in deg) 11 | REAL*4 P !Value returned 12 | 13 | !INCLUDE STATEMENTS: 14 | 15 | !LOCAL VARIABLES: 16 | 17 | INTEGER*4 S 18 | REAL*4 APR,RS 19 | 20 | !FUNCTION DEFINITIONS: 21 | 22 | !DATA STATEMENTS: 23 | 24 | !CODE: 25 | 26 | P = 0.0 27 | DPDPS = 0.0 28 | IF ( MOD(ABS(M),2).EQ.0 ) THEN 29 | DO S=0,L,2 30 | CALL APLMS(L,M,S,APR) 31 | RS = S 32 | P = P+APR*COSD(RS*PSI) 33 | DPDPS = DPDPS-RS*APR*SIND(RS*PSI) 34 | END DO 35 | ELSE 36 | DO S=2,L,2 37 | CALL APLMS(L,M,S,APR) 38 | RS = S 39 | P = P+APR*SIND(RS*PSI) 40 | DPDPS = DPDPS+RS*APR*COSD(RS*PSI) 41 | END DO 42 | END IF 43 | RETURN 44 | END 45 | 46 | -------------------------------------------------------------------------------- /sources/texturesubs/qlmn.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE QLMN(L,MM,NN,Q) 2 | 3 | !PURPOSE: Compute Ql,m,n for spherical harmonics from lookup table 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | !CALLING ARGUMENTS: 8 | 9 | INTEGER*4 L,MM,NN !order & subindices (m may be <0) 10 | REAL*4 Q !Output value 11 | 12 | !INCLUDE STATEMENTS: 13 | 14 | REAL*4 QT 15 | COMMON /QLMNVAL/QT(2109) 16 | 17 | 18 | !LOCAL VARIABLES: 19 | 20 | REAL*8 SUM,TEMP,TEMP1 21 | INTEGER*4 LMN,I,J,M,N 22 | 23 | !FUNCTION DEFINITIONS: 24 | 25 | REAL*8 FACTLN !Compute ln-factorial & binominal coeffs. 26 | 27 | !DATA STATEMENTS: 28 | 29 | !CODE: 30 | 31 | M = ABS(MM) 32 | N = ABS(NN) 33 | IF ( N.GT.M ) THEN 34 | I = M 35 | M = N 36 | N = I 37 | END IF 38 | IF ( MOD(N,2).EQ.0 .AND. MOD(L,2).EQ.0 ) THEN !Even L,N - do lookup 39 | J = 0 40 | DO I=2,L,2 41 | J = J+(I/2)**2 !points to last term in L-2 block 42 | END DO 43 | J = J+1 44 | DO I=0,M-1 45 | J = J+(I+2)/2 !points to 1st term in M block 46 | END DO 47 | J = J+N/2 !offset to N term 48 | ! PRINT '(A,I4,F12.8)',' J,Q ',J,QT(J) 49 | Q = QT(J) 50 | ELSE !Odd L or N - calculate Q 51 | LMN = L-M-N 52 | TEMP = 0.5D0*(FACTLN(L+N)+FACTLN(L+M)+ 53 | 1 FACTLN(L-M)+FACTLN(L-N)) 54 | SUM = 0.0D0 55 | DO I=0,L-N 56 | IF ( (L-M-I).GE.0 .AND. (M+N+I).GE.0 ) THEN 57 | TEMP1 = TEMP-FACTLN(I)-FACTLN(L-M-I)- 58 | 1 FACTLN(L-N-I)-FACTLN(M+N+I) 59 | TEMP1 = DEXP(TEMP1) 60 | IF ( MOD(I,2).NE.0 ) TEMP1 = -TEMP1 61 | SUM = SUM+TEMP1 62 | END IF 63 | END DO 64 | Q = SUM/2.**(1.*L) 65 | IF ( MOD(LMN,2).NE.0 ) Q = -Q 66 | ! PRINT '(A,3I4,F12.8)',' l,m,n,Q(lmn)',L,M,N,Q 67 | END IF 68 | IF ( MM.LT.0 .AND. MOD(L+NN,2).NE.0 ) Q = -Q 69 | IF ( NN.LT.0 .AND. MOD(L+MM,2).NE.0 ) Q = -Q 70 | RETURN 71 | END 72 | 73 | -------------------------------------------------------------------------------- /sources/texturesubs/qlmninit.for: -------------------------------------------------------------------------------- 1 | SUBROUTINE QLMNINIT 2 | 3 | !PURPOSE: Compute Ql,m,n for spherical harmonics up to L=34 - only does even orders 4 | ! and only even N terms - by R.I. Sheldon & modified by R. Von Dreele for GSAS 5 | 6 | INCLUDE '../INCLDS/COPYRIGT.FOR' 7 | 8 | !CALLING ARGUMENTS: 9 | 10 | !INCLUDE STATEMENTS: 11 | 12 | REAL*4 QT 13 | COMMON /QLMNVAL/QT(2109) 14 | 15 | !LOCAL VARIABLES: 16 | 17 | REAL*8 SUM,TEMP,TEMP1 18 | INTEGER*4 I,LMN,M,MM 19 | 20 | !FUNCTION DEFINITIONS: 21 | 22 | REAL*8 FACTLN !Compute ln-factorial & binominal coeffs. 