Add diffusion simulation with Molecular Dynamics (#2)

* Add/update files in bin/ folder Signed-off-by: Vassilis Vassiliadis <[email protected]> * Add/update forcefield/ folder Signed-off-by: Vassilis Vassiliadis <[email protected]> * Rename FlowIR YAML file Signed-off-by: Vassilis Vassiliadis <[email protected]> * Add new experiments Signed-off-by: Vassilis Vassiliadis <[email protected]> * Update original FlowIR YAML Signed-off-by: Vassilis Vassiliadis <[email protected]> * Update container image registry to Quay.io Signed-off-by: Vassilis Vassiliadis <[email protected]> * Remove outdate instructions from conf/ Signed-off-by: Vassilis Vassiliadis <[email protected]> * Add/update files in hooks/ folder Signed-off-by: Vassilis Vassiliadis <[email protected]> * Update dependencies Signed-off-by: Vassilis Vassiliadis <[email protected]> * Update conf/ folder Signed-off-by: Vassilis Vassiliadis <[email protected]> * Update notebook Signed-off-by: Vassilis Vassiliadis <[email protected]> * Update Markdown files Signed-off-by: Vassilis Vassiliadis <[email protected]> * Update WhiteSource branch Signed-off-by: Vassilis Vassiliadis <[email protected]> * Remove manifest YAML Signed-off-by: Vassilis Vassiliadis <[email protected]> * Update README.md Signed-off-by: Rodrigo Neumann <[email protected]> Signed-off-by: Vassilis Vassiliadis <[email protected]> * docs: tidyup packages layout and documentation (#3) Signed-off-by: Vassilis Vassiliadis <[email protected]> * feat: use strongly versioned images It's best to use a specific version of an image rather than :latest. Overtime :latest can drift and that can cause problems when your components expect a different version of the containers than the one currently on your container registry Signed-off-by: Vassilis Vassiliadis <[email protected]> * fix: replace \" with " in value of gasComposition Signed-off-by: Vassilis Vassiliadis <[email protected]> * fix: JSON payload for api.experiment_push() Signed-off-by: Vassilis Vassiliadis <[email protected]> * docs: fix typo Signed-off-by: Vassilis Vassiliadis <[email protected]> * docs: undo change about manifest.yaml Signed-off-by: Vassilis Vassiliadis <[email protected]> * docs: remove deprecated instructions for docker Signed-off-by: Vassilis Vassiliadis <[email protected]> * Update path to scripts * Pin Python dependency versions * Fix path to be linted by TravisCI --------- Signed-off-by: Vassilis Vassiliadis <[email protected]> Signed-off-by: Rodrigo Neumann <[email protected]> Co-authored-by: Vassilis Vassiliadis <[email protected]> Co-authored-by: Vassilis Vassiliadis <[email protected]>
st4sd · Dec 11, 2024 · 9348fe0 · 9348fe0
1 parent 3d19176
commit 9348fe0
Show file tree

Hide file tree

Showing 59 changed files with 2,171 additions and 561 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -33,7 +33,7 @@ before_script:
 
 script:
   # Run Python linter
-  - flake8 --max-line-length=100 bin/
+  - flake8 --max-line-length=100 reference-scripts/
 
   # Connect to quay.io
   - docker login -u "$QUAY_USERNAME" -p "$QUAY_API_KEY" quay.io

diff --git a/.whitesource b/.whitesource
@@ -1,3 +1,3 @@
 {
-  "settingsInheritedFrom": "whitesource-config/whitesource-config@python3"
-}
+  "settingsInheritedFrom": "whitesource-config/whitesource-config@master"
+}
diff --git a/MAINTAINERS.md b/MAINTAINERS.md
@@ -2,6 +2,6 @@
 
 Following is the current list of maintainers on this project (in alphabetical order):
 
-- Manuela Blanco ([manuela-blanco](https://github.com/manuela-blanco))
 - Rodrigo Neumann ([neumannrf](https://github.com/neumannrf))
 - Felipe Lopes de Oliveira ([lipelopesoliveira](https://github.com/lipelopesoliveira))
+- Manuela Blanco Rodriguez ([manuela-blanco](https://github.com/manuela-blanco))
diff --git a/Pipfile b/Pipfile
@@ -7,13 +7,14 @@ verify_ssl = true
 python_version = "3.9"
 
