From 5889bdde3bcddda387da0b537f9669d27a0e9715 Mon Sep 17 00:00:00 2001 From: ramanishsingh Date: Sat, 21 Sep 2024 01:42:39 -0500 Subject: [PATCH 1/3] update MW for density calc --- .pre-commit-config.yaml | 17 ++++++++--------- .../mdmc_ethanol_subproject/clear_folder.py | 5 +++-- .../src/engines/mcccs/project.py | 2 +- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c09ead25..60eca64a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,7 +1,6 @@ ci: autofix_commit_msg: | [pre-commit.ci] auto fixes from pre-commit.com hooks - for more information, see https://pre-commit.ci autofix_prs: true autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate' @@ -9,25 +8,25 @@ ci: skip: [] submodules: false repos: -- repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 +- repo: git@github.com:pre-commit/pre-commit-hooks + rev: v4.0.1 hooks: - id: check-yaml - id: end-of-file-fixer - id: trailing-whitespace -- repo: https://github.com/psf/black - rev: 24.4.2 +- repo: git@github.com:psf/black + rev: 22.3.0 hooks: - id: black args: [--line-length=80, --target-version=py38] -- repo: https://github.com/pycqa/isort - rev: 5.13.2 +- repo: git@github.com:pycqa/isort + rev: 5.11.5 hooks: - id: isort name: isort (python) args: [--profile=black, --line-length=80] -- repo: https://github.com/pycqa/pydocstyle - rev: '6.3.0' +- repo: git@github.com:pycqa/pydocstyle + rev: '6.1.1' hooks: - id: pydocstyle args: [--convention=numpy] diff --git a/reproducibility_project/mdmc_ethanol_subproject/clear_folder.py b/reproducibility_project/mdmc_ethanol_subproject/clear_folder.py index 461e8d95..146153bf 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/clear_folder.py +++ b/reproducibility_project/mdmc_ethanol_subproject/clear_folder.py @@ -51,8 +51,9 @@ def main(): for job in group: os.chdir(job.workspace()) - os.chdir("..") - os.system("rm -rf {}".format(job)) + print(job) + # os.chdir("..") + os.system("rm -rf log-npt.txt") # print(os.listdir()) # os.system("cat sig*state*json") # os.system("cat sig*state*json") diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/project.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/project.py index 8eec0f70..2b3978f6 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/project.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/project.py @@ -329,7 +329,7 @@ def sanitize_gemc_log(step, job): """Sanitize the output logs for gemc simulations.""" import numpy as np - mw = job.sp.mass + mw = 46.068672 files = sorted(glob("fort*12*{}*".format(step))) arrays_box1 = [] arrays_box2 = [] From 8d95ca22064a5f570c7e1c9e166092e0a8a7d9e8 Mon Sep 17 00:00:00 2001 From: ramanishsingh Date: Sat, 21 Sep 2024 02:08:48 -0500 Subject: [PATCH 2/3] update MW in MCCCS-MN density calc --- .../mdmc_ethanol_subproject/src/engines/mcccs/project.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/project.py b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/project.py index 2b3978f6..dc3f7c2c 100644 --- a/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/project.py +++ b/reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/project.py @@ -287,7 +287,8 @@ def sanitize_npt_log(step, job): """Sanitize the output logs for NPT simulations.""" import numpy as np - mw = job.sp.mass + mw = 46.068672 + print("sanitizing for", job, "molecule =", job.sp.molecule, "mw=", mw) temp = job.sp.temperature files = sorted(glob("fort*12*{}*".format(step))) arrays = [] From 3a45ff60a24a0bd4d844a0e5b15832edbb95f454 Mon Sep 17 00:00:00 2001 From: Ramanish Singh <48493179+ramanishsingh@users.noreply.github.com> Date: Sat, 21 Sep 2024 00:10:01 -0700 Subject: [PATCH 3/3] Update .pre-commit-config.yaml --- .pre-commit-config.yaml | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 60eca64a..c09ead25 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,7 @@ ci: autofix_commit_msg: | [pre-commit.ci] auto fixes from pre-commit.com hooks + for more information, see https://pre-commit.ci autofix_prs: true autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate' @@ -8,25 +9,25 @@ ci: skip: [] submodules: false repos: -- repo: git@github.com:pre-commit/pre-commit-hooks - rev: v4.0.1 +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.6.0 hooks: - id: check-yaml - id: end-of-file-fixer - id: trailing-whitespace -- repo: git@github.com:psf/black - rev: 22.3.0 +- repo: https://github.com/psf/black + rev: 24.4.2 hooks: - id: black args: [--line-length=80, --target-version=py38] -- repo: git@github.com:pycqa/isort - rev: 5.11.5 +- repo: https://github.com/pycqa/isort + rev: 5.13.2 hooks: - id: isort name: isort (python) args: [--profile=black, --line-length=80] -- repo: git@github.com:pycqa/pydocstyle - rev: '6.1.1' +- repo: https://github.com/pycqa/pydocstyle + rev: '6.3.0' hooks: - id: pydocstyle args: [--convention=numpy]