23 | 24 | !DATA STATEMENTS: 25 | 26 | !CODE: 27 | 28 | J = 1 29 | QT(1) = 1.0 30 | DO L=2,34,2 31 | DO M=0,L 32 | DO N=0,M,2 33 | J = J+1 34 | LMN = L-M-N 35 | TEMP = 0.5D0*(FACTLN(L+N)+FACTLN(L+M)+ 36 | 1 FACTLN(L-M)+FACTLN(L-N)) 37 | SUM = 0.0D0 38 | DO I=0,L-N 39 | IF ( (L-M-I).GE.0 .AND. (M+N+I).GE.0 ) THEN 40 | TEMP1 = TEMP-FACTLN(I)-FACTLN(L-M-I)- 41 | 1 FACTLN(L-N-I)-FACTLN(M+N+I) 42 | TEMP1 = DEXP(TEMP1) 43 | IF ( MOD(I,2).NE.0 ) TEMP1 = -TEMP1 44 | SUM = SUM+TEMP1 45 | END IF 46 | END DO 47 | QT(J) = SUM/2.**(1.*L) 48 | IF ( MOD(LMN,2).NE.0 ) QT(J) = -QT(J) 49 | ! PRINT '(A,3I4,F12.8)',' l,m,n,Q(lmn)',L,M,N,QT(J) 50 | END DO 51 | END DO 52 | END DO 53 | RETURN 54 | END 55 | 56 | -------------------------------------------------------------------------------- /sources/texturesubs/sind.for: -------------------------------------------------------------------------------- 1 | REAL*4 FUNCTION SIND(ARG) 2 | 3 | !PURPOSE: Calculate sine from angle in deg. 4 | 5 | INCLUDE '../INCLDS/COPYRIGT.FOR' 6 | 7 | !CALLING ARGUMENTS: 8 | 9 | REAL*4 ARG !Sine argument in degrees 10 | 11 | !INCLUDE STATEMENTS: 12 | 13 | !LOCAL VARIABLES: 14 | 15 | !FUNCTION DEFINITIONS: 16 | 17 | !DATA STATEMENTS: 18 | 19 | DATA RPD/0.017453292519943/ 20 | 21 | !CODE: 22 | 23 | SIND = SIN(ARG*RPD) 24 | RETURN 25 | END 26 | -------------------------------------------------------------------------------- /tests/run_pypowder.py: -------------------------------------------------------------------------------- 1 | # compute a single peak with pypowder 2 | import os 3 | import sys 4 | import importlib.util 5 | import numpy as np 6 | 7 | home = os.path.dirname(__file__) 8 | G2loc = None 9 | try: 10 | G2loc = importlib.util.find_spec('GSASII.GSASIIscriptable') 11 | except ModuleNotFoundError: 12 | print('ModuleNotFound for GSASII.GSASIIscriptable') 13 | 14 | if G2loc is None: # fixup path if GSASII not installed into Python 15 | print('GSAS-II not installed in Python; Hacking sys.path') 16 | sys.path.append(os.path.dirname(home)) 17 | 18 | from GSASII import GSASIIpath 19 | GSASIIpath.SetBinaryPath() 20 | 21 | if GSASIIpath.binaryPath: 22 | import pypowder as pyd 23 | else: 24 | from . import pypowder as pyd 25 | 26 | # these values generate a nearly symmetric peak 27 | xdata = np.arange(18,22,.05) 28 | pos = 20. 29 | sig = 525.9994695543994 30 | gam = 2.1444606947716025 31 | shl = 0.002 32 | ydata = pyd.pypsvfcjo(len(xdata),xdata-pos,pos,sig,gam,shl) 33 | 34 | # these values generate a peak with significant low-angle broadening 35 | #xdata = np.arange(0.1,5,.05) 36 | #pos = 2 37 | #sig = 525.9994695543994 38 | #gam = 2.1444606947716025 39 | #shl = 0.035 40 | #ydata = pyd.pypsvfcjo(len(xdata),xdata-pos,pos,sig,gam,shl) 41 | 42 | import matplotlib.pyplot as plt 43 | plt.plot(xdata,ydata) 44 | plt.show() 45 | 46 | -------------------------------------------------------------------------------- /tests/test_elm.py: -------------------------------------------------------------------------------- 1 | ''' 2 | test_elm.py 3 | ============== 4 | Performs a very simple test on the element tables. 