From b139e5bd1826f459016e45a8f2bd88f38942ec05 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 24 Jul 2024 04:25:33 +0000 Subject: [PATCH 1/3] Bump pylammpsmpi from 0.2.21 to 0.2.22 Bumps [pylammpsmpi](https://github.com/pyiron/pylammpsmpi) from 0.2.21 to 0.2.22. - [Release notes](https://github.com/pyiron/pylammpsmpi/releases) - [Commits](https://github.com/pyiron/pylammpsmpi/compare/pylammpsmpi-0.2.21...pylammpsmpi-0.2.22) --- updated-dependencies: - dependency-name: pylammpsmpi dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index c1594b21..892c560b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -46,12 +46,12 @@ gpaw = [ "gpaw==24.6.0", ] lammps = [ - "pylammpsmpi==0.2.21", + "pylammpsmpi==0.2.22", "jinja2==3.1.4", "pandas==2.2.2", ] lammps_phonons = [ - "pylammpsmpi==0.2.21", + "pylammpsmpi==0.2.22", "jinja2==3.1.4", "pandas==2.2.2", "dynaphopy==1.17.16", From 6f06de910c87a3048209c506d103ac69f092bb1d Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 24 Jul 2024 04:27:31 +0000 Subject: [PATCH 2/3] [dependabot skip] Update environment --- .ci_support/environment-docs.yml | 2 +- .ci_support/environment-lammps.yml | 2 +- .ci_support/environment-notebooks.yml | 2 +- binder/environment.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index 43c49588..4d4f59e1 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -16,6 +16,6 @@ dependencies: - seekpath =2.1.0 - lammps =2023.11.21 - pandas =2.2.2 -- pylammpsmpi =0.2.21 +- pylammpsmpi =0.2.22 - jinja2 =3.1.4 - jupyter-book =1.0.0 diff --git a/.ci_support/environment-lammps.yml b/.ci_support/environment-lammps.yml index 51618143..76237ef6 100644 --- a/.ci_support/environment-lammps.yml +++ b/.ci_support/environment-lammps.yml @@ -3,7 +3,7 @@ channels: dependencies: - lammps =2024.02.07 - pandas =2.2.2 -- pylammpsmpi =0.2.21 +- pylammpsmpi =0.2.22 - jinja2 =3.1.4 - iprpy-data =2023.07.25 - dynaphopy =1.17.16 diff --git a/.ci_support/environment-notebooks.yml b/.ci_support/environment-notebooks.yml index 475c0419..1e93db16 100644 --- a/.ci_support/environment-notebooks.yml +++ b/.ci_support/environment-notebooks.yml @@ -6,6 +6,6 @@ dependencies: - gpaw =24.6.0 - lammps =2024.02.07 - pandas =2.2.2 -- pylammpsmpi =0.2.21 +- pylammpsmpi =0.2.22 - jinja2 =3.1.4 - dynaphopy =1.17.16 diff --git a/binder/environment.yml b/binder/environment.yml index 217aa2a0..a27b5ff9 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -11,7 +11,7 @@ dependencies: - gpaw =24.6.0 - lammps =2024.02.07 - pandas =2.2.2 -- pylammpsmpi =0.2.21 +- pylammpsmpi =0.2.22 - jinja2 =3.1.4 - dynaphopy =1.17.16 - tqdm =4.66.4 From bec3455617e9fdfbd97bacc239a8d225ccc11e5c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Jan=C3=9Fen?= Date: Wed, 24 Jul 2024 07:31:09 +0200 Subject: [PATCH 3/3] Fix tests --- tests/test_elastic_lammps.py | 44 ++++++++++++------------- tests/test_elastic_lammps_functional.py | 44 ++++++++++++------------- 2 files changed, 44 insertions(+), 44 deletions(-) diff --git a/tests/test_elastic_lammps.py b/tests/test_elastic_lammps.py index 325de1f9..32ac6ec1 100644 --- a/tests/test_elastic_lammps.py +++ b/tests/test_elastic_lammps.py @@ -50,9 +50,9 @@ def test_calc_elastic(self): [114.10311701, 60.51102935, 60.51102935, 0.0, 0.0, 0.0], [60.51102935, 114.10311701, 60.51102935, 0.0, 0.0, 0.0], [60.51102935, 60.51102935, 114.10311701, 0.0, 0.0, 0.0], - [0.0, 0.0, 0.0, 51.23853765, 0.0, 0.0], - [0.0, 0.0, 0.0, 0.0, 51.23853765, 0.0], - [0.0, 0.0, 0.0, 0.0, 0.0, 51.23853765], + [0.0, 0.0, 0.0, 31.67489592, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 