From f7844de9ffccc312f6efe3f874aca47d1c9b7ee5 Mon Sep 17 00:00:00 2001 From: Lars Pastewka Date: Thu, 29 Jul 2021 09:17:08 +0200 Subject: [PATCH] TST: Increase cutoff --- .gitattributes | 4 +- docs/make.bat | 484 +++++++++++++-------------- matscipy/dislocation.py | 24 +- matscipy/fracture_mechanics/crack.py | 2 +- tests/test_bop.py | 8 +- 5 files changed, 262 insertions(+), 260 deletions(-) diff --git a/.gitattributes b/.gitattributes index a679b9c4..ecc65f31 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,3 +1,5 @@ matscipy/_version.py export-subst *.fs -linguist-detectable -*.py text eol=lf \ No newline at end of file +.gitattributes text eol=lf +*.py text eol=lf +*.sh text eol=lf diff --git a/docs/make.bat b/docs/make.bat index 327d0364..00b086d6 100644 --- a/docs/make.bat +++ b/docs/make.bat @@ -1,242 +1,242 @@ -@ECHO OFF - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set BUILDDIR=_build -set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . -set I18NSPHINXOPTS=%SPHINXOPTS% . -if NOT "%PAPER%" == "" ( - set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% - set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% -) - -if "%1" == "" goto help - -if "%1" == "help" ( - :help - echo.Please use `make ^` where ^ is one of - echo. html to make standalone HTML files - echo. dirhtml to make HTML files named index.html in directories - echo. singlehtml to make a single large HTML file - echo. pickle to make pickle files - echo. json to make JSON files - echo. htmlhelp to make HTML files and a HTML help project - echo. qthelp to make HTML files and a qthelp project - echo. devhelp to make HTML files and a Devhelp project - echo. epub to make an epub - echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter - echo. text to make text files - echo. man to make manual pages - echo. texinfo to make Texinfo files - echo. gettext to make PO message catalogs - echo. changes to make an overview over all changed/added/deprecated items - echo. xml to make Docutils-native XML files - echo. pseudoxml to make pseudoxml-XML files for display purposes - echo. linkcheck to check all external links for integrity - echo. doctest to run all doctests embedded in the documentation if enabled - goto end -) - -if "%1" == "clean" ( - for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i - del /q /s %BUILDDIR%\* - goto end -) - - -%SPHINXBUILD% 2> nul -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ - exit /b 1 -) - -if "%1" == "html" ( - %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/html. - goto end -) - -if "%1" == "dirhtml" ( - %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. - goto end -) - -if "%1" == "singlehtml" ( - %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. 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The epub file is in %BUILDDIR%/epub. - goto end -) - -if "%1" == "latex" ( - %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. - goto end -) - -if "%1" == "latexpdf" ( - %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex - cd %BUILDDIR%/latex - make all-pdf - cd %BUILDDIR%/.. - echo. - echo.Build finished; the PDF files are in %BUILDDIR%/latex. - goto end -) - -if "%1" == "latexpdfja" ( - %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex - cd %BUILDDIR%/latex - make all-pdf-ja - cd %BUILDDIR%/.. - echo. - echo.Build finished; the PDF files are in %BUILDDIR%/latex. - goto end -) - -if "%1" == "text" ( - %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The text files are in %BUILDDIR%/text. - goto end -) - -if "%1" == "man" ( - %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The manual pages are in %BUILDDIR%/man. - goto end -) - -if "%1" == "texinfo" ( - %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. - goto end -) - -if "%1" == "gettext" ( - %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The message catalogs are in %BUILDDIR%/locale. - goto end -) - -if "%1" == "changes" ( - %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes - if errorlevel 1 exit /b 1 - echo. - echo.The overview file is in %BUILDDIR%/changes. - goto end -) - -if "%1" == "linkcheck" ( - %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck - if errorlevel 1 exit /b 1 - echo. - echo.Link check complete; look for any errors in the above output ^ -or in %BUILDDIR%/linkcheck/output.txt. - goto end -) - -if "%1" == "doctest" ( - %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest - if errorlevel 1 exit /b 1 - echo. - echo.Testing of doctests in the sources finished, look