5 | ''' 6 | 7 | import os 8 | import sys 9 | import importlib.util 10 | if importlib.util.find_spec('GSASII') is None: # hack path if GSASII not installed into Python 11 | home = os.path.dirname(__file__) 12 | sys.path.append(os.path.dirname(home)) 13 | 14 | from GSASII import GSASIIElem 15 | 16 | def test_get_xsection(): 17 | 'Test that a cross-section for a single element is read' 18 | xsection = GSASIIElem.GetXsectionCoeff('Fe') 19 | assert len(xsection) > 0 20 | 21 | if __name__ == '__main__': 22 | # run self-tests 23 | test_get_xsection() 24 | print ("OK") 25 | -------------------------------------------------------------------------------- /tests/testinp/INST_XRY.PRM: -------------------------------------------------------------------------------- 1 | 123456789012345678901234567890123456789012345678901234567890 2 | INS BANK 1 3 | INS HTYPE PXCR 4 | INS 1 IRAD 3 5 | INS 1 ICONS 1.540500 1.544300 0.0 0 0.7 0 0.5 6 | INS 1I HEAD DUMMY INCIDENT SPECTRUM FOR X-RAY DIFFRACTOMETER 7 | INS 1I ITYP 0 0.0000 180.0000 1 8 | INS 1PRCF1 3 8 0.01 9 | INS 1PRCF11 2.000000E+00 -2.000000E+00 5.000000E+00 0.100000E+00 10 | INS 1PRCF12 0.000000E+00 0.000000E+00 0.150000E-01 0.150000E-01 11 | -------------------------------------------------------------------------------- /tests/testinp/PbSO4-Wyckoff.cif: -------------------------------------------------------------------------------- 1 | 2 | ###################################################################### 3 | data_pbso4-phase 4 | 5 | # phase info for PbSO4 follows 6 | _pd_phase_name PbSO4 7 | _cell_length_a 8.48 8 | _cell_length_b 5.398 9 | _cell_length_c 6.958 10 | _cell_angle_alpha 90 11 | _cell_angle_beta 90 12 | _cell_angle_gamma 90 13 | _cell_volume 318.503 14 | _symmetry_cell_setting orthorhombic 15 | _symmetry_space_group_name_H-M "P n m a" 16 | loop_ 17 | _space_group_symop_id 18 | _space_group_symop_operation_xyz 19 | 1 x,y,z 20 | 2 1/2-x,1/2+y,1/2+z 21 | 3 x,1/2-y,z 22 | 4 1/2-x,-y,1/2+z 23 | 5 -x,-y,-z 24 | 6 1/2+x,1/2-y,1/2-z 25 | 7 -x,1/2+y,-z 26 | 8 1/2+x,y,1/2-z 27 | 28 | # ATOMIC COORDINATES AND DISPLACEMENT PARAMETERS 29 | loop_ 30 | _atom_site_label 31 | _atom_site_type_symbol 32 | _atom_site_fract_x 33 | _atom_site_fract_y 34 | _atom_site_fract_z 35 | _atom_site_occupancy 36 | _atom_site_adp_type 37 | _atom_site_U_iso_or_equiv 38 | _atom_site_symmetry_multiplicity 39 | Pb Pb 0.18820 0.25000 0.16700 1.000 Uiso 0.010 4 40 | S S 0.06300 0.25000 0.68600 1.000 Uiso 0.010 4 41 | O1 O -0.09500 0.25000 0.60000 1.000 Uiso 0.010 4 42 | O2 O 0.18100 0.25000 0.54300 1.000 Uiso 0.010 4 43 | O3 O 0.08500 0.02600 0.80600 1.000 Uiso 0.010 8 44 | 45 | loop_ _atom_type_symbol _atom_type_number_in_cell 46 | O 16 47 | Pb 4 48 | S 4 49 | 50 | # Note that Z affects _cell_formula_sum and _weight 51 | _cell_formula_units_Z 4 52 | _chemical_formula_sum "O4 Pb S" 53 | _chemical_formula_weight 303.26 54 | -------------------------------------------------------------------------------- /tests/testinp/gencelltests.py: -------------------------------------------------------------------------------- 1 | #!