From 49256eeaa987564cc500eccf16d265aea72558de Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sat, 23 Jul 2022 19:24:01 +0000 Subject: [PATCH] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/Makefile | 1 - docs/_images/pyMDMC_GITHUB_2021.bib | 1 - docs/_images/pyMDMC_GITHUB_2021.ris | 2 +- docs/_images/pyMDMC_PAPER_2022.bib | 1 - docs/_images/pyMDMC_ZENODO_2021.bib | 1 - docs/_images/pyMDMC_ZENODO_2021.ris | 2 +- docs/citing_MDMC_PYTHON.rst | 1 - docs/docs-env.yml | 1 - docs/example_simulation.rst | 1 - docs/generating_systems.rst | 1 - docs/index.rst | 1 - docs/installation.rst | 1 - docs/make.bat | 1 - docs/requirements.txt | 1 - docs/running_analysis_code.rst | 1 - docs/running_the_simulation.rst | 1 - docs/simulation_analysis.rst | 1 - docs/simulation_output.rst | 1 - docs/simulation_parameters_files.rst | 1 - 19 files changed, 2 insertions(+), 19 deletions(-) diff --git a/docs/Makefile b/docs/Makefile index 9e10b66..0e0d28a 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -175,4 +175,3 @@ pseudoxml: $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml @echo @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." - diff --git a/docs/_images/pyMDMC_GITHUB_2021.bib b/docs/_images/pyMDMC_GITHUB_2021.bib index 513e43c..ace63c1 100644 --- a/docs/_images/pyMDMC_GITHUB_2021.bib +++ b/docs/_images/pyMDMC_GITHUB_2021.bib @@ -4,4 +4,3 @@ @Inbook{pyMDMC_GITHUB_2021 year = "2021", url = "https://github.com/GOMC-WSU/py-MCMD" } - diff --git a/docs/_images/pyMDMC_GITHUB_2021.ris b/docs/_images/pyMDMC_GITHUB_2021.ris index 8efe68d..00276d1 100644 --- a/docs/_images/pyMDMC_GITHUB_2021.ris +++ b/docs/_images/pyMDMC_GITHUB_2021.ris @@ -1,7 +1,7 @@ TY - AU - Crawford, B. AU - Potoff J. -AU - +AU - AU - AU - AU - diff --git a/docs/_images/pyMDMC_PAPER_2022.bib b/docs/_images/pyMDMC_PAPER_2022.bib index 82354f7..373332e 100644 --- a/docs/_images/pyMDMC_PAPER_2022.bib +++ b/docs/_images/pyMDMC_PAPER_2022.bib @@ -5,4 +5,3 @@ @article{pyMDMC_PAPER_2021 doi = "https://doi.org/10.1021/acs.jctc.1c00911" url = "https://pubs.acs.org/doi/10.1021/acs.jctc.1c00911" } - diff --git a/docs/_images/pyMDMC_ZENODO_2021.bib b/docs/_images/pyMDMC_ZENODO_2021.bib index ef62323..76b7c74 100644 --- a/docs/_images/pyMDMC_ZENODO_2021.bib +++ b/docs/_images/pyMDMC_ZENODO_2021.bib @@ -5,4 +5,3 @@ @Inbook{pyMDMC_ZENODO_2021 url = "https://doi.org/10.5281/zenodo.5142483" doi = "10.5281/zenodo.5142483" } - diff --git a/docs/_images/pyMDMC_ZENODO_2021.ris b/docs/_images/pyMDMC_ZENODO_2021.ris index ac32fc4..f9b1d89 100644 --- a/docs/_images/pyMDMC_ZENODO_2021.ris +++ b/docs/_images/pyMDMC_ZENODO_2021.ris @@ -1,7 +1,7 @@ TY - AU - Crawford, B. AU - Potoff J. -AU - +AU - AU - AU - AU - diff --git a/docs/citing_MDMC_PYTHON.rst b/docs/citing_MDMC_PYTHON.rst index 186c007..da737e2 100644 --- a/docs/citing_MDMC_PYTHON.rst +++ b/docs/citing_MDMC_PYTHON.rst @@ -73,4 +73,3 @@ We also recommend citing the `Concatenate DCD files (CatDCD) - diff --git a/docs/generating_systems.rst b/docs/generating_systems.rst index fb52fba..36d5a05 100644 --- a/docs/generating_systems.rst +++ b/docs/generating_systems.rst @@ -26,4 +26,3 @@ Non-Traditional Chemical Engineering Systems ------- Non-Traditional chemical engineering systems are proteins or other molecules requiring multiple residue names per molecule. Currently, the GOMC-MoSDeF software is not compatible with these systems. Therefore, these systems should be constructed using different software, such as `Visual Molecular Dynamics (VMD) `_, or other similar software. - diff --git a/docs/index.rst b/docs/index.rst index e658f43..fdf6a4f 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -32,4 +32,3 @@ The py-MCMD Python package consists of two (2) different licenses (:download:`Co CatDCD_instructions_license generating_systems citing_MDMC_PYTHON - diff --git a/docs/installation.rst b/docs/installation.rst index f795e98..ef13b80 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -30,4 +30,3 @@ This Python code is currently compatible only with `NAMD version 2.14 both box 0 and box 1). The GCMC, NVT, NPT, or the GEMC ensembles when using only one (1) NAMD simulation box (i.e., only_use_box_0_for_namd_for_gemc = True --> only box 0) are always run in series, since there is nothing to run in parallel. Note: This feature was added so the user can minimize the load on the GPU by running both NAMD simulations in parallel. - diff --git a/docs/simulation_analysis.rst b/docs/simulation_analysis.rst index eb4ea1a..759f821 100644 --- a/docs/simulation_analysis.rst +++ b/docs/simulation_analysis.rst @@ -154,4 +154,3 @@ The variables below are contained in the *"user_input_combine_data_NAMD_GOMC.jso This input is used when combining the 'Hybrid' data. This is required when combining the 'GOMC-only', or 'NAMD-only' data, but is not used. - diff --git a/docs/simulation_output.rst b/docs/simulation_output.rst index 227b06d..8409e16 100644 --- a/docs/simulation_output.rst +++ b/docs/simulation_output.rst @@ -26,4 +26,3 @@ The hybrid simulation Python code outputs the main NAMD and GOMC folders, each c Retaining all the individual simulation runs can add up to considerable storage requirements. Therefore, we recommended optimizing the number of steps and moves for each simulation engine and calculating the entire run's storage requirements before starting the production runs. *In the future, we plan on programming an auto-cleanup and that will combine all the individual runs on the fly and minimize the storage requirement.* - diff --git a/docs/simulation_parameters_files.rst b/docs/simulation_parameters_files.rst index 500a212..786f4d3 100644 --- a/docs/simulation_parameters_files.rst +++ b/docs/simulation_parameters_files.rst @@ -260,4 +260,3 @@ The MD/MC Hybrid input file is in the `json