at the ^ -results in %BUILDDIR%/doctest/output.txt. - goto end -) - -if "%1" == "xml" ( - %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The XML files are in %BUILDDIR%/xml. - goto end -) - -if "%1" == "pseudoxml" ( - %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml. - goto end -) - -:end +@ECHO OFF + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set BUILDDIR=_build +set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . +set I18NSPHINXOPTS=%SPHINXOPTS% . +if NOT "%PAPER%" == "" ( + set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% + set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% +) + +if "%1" == "" goto help + +if "%1" == "help" ( + :help + echo.Please use `make ^` where ^ is one of + echo. html to make standalone HTML files + echo. dirhtml to make HTML files named index.html in directories + echo. singlehtml to make a single large HTML file + echo. pickle to make pickle files + echo. json to make JSON files + echo. htmlhelp to make HTML files and a HTML help project + echo. qthelp to make HTML files and a qthelp project + echo. devhelp to make HTML files and a Devhelp project + echo. epub to make an epub + echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter + echo. text to make text files + echo. man to make manual pages + echo. texinfo to make Texinfo files + echo. gettext to make PO message catalogs + echo. changes to make an overview over all changed/added/deprecated items + echo. xml to make Docutils-native XML files + echo. pseudoxml to make pseudoxml-XML files for display purposes + echo. linkcheck to check all external links for integrity + echo. doctest to run all doctests embedded in the documentation if enabled + goto end +) + +if "%1" == "clean" ( + for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i + del /q /s %BUILDDIR%\* + goto end +) + + +%SPHINXBUILD% 2> nul +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "html" ( + %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/html. + goto end +) + +if "%1" == "dirhtml" ( + %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. + goto end +) + +if "%1" == "singlehtml" ( + %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. + goto end +) + +if "%1" == "pickle" ( + %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the pickle files. + goto end +) + +if "%1" == "json" ( + %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the JSON files. + goto end +) + +if "%1" == "htmlhelp" ( + %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run HTML Help Workshop with the ^ +.hhp project file in %BUILDDIR%/htmlhelp. + goto end +) + +if "%1" == "qthelp" ( + %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run "qcollectiongenerator" with the ^ +.qhcp project file in %BUILDDIR%/qthelp, like this: + echo.^> qcollectiongenerator %BUILDDIR%\qthelp\matscipy.qhcp + echo.To view the help file: + echo.^> assistant -collectionFile %BUILDDIR%\qthelp\matscipy.ghc + goto end +) + +if "%1" == "devhelp" ( + %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. + goto end +) + +if "%1" == "epub" ( + %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The epub file is in %BUILDDIR%/epub. + goto end +) + +if "%1" == "latex" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "latexpdf" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + cd %BUILDDIR%/latex + make all-pdf + cd %BUILDDIR%/.. + echo. + echo.Build finished; the PDF files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "latexpdfja" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + cd %BUILDDIR%/latex + make all-pdf-ja + cd %BUILDDIR%/.. + echo. + echo.Build finished; the PDF files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "text" ( + %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The text files are in %BUILDDIR%/text. + goto end +) + +if "%1" == "man" ( + %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The manual pages are in %BUILDDIR%/man. + goto end +) + +if "%1" == "texinfo" ( + %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. + goto end +) + +if "%1" == "gettext" ( + %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The message catalogs are in %BUILDDIR%/locale. + goto end +) + +if "%1" == "changes" ( + %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes + if errorlevel 1 exit /b 1 + echo. + echo.The overview file is in %BUILDDIR%/changes. + goto end +) + +if "%1" == "linkcheck" ( + %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck + if errorlevel 1 exit /b 1 + echo. + echo.Link check complete; look