Converting to flowerMD code

README.md

@@ -1,58 +1,6 @@
 # PhantomWalk
-Polymer system initialization workflow that utilizes a random walk and dissipative particle dynamics as a soft push potential.
+This repository has supporting data and examples for the PhantomWalk workflow that is implemented in flowerMD. PhantomWalk is a polymer system initialization workflow that utilizes a random walk and dissipative particle dynamics as a soft push potential.
 
 ## Environment
 
-Build a software environment using the `environment.yml` file and the command ```conda env create -f environment.yml```
-
-## Examples
-1 - Run a dpd simulation and check the bond lengths and inter-particle distances.
-2 - Run a dpd simulation with an energy stabilization cutoff. Write out simulation to trajectory file.
-3 - Run a dpd simulation with option for angles and dihedrals. Write out to trajectory file. Start a Lennard-Jones WCA simulation with optional angles and dihedrals.
-4 - Replace the random walk in the DPD workflow with mbuild self-avoiding random walk.
-5 - Run DPD on a rigid body model used for anisotropic coarse-graining. Based on flowerMD classes.
-
-## Installation
-
-First, clone the PhantomWalk repository:
-
-``` sh
-git clone git@github.com:cmelab/PhantomWalk
-cd PhantomWalk
-```
-
-Set up & activate the conda environment shipped with PhantomWalk:
-
-``` sh
-conda env create -f ./environment.yml
-conda activate phantomwalk
-```
-
-Install PhantomWalk into the environment with `pip`:
-
-``` sh
-python -m pip install -e .
-```
-
-### Development Environment
-
-If PhantomWalk is being installed for development purposes, the dev environment
-should be used instead, which provides packages necessary for [testing](#tests).
-
-``` sh
-conda env create -f ./environment-dev.yml
-conda activate
-```
-
-## Tests
-
-Before running tests, ensure you have activated the [PhantomWalk dev environment](#development-environment).
-
-PhantomWalk tests can be run by invoking `pytest` in the PhantomWalk repo:
-
-``` sh
-pytest
-```
-
-See the [pytest documentation](https://docs.pytest.org/en/latest/contents.html)
-for more details on how `pytest` works and how to use it.
+Build a software environment using the `environment-dev.yml' file and instructions in flowerMD[https://github.com/cmelab/flowerMD].

phantomwalk/conda-envs/environment-signac.yml

@@ -0,0 +1,41 @@
+name: phantomwalk-signac
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+    # Basic Python dependencies
+    # - python>=3.12
+    - python>=3.11,<3.14
+    - pip
+    - jupyterlab
+
+    # Mathematics and scientific computing
+    - numpy>=2.0
+    - scipy>=1.16.0 # required to allow use of RigidTransform
+    - sympy
+
+    # Visualization
+    - matplotlib
+    - py3Dmol
+
+    # Chemistry
+    - rdkit
+    - periodictable
+    - openbabel>=3
+
+    # Molecular Dynamics toolkits
+    ## HOOMD
+    - hoomd>=5.0,!=5.3.0
+    - gsd>=3.0,<5
+    - freud
+    - fresnel
+    - cmeutils>=1.3
+    - grits >=0.6.0
+
+    - signac=2.1.0
+
+    - pip:
+      - "flowermd @ git+https://github.com/cmelab/flowerMD.git" # experimental DPD functionality not yet in FlowerMD conda releases
+      - "gmso @ git+https://github.com/mosdef-hub/gmso.git"
+      - "mbuild @ git+https://github.com/mosdef-hub/mbuild.git@develop"
+      - "signac-flow @ git+https://github.com/glotzerlab/signac-flow.git@61fe01b" 

phantomwalk/conda-envs/environment.yml

@@ -0,0 +1,37 @@
+name: phantomwalk
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+    # Basic Python dependencies
+    - python>=3.11,<3.14 
+    - pip 
+    - jupyterlab 
+
+    # Mathematics and scientific computing 
+    - numpy>=2.0 
+    - scipy>=1.16.0 # required to allow use of RigidTransform 
+    - sympy 
+
+    # Visualization 
+    - matplotlib 
+    - py3Dmol 
+
+    # Chemistry 
+    - rdkit 
+    - periodictable 
+    - openbabel>=3 
+
+    # Molecular Dynamics toolkits 
+    ## HOOMD 
+    - hoomd>=5.0,!=5.3.0 
+    - gsd>=3.0,<5 
+    - freud 
+    - fresnel 
+    - cmeutils>=1.3 
+    - grits >=0.6.0 
+
+    - pip: 
+      - "flowermd @ git+https://github.com/cmelab/flowerMD.git" # experimental DPD functionality not yet in FlowerMD conda releases 
+      - "gmso @ git+https://github.com/mosdef-hub/gmso.git" 
+      - "mbuild @ git+https://github.com/mosdef-hub/mbuild.git@develop"