Merge pull request #42 from bc118/update_docs_2

changed the NAMD_GOMC titles and file names py-MCMD. Added citation f…

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+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'
+    autoupdate_schedule: weekly
+    skip: []
+    submodules: false
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.1.0
+  hooks:
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+      exclude: setup.cfg
+- repo: https://github.com/psf/black
+  rev: 22.3.0
+  hooks:
+    - id: black
+      args: [--line-length=80]
+- repo: https://github.com/pycqa/isort
+  rev: 5.10.1
+  hooks:
+    - id: isort
+      name: isort (python)
+      args: [--profile=black, --line-length=80]

CITATION.cff

@@ -1,12 +1,14 @@
-cff-version: 1.1.0
+cff-version: 1.2.0
 message: "If you use this software, please cite it as below."
 authors:
   - family-names: Crawford
     given-names: Brad
     orcid: https://orcid.org/0000-0003-0638-7333
-  - family-names: Potoff 
+  - family-names: Potoff
     given-names: Jeffrey
     orcid: https://orcid.org/0000-0002-4421-8787
 title: py-MCMD: A Python Library for Performing Hybrid Monte Carlo - Molecular Dynamics Simulations with GOMC and NAMD
-version: 0.0.1
+        url: https://doi.org/10.5281/zenodo.5142483
+	doi: 10.5281/zenodo.5142483
+version: 0.0.2
 date-released: 2021-7-28

LICENSE

@@ -1,4 +1,4 @@
-Note: There are 2 different licenses, one (1) for NAMD_GOMC and 
+Note: There are 2 different licenses, one (1) for NAMD_GOMC and
 one (1) the CatDCD - Concatenate DCD files
 
 NAMD_GOMC LICENSE:

README.md

@@ -2,8 +2,6 @@
 --------
 
 This Python code enables hybrid molecular dynamics/Monte Carlo (MD/MC) simulations using [NAMD](https://www.ks.uiuc.edu/Research/namd/) and the [GPU Optimized Monte Carlo (GOMC)](http://gomc.eng.wayne.edu) software.
-The Python code allows users to switch back and forth between the NAMD and GOMC simulation engines, with one (1) iteration of each NAMD and GOMC consisting of a cycle.  The user programs the number of cycles and the number of NAMD and GOMC steps per cycle.  Combining the MD/MC simulations allows the best of both types of simulations while minimizing the downsides, and in some cases, enabling simulations that were previously not feasible. This code allows the modification of the NAMD and GOMC control files, maximizing user flexibility and functionality. 
+The Python code allows users to switch back and forth between the NAMD and GOMC simulation engines, with one (1) iteration of each NAMD and GOMC consisting of a cycle.  The user programs the number of cycles and the number of NAMD and GOMC steps per cycle.  Combining the MD/MC simulations allows the best of both types of simulations while minimizing the downsides, and in some cases, enabling simulations that were previously not feasible. This code allows the modification of the NAMD and GOMC control files, maximizing user flexibility and functionality.
 
 Please see the [py-MCMD Read the Docs](https://py-mcmd.readthedocs.io/en/latest/) webpage for more information and instructions.
-
-