 [dev-packages]
-raspa2 = "*"
+raspa2 = "==2.0.4"
 
 [packages]
-gemmi = "*"
-numpy = "*"
-pandas = "*"
-pyeqeq = "*"
-pymser = "*"
-requests = "*"
-scipy = "*"
+gemmi = "==0.6.3"
+numpy = "==1.25.2"
+pandas = "==2.1.0"
+pyeqeq = "==0.0.10"
+pymatgen = "==2023.9.10"
+pymser = "==1.0.19"
+requests = "==2.25.1"
+scipy = "==1.11.2"
diff --git a/README.md b/README.md
@@ -12,11 +12,45 @@ Automated virtual experiment that simulates adsorption isotherms on nanoporous m
 
 ## Launching the virtual experiment
 
-First you need to import the virtual experiment in your ST4SD registry [from the global ST4SD registry](https://st4sd.github.io/overview/using-the-virtual-experiments-registry-ui). You will then be able to start the parameterised package `nanopore-adsorption-experiment` in your private ST4SD registry (see [example notebook](nanopore-adsorption-experiment.ipynb) or [instructions to run experiment using docker](run-using-docker.md)).
+### On a local machine
+
+## Instructions
+
+If you have a container runtime such as docker, podman, rancher desktop, etc available on your system you can execute the experiment by:
+
+1. creating a python virtual environment, activating it, and installing the python module `st4sd-runtime-core[develop]>=2.2.0`
+2. cloning this repository
+3. launching the experiment
+For example:
+
+```bash
+#!/usr/bin/env sh
+: # Download virtual experiment
+git clone https://github.com/st4sd/nanopore-adsorption-experiment.git
+: # Setup ST4SD runtime-core
+python3 -m venv --copies venv
+. venv/bin/activate
+python3 -m pip install "st4sd-runtime-core[develop]>=2.2.0"
+: # Go inside the directory of this repository. 
+: # The next command executes the experiment in there
+cd nanopore-adsorption-experiment
+: # Run the experiment
+elaunch.py --applicationDependencySource="nanopore-database=cif:copy" \
+      --manifest=manifest.yaml \
+      --input=docker_example/cif_files.dat \
+      workflow_definitions/adsorption.yaml
+```
+
+**Note**: Make sure you run the `git clone` command in a directory that your container runtime (e.g.`docker`, `podman`, etc) can mount later when you execute the experiment.
+**Note**: Using a container runtime is intended for small scale experiments and/or debugging your experiments. Use the `kubernetes` example below to launch larger experiments.
+
+### On Kubernetes
+
+Follow our end to end [example notebook](nanopore-adsorption-experiment.ipynb) to launch our `nanopore-adsorption-experiment` experiment on your ST4SD Cloud instance.
 
 ## Using custom database of CIF files
 
-You may download the CIF files of your choosing to a PVC inside your OpenShift cluster (below we use the name `nanopore-database-pvc`), mount it as a volume and ask the virtual experiment instance to use the contents of the PVC as the contents of the `nanopore-database` application-dependency. You will also need to remove the line related to `nanopore-database` from the `manifest.yaml` to enable the use of the PVC.
+You may download the CIF files of your choosing to a PVC inside your OpenShift cluster (below we use the name `nanopore-database-pvc`), mount it as a volume and ask the virtual experiment instance to use the contents of the PVC as the contents of the `nanopore-database` application-dependency.
 
 ```Python
 file_names = [""]

diff --git a/bin/charge_equilibration.sh b/bin/charge_equilibration.sh
diff --git a/bin/create_supercell.py b/bin/create_supercell.py
diff --git a/bin/create_supercell.sh b/bin/create_supercell.sh
diff --git a/bin/make_grid.sh b/bin/make_grid.sh
diff --git a/bin/modules/calculate_properties.py b/bin/modules/calculate_properties.py