31.67489592, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0, 31.67489592], ] ), ).all() @@ -84,14 +84,14 @@ def test_calc_elastic(self): (-0.0025, -13.439544638502628), (0.0, -13.439999952735112), (0.0024999999999999996, -13.43954822781134), - (0.005, -13.438204192615181), + (0.005, -13.438204192615178), ], [ - (-0.005, -13.436741954502294), - (-0.0025, -13.439195465714551), + (-0.005, -13.437971451918395), + (-0.0025, -13.439501038418321), (0.0, -13.439999952735112), - (0.0024999999999999996, -13.439213491269701), - (0.005, -13.436885713447486), + (0.0024999999999999996, -13.439515785430654), + (0.005, -13.438089441277942), ], ] ), @@ -99,13 +99,13 @@ def test_calc_elastic(self): ) self.assertTrue( np.isclose( - workflow._data["A2"], np.array([2.20130388, 1.08985578, 1.91883479]) + workflow._data["A2"], np.array([2.20130388, 1.08985578, 1.1861949]) ).all() ) self.assertAlmostEqual(elastic_dict["bulkmodul_voigt"], 78.37505857279467) - self.assertAlmostEqual(elastic_dict["shearmodul_voigt"], 41.46154012284969) - self.assertAlmostEqual(elastic_dict["youngsmodul_voigt"], 105.73882997912072) - self.assertAlmostEqual(elastic_dict["poissonsratio_voigt"], 0.2751435386362729) + self.assertAlmostEqual(elastic_dict["shearmodul_voigt"], 29.723355082523486) + self.assertAlmostEqual(elastic_dict["youngsmodul_voigt"], 79.16270932956571) + self.assertAlmostEqual(elastic_dict["poissonsratio_voigt"], 0.3316583728482119) self.assertTrue( np.isclose( elastic_dict["elastic_matrix_inverse"], @@ -114,19 +114,19 @@ def test_calc_elastic(self): [0.01385733, -0.00480214, -0.00480214, 0.0, 0.0, 0.0], [-0.00480214, 0.01385733, -0.00480214, 0.0, 0.0, 0.0], [-0.00480214, -0.00480214, 0.01385733, 0.0, 0.0, 0.0], - [0.0, 0.0, 0.0, 0.01951656, 0.0, 0.0], - [0.0, 0.0, 0.0, 0.0, 0.01951656, 0.0], - [0.0, 0.0, 0.0, 0.0, 0.0, 0.01951656], + [0.0, 0.0, 0.0, 0.03157074, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.03157074, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0, 0.03157074], ] ), ).all() ) self.assertAlmostEqual(elastic_dict["bulkmodul_reuss"], 78.37505857279469) - self.assertAlmostEqual(elastic_dict["shearmodul_reuss"], 37.54104251720356) - self.assertAlmostEqual(elastic_dict["youngsmodul_reuss"], 97.11702764970639) - self.assertAlmostEqual(elastic_dict["poissonsratio_reuss"], 0.29347803281170937) + self.assertAlmostEqual(elastic_dict["shearmodul_reuss"], 29.524633432574454) + self.assertAlmostEqual(elastic_dict["youngsmodul_reuss"], 78.69249533327846) + self.assertAlmostEqual(elastic_dict["poissonsratio_reuss"], 0.3326582955380103) self.assertAlmostEqual(elastic_dict["bulkmodul_hill"], 78.37505857279467) - self.assertAlmostEqual(elastic_dict["shearmodul_hill"], 39.501291320026624) - self.assertAlmostEqual(elastic_dict["youngsmodul_hill"], 101.45869947879392) - self.assertAlmostEqual(elastic_dict["poissonsratio_hill"], 0.2842453510798992) - self.assertAlmostEqual(elastic_dict["AVR"], 4.962492964955925) + self.assertAlmostEqual(elastic_dict["shearmodul_hill"], 29.623994257548972) + self.assertAlmostEqual(elastic_dict["youngsmodul_hill"], 78.9276905674883) + self.assertAlmostEqual(elastic_dict["poissonsratio_hill"], 0.33215814655674686) + self.assertAlmostEqual(elastic_dict["AVR"], 0.3354065765429198) diff --git a/tests/test_elastic_lammps_functional.py b/tests/test_elastic_lammps_functional.py index e8ae5d50..af4aa3fe 100644 --- a/tests/test_elastic_lammps_functional.py +++ b/tests/test_elastic_lammps_functional.py @@ -56,9 +56,9 @@ def test_calc_elastic_functions(self): [114.10311701, 60.51102935, 60.51102935, 0.0, 0.0, 0.0], [60.51102935, 