/Users/toby/build/cctbx_build/bin/python 2 | import sys 3 | import cctbx.uctbx as uc 4 | import numpy as np 5 | import datetime 6 | 7 | fp = sys.stdout 8 | fp.write("# output from uctbx (cctbx) computed on platform %s on %s\n" % 9 | (sys.platform, datetime.date.today()) ) 10 | fp.write("#import numpy as np\n") 11 | fp.write("array = np.array\n\n") 12 | fp.write("CellTestData = [\n") 13 | 14 | for cell in [ 15 | (4,4,4,90,90,90), 16 | (4.1,5.2,6.3,100,80,130), 17 | (3.5,3.5,6,90,90,120), 18 | ]: 19 | fp.write("# cell, g, G, cell*, V, V*\n") 20 | result = [] 21 | result.append(cell) 22 | mm = uc.unit_cell(cell).metrical_matrix() 23 | result.append( 24 | np.array([mm[i] for i in (0,3,4,3,1,5,4,5,2)]).reshape(3,3) 25 | ) 26 | rmm = uc.unit_cell(cell).reciprocal_metrical_matrix() 27 | result.append( 28 | np.array([rmm[i] for i in (0,3,4,3,1,5,4,5,2)]).reshape(3,3) 29 | ) 30 | result.append( 31 | uc.unit_cell(cell).reciprocal().parameters() 32 | ) 33 | result.append( 34 | uc.unit_cell(cell).volume() 35 | ) 36 | result.append( 37 | uc.unit_cell(cell).reciprocal().volume() 38 | ) 39 | fp.write(" %s,\n" % result) 40 | fp.write("]\n") 41 | 42 | fp.write("CoordTestData = [\n") 43 | for cell in [ 44 | (4,4,4,90,90,90), 45 | (4.1,5.2,6.3,100,80,130), 46 | (3.5,3.5,6,90,90,120), 47 | ]: 48 | fp.write("# cell, ((frac, ortho),...)\n") 49 | fp.write(" ((%s,%s,%s,%s,%s,%s,), [\n" % cell) 50 | for frac in [ 51 | (0.1,0.,0.), 52 | (0.,0.1,0.), 53 | (0.,0.,0.1), 54 | (0.1,0.2,0.3), 55 | (0.2,0.3,0.1), 56 | (0.3,0.2,0.1), 57 | (0.5,0.5,0.5), 58 | ]: 59 | fp.write(" (%s,%s),\n" % (frac, uc.unit_cell(cell).orthogonalize(frac))) 60 | fp.write("]),\n") 61 | fp.write("]\n") 62 | 63 | sys.exit() 64 | -------------------------------------------------------------------------------- /tests/testinp/inst_d1a.prm: -------------------------------------------------------------------------------- 1 | 123456789012345678901234567890123456789012345678901234567890 2 | INS BANK 1 3 | INS HTYPE PNCR 4 | INS 1 ICONS 1.909000 0.000000 -0.1 0 0.0 0 0.0 5 | INS 1I HEAD DUMMY INCIDENT SPECTRUM FOR DIFFRACTOMETER D1A 6 | INS 1I ITYP 0 0.0000 180.0000 1 7 | INS 1PRCF1 1 6 0.01 8 | INS 1PRCF11 0.354031E+03 -0.760404E+03 0.651592E+03 0.000000E+00 9 | INS 1PRCF12 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 10 | INS 1PRCF2 2 6 0.01 11 | INS 1PRCF21 0.354031E+03 -0.760404E+03 0.651592E+03 0.000000E+00 12 | INS 1PRCF22 0.000000E+00 0.000000E+00 -------------------------------------------------------------------------------- /tests/testinp/nx09_strain_011.imctrl: -------------------------------------------------------------------------------- 1 | type:PWDR 2 | color:GSPaired 3 | wavelength:0.12398 4 | calibrant:CeO2 SRM674b 5 | distance:1118.8555366950047 6 | center:[np.float64(168.59496999985376), np.float64(173.45708080489564)] 7 | Oblique:[0.5, False] 8 | tilt:1.2679918237395627 9 | rotation:94.80104622234859 10 | azmthOff:0.0 11 | fullIntegrate:True 12 | LRazimuth:[0.0, 360.0] 13 | setdist:100.0 14 | IOtth:[1.5, 9.0] 15 | outChannels:2500 16 | outAzimuths:1 17 | invert_x:False 18 | invert_y:True 19 | DetDepth:0.0 20 | calibskip:0 21 | pixLimit:2 22 | cutoff:1.0 23 | calibdmin:1.09 24 | Flat Bkg:0.0 25 | varyList:{'dist': True, 'det-X': True, 'det-Y': True, 'tilt': True, 'phi': True, 'dep': False, 'wave': False} 26 | binType:2-theta 27 | SampleShape:Cylinder 28 | PolaVal:[0.99, False] 29 | SampleAbs:[0.0, False] 30 | dark image:['', -1.0] 31 | background image:['', -1.0] 32 | --------------------------------------------------------------------------------