From eeb347dd6c5fffbae72bcc8b475950e8c4449566 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 26 Jun 2024 07:59:01 +0200 Subject: [PATCH 1/8] Update pyproject.toml --- pyproject.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e77b284c3..25aa9735c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ classifiers = [ ] dependencies = [ "ase==3.23.0", - "atomistics==0.1.29", + "atomistics==0.1.30", "defusedxml==0.7.1", "h5py==3.11.0", "matplotlib==3.8.4", @@ -38,11 +38,11 @@ dependencies = [ "pyiron_base==0.9.4", "pyiron_snippets==0.1.2", "pylammpsmpi==0.2.19", - "scipy==1.13.1", + "scipy==1.14.0", "scikit-learn==1.5.0", "seekpath==2.1.0", "spglib==2.4.0", - "structuretoolkit==0.0.25", + "structuretoolkit==0.0.26", ] dynamic = ["version"] From a54c81efa837a8689c5087aeff2c8783c35143c8 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 26 Jun 2024 07:59:45 +0200 Subject: [PATCH 2/8] Update environment.yml --- .ci_support/environment.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index fd599bd57..9c216a728 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -3,7 +3,7 @@ channels: dependencies: - aimsgb =1.1.0 - ase =3.23.0 -- atomistics =0.1.29 +- atomistics =0.1.30 - coverage - codacy-coverage - defusedxml =0.7.1 @@ -20,8 +20,8 @@ dependencies: - pylammpsmpi =0.2.19 - pyscal =2.10.18 - scikit-learn =1.5.0 -- scipy =1.13.1 +- scipy =1.14.0 - seekpath =2.1.0 - spglib =2.4.0 -- structuretoolkit =0.0.25 +- structuretoolkit =0.0.26 - pyxtal =0.6.2 From 4ef68c89c076d505d2eb79153bd00a10874d8e7d Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 26 Jun 2024 08:00:18 +0200 Subject: [PATCH 3/8] Update environment-docs.yml --- .ci_support/environment-docs.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index b7a1e1495..3571c8e02 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -7,7 +7,7 @@ dependencies: - myst-parser - aimsgb =1.1.0 - ase =3.23.0 -- atomistics =0.1.29 +- atomistics =0.1.30 - defusedxml =0.7.1 - h5py =3.11.0 - matplotlib-base =3.8.4 @@ -22,9 +22,9 @@ dependencies: - pylammpsmpi =0.2.19 - pyscal =2.10.18 - scikit-learn =1.5.0 -- scipy =1.13.1 +- scipy =1.14.0 - seekpath =2.1.0 - spglib =2.4.0 -- structuretoolkit =0.0.25 +- structuretoolkit =0.0.26 - pyxtal =0.6.2 - jupyter-book =1.0.0 From 5ac66f27a93664e32735b51c1418287b91a41368 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 26 Jun 2024 08:01:33 +0200 Subject: [PATCH 4/8] Update environment.yml --- binder/environment.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/binder/environment.yml b/binder/environment.yml index c8ecd90e4..dcffb5bfd 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -3,7 +3,7 @@ channels: dependencies: - aimsgb =1.1.0 - ase =3.23.0 -- atomistics =0.1.29 +- atomistics =0.1.30 - defusedxml =0.7.1 - h5py =3.11.0 - matplotlib-base =3.8.4 @@ -15,13 +15,13 @@ dependencies: - pint =0.24 - pyiron_base =0.9.4 - pyiron_snippets =0.1.2 -- pylammpsmpi =0.2.19 +- pylammpsmpi =0.2.20 - pyscal =2.10.18 - scikit-learn =1.5.0 -- scipy =1.13.1 +- scipy =1.14.0 - seekpath =2.1.0 - spglib =2.4.0 -- structuretoolkit =0.0.25 +- structuretoolkit =0.0.26 - pyxtal =0.6.2 - pyiron-data >=0.0.22 - sqsgenerator From d2a6459e604e12a3f33648bd83a2a6cb0c0b3122 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 26 Jun 2024 08:01:49 +0200 Subject: [PATCH 5/8] Update environment.yml --- .ci_support/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 9c216a728..179e94547 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -17,7 +17,7 @@ dependencies: - pint =0.24 - pyiron_base =0.9.4 - pyiron_snippets =0.1.2 -- pylammpsmpi =0.2.19 +- pylammpsmpi =0.2.20 - pyscal =2.10.18 - scikit-learn =1.5.0 - scipy =1.14.0 From dc5564626e582b72d131fc547004f2e046f668c6 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 26 Jun 2024 08:02:02 +0200 Subject: [PATCH 6/8] Update environment-docs.yml --- .ci_support/environment-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml index 3571c8e02..c409ac949 100644 --- a/.ci_support/environment-docs.yml +++ b/.ci_support/environment-docs.yml @@ -19,7 +19,7 @@ dependencies: - pint =0.24 - pyiron_base =0.9.4 - pyiron_snippets =0.1.2 -- pylammpsmpi =0.2.19 +- pylammpsmpi =0.2.20 - pyscal =2.10.18 - scikit-learn =1.5.0 - scipy =1.14.0 From 9da9e189cbb9181aa3dc4c3a797065d41f1db4b4 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 26 Jun 2024 08:02:20 +0200 Subject: [PATCH 7/8] Update pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 25aa9735c..8ff5c0648 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,7 +37,7 @@ dependencies = [ "pint==0.24", "pyiron_base==0.9.4", "pyiron_snippets==0.1.2", - "pylammpsmpi==0.2.19", + "pylammpsmpi==0.2.20", "scipy==1.14.0", "scikit-learn==1.5.0", "seekpath==2.1.0", From 194f7e78b6b269b414c25e2a2032a5bb75db0b09 Mon Sep 17 00:00:00 2001 From: Jan Janssen Date: Wed, 26 Jun 2024 08:08:59 +0200 Subject: [PATCH 8/8] Update report.py --- pyiron_atomistics/vasp/parser/report.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyiron_atomistics/vasp/parser/report.py b/pyiron_atomistics/vasp/parser/report.py index 0065c6258..fe6d15d1f 100644 --- a/pyiron_atomistics/vasp/parser/report.py +++ b/pyiron_atomistics/vasp/parser/report.py @@ -3,7 +3,7 @@ # Distributed under the terms of "New BSD License", see the LICENSE file. import numpy as np -from scipy.integrate import cumtrapz +from scipy.integrate import cumulative_trapezoid __author__ = "Sudarsan Surendralal" __copyright__ = ( @@ -43,7 +43,7 @@ def from_file(self, filename="REPORT"): ] rel_lines = [lines[i] for i, line in enumerate(lines) if "cc>" in line] cv = np.genfromtxt(rel_lines, usecols=[2]) - fe = cumtrapz(lam, cv) + fe = cumulative_trapezoid(lam, cv) self.parse_dict["cv_full"] = cv self.parse_dict["derivative"] = lam self.parse_dict["cv"] = cv[:-1]