114.10311701, 60.51102935, 0.0, 0.0, 0.0], [60.51102935, 60.51102935, 114.10311701, 0.0, 0.0, 0.0], - [0.0, 0.0, 0.0, 51.23853765, 0.0, 0.0], - [0.0, 0.0, 0.0, 0.0, 51.23853765, 0.0], - [0.0, 0.0, 0.0, 0.0, 0.0, 51.23853765], + [0.0, 0.0, 0.0, 31.67489592, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 31.67489592, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0, 31.67489592], ] ), ).all() @@ -90,14 +90,14 @@ def test_calc_elastic_functions(self): (-0.0025, -13.439544638502628), (0.0, -13.439999952735112), (0.0024999999999999996, -13.43954822781134), - (0.005, -13.438204192615181), + (0.005, -13.438204192615178), ], [ - (-0.005, -13.436741954502294), - (-0.0025, -13.439195465714551), + (-0.005, -13.437971451918395), + (-0.0025, -13.439501038418321), (0.0, -13.439999952735112), - (0.0024999999999999996, -13.439213491269701), - (0.005, -13.436885713447486), + (0.0024999999999999996, -13.439515785430654), + (0.005, -13.438089441277942), ], ] ), @@ -105,13 +105,13 @@ def test_calc_elastic_functions(self): ) self.assertTrue( np.isclose( - sym_dict["A2"], np.array([2.20130388, 1.08985578, 1.91883479]) + sym_dict["A2"], np.array([[2.20130388, 1.08985578, 1.1861949]]) ).all() ) self.assertAlmostEqual(elastic_dict["bulkmodul_voigt"], 78.37505857279467) - self.assertAlmostEqual(elastic_dict["shearmodul_voigt"], 41.46154012284969) - self.assertAlmostEqual(elastic_dict["youngsmodul_voigt"], 105.73882997912072) - self.assertAlmostEqual(elastic_dict["poissonsratio_voigt"], 0.2751435386362729) + self.assertAlmostEqual(elastic_dict["shearmodul_voigt"], 29.723355082523486) + self.assertAlmostEqual(elastic_dict["youngsmodul_voigt"], 79.16270932956571) + self.assertAlmostEqual(elastic_dict["poissonsratio_voigt"], 0.3316583728482119) self.assertTrue( np.isclose( elastic_dict["elastic_matrix_inverse"], @@ -120,19 +120,19 @@ def test_calc_elastic_functions(self): [0.01385733, -0.00480214, -0.00480214, 0.0, 0.0, 0.0], [-0.00480214, 0.01385733, -0.00480214, 0.0, 0.0, 0.0], [-0.00480214, -0.00480214, 0.01385733, 0.0, 0.0, 0.0], - [0.0, 0.0, 0.0, 0.01951656, 0.0, 0.0], - [0.0, 0.0, 0.0, 0.0, 0.01951656, 0.0], - [0.0, 0.0, 0.0, 0.0, 0.0, 0.01951656], + [0.0, 0.0, 0.0, 0.03157074, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.03157074, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0, 0.03157074], ] ), ).all() ) self.assertAlmostEqual(elastic_dict["bulkmodul_reuss"], 78.37505857279469) - self.assertAlmostEqual(elastic_dict["shearmodul_reuss"], 37.54104251720356) - self.assertAlmostEqual(elastic_dict["youngsmodul_reuss"], 97.11702764970639) - self.assertAlmostEqual(elastic_dict["poissonsratio_reuss"], 0.29347803281170937) + self.assertAlmostEqual(elastic_dict["shearmodul_reuss"], 29.524633432574454) + self.assertAlmostEqual(elastic_dict["youngsmodul_reuss"], 78.69249533327846) + self.assertAlmostEqual(elastic_dict["poissonsratio_reuss"], 0.3326582955380103) self.assertAlmostEqual(elastic_dict["bulkmodul_hill"], 78.37505857279467) - self.assertAlmostEqual(elastic_dict["shearmodul_hill"], 39.501291320026624) - self.assertAlmostEqual(elastic_dict["youngsmodul_hill"], 101.45869947879392) - self.assertAlmostEqual(elastic_dict["poissonsratio_hill"], 0.2842453510798992) - self.assertAlmostEqual(elastic_dict["AVR"], 4.962492964955925) + self.assertAlmostEqual(elastic_dict["shearmodul_hill"], 29.623994257548972) + self.assertAlmostEqual(elastic_dict["youngsmodul_hill"], 78.9276905674883) + self.assertAlmostEqual(elastic_dict["poissonsratio_hill"], 0.33215814655674686) + self.assertAlmostEqual(elastic_dict["AVR"], 0.3354065765429198)