for any errors in the above output ^ +or in %BUILDDIR%/linkcheck/output.txt. + goto end +) + +if "%1" == "doctest" ( + %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest + if errorlevel 1 exit /b 1 + echo. + echo.Testing of doctests in the sources finished, look at the ^ +results in %BUILDDIR%/doctest/output.txt. + goto end +) + +if "%1" == "xml" ( + %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The XML files are in %BUILDDIR%/xml. + goto end +) + +if "%1" == "pseudoxml" ( + %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml. + goto end +) + +:end diff --git a/matscipy/dislocation.py b/matscipy/dislocation.py index a4bb69e1..06c305e5 100644 --- a/matscipy/dislocation.py +++ b/matscipy/dislocation.py @@ -382,26 +382,26 @@ def show_configuration(disloc, bulk, u, fixed_mask=None): fig = plt.figure(figsize=(16, 4)) ax1 = fig.add_subplot(131) - ax1.set_title("z displacement, $\AA$") + ax1.set_title(r"z displacement, $\AA$") sc = ax1.scatter(bulk.positions[:, 0], bulk.positions[:, 1], c=u.T[2]) ax1.axvline(0.0, color="red", linestyle="dashed") - ax1.set_xlabel("x, $\AA$") - ax1.set_ylabel("y, $\AA$") + ax1.set_xlabel(r"x, $\AA$") + ax1.set_ylabel(r"y, $\AA$") plt.colorbar(sc) ax2 = fig.add_subplot(132) - ax2.set_title("x displacement, $\AA$") + ax2.set_title(r"x displacement, $\AA$") sc = ax2.scatter(bulk.positions[:, 0], bulk.positions[:, 1], c=u.T[0]) - ax2.set_xlabel("x, $\AA$") - ax2.set_ylabel("y, $\AA$") + ax2.set_xlabel(r"x, $\AA$") + ax2.set_ylabel(r"y, $\AA$") plt.colorbar(sc, format="%.1e") ax3 = fig.add_subplot(133) - ax3.set_title("y displacement, $\AA$") + ax3.set_title(r"y displacement, $\AA$") sc = ax3.scatter(bulk.positions[:, 0], bulk.positions[:, 1], c=u.T[1]) plt.colorbar(sc, format="%.1e") - ax3.set_xlabel("x, $\AA$") - ax3.set_ylabel("y, $\AA$") + ax3.set_xlabel(r"x, $\AA$") + ax3.set_ylabel(r"y, $\AA$") if fixed_mask is not None: @@ -1366,7 +1366,7 @@ def make_screw_quadrupole(alat, right_shift=0, n1u=5, symbol="W"): - """Generates a screw dislocation dipole configuration + r"""Generates a screw dislocation dipole configuration for effective quadrupole arrangement. Works for BCC systems. Parameters @@ -2204,8 +2204,8 @@ def plot_unit_cell(self, ms=250, ax=None): c="b") ax.legend(handles=[bulk_atoms, core1, core2], fontsize=12) - ax.set_xlabel("$\AA$") - ax.set_ylabel("$\AA$") + ax.set_xlabel(r"$\AA$") + ax.set_ylabel(r"$\AA$") def displacements(self, bulk_positions, center, self_consistent=True, diff --git a/matscipy/fracture_mechanics/crack.py b/matscipy/fracture_mechanics/crack.py index 147f3f41..fc008e6f 100755 --- a/matscipy/fracture_mechanics/crack.py +++ b/matscipy/fracture_mechanics/crack.py @@ -2030,7 +2030,7 @@ def plot_stress_fields(atoms, r_range=None, initial_params=None, fix_params=None clf() for i, (ii, jj), label in zip(range(3), [(0,0), (1,1), (0,1)], - ['\sigma_{xx}', r'\sigma_{yy}', r'\sigma_{xy}']): + [r'\sigma_{xx}', r'\sigma_{yy}', r'\sigma_{xy}']): subplot(3,3,i+1) gca().set_aspect('equal') contourf(X, Y, grid_sigma[...,i]*GPA, contours[i]) diff --git a/tests/test_bop.py b/tests/test_bop.py index cbac2fee..123cf25d 100644 --- a/tests/test_bop.py +++ b/tests/test_bop.py @@ -225,7 +225,7 @@ def d22_term5(test_cutoff): @pytest.mark.parametrize('term', [term1, term4, d11_term5, d22_term5]) -@pytest.mark.parametrize('test_cutoff', [2.4]) +@pytest.mark.parametrize('test_cutoff', [3.0]) def test_generic_potential_form1(test_cutoff, term): d = 2.0 # Si2 bondlength small = Atoms([14] * 4, [(d, 0, d / 2), (0, 0, 0), (d, 0, 0), (0, 0, d)], cell=(100, 100, 100)) @@ -234,7 +234,7 @@ def test_generic_potential_form1(test_cutoff, term): @pytest.mark.parametrize('term', [term1, term4, d11_term5, d22_term5]) -@pytest.mark.parametrize('test_cutoff', [2.4]) +@pytest.mark.parametrize('test_cutoff', [3.5]) def test_generic_potential_form2(test_cutoff, term): d = 2.0 # Si2 bondlength small2 = Atoms([14] * 5, [(d, 0, d / 2), (0, 0, 0), (d, 0, 0), (0, 0, d), (0, d, d)], cell=(100, 100, 100)) @@ -263,8 +263,8 @@ def compute_forces_and_hessian(a, par): np.testing.assert_allclose(ana_forces, num_forces, atol=1e-3) # Hessian - ana_hessian = calculator.get_hessian(a).todense() - num_hessian = fd_hessian(a, dx=1e-5, indices=None).todense() + ana_hessian = np.array(calculator.get_hessian(a).todense()) + num_hessian = np.array(fd_hessian(a, dx=1e-5, indices=None).todense()) # print('ana\n', ana_hessian) # print('num\n', num_hessian) # print('ana - num\n', (np.abs(ana_hessian - num_hessian) > 1e-6).astype(int))