Add example file for cyanobacterial co-culture

.github/workflows/docker-image-ci.yml

@@ -0,0 +1,33 @@
+name: Docker Image CI
+
+on:
+  push:
+    branches: [ cyano ]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      -
+        name: Checkout 
+        uses: actions/checkout@v2
+      -
+        name: Login to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Build and push
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: ${{ secrets.DOCKER_HUB_USERNAME }}/nufeb:latest

.github/workflows/sync.yml

@@ -0,0 +1,43 @@
+name: Merge Upstream
+
+# Controls when the action will run. 
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  schedule:
+    - cron: '*/30 * * * *' # every 30 minutes
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  merge-master:
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v2
+        - name: Merge upstream
+          run: |
+            git config --global user.name Jsakkos
+            git config --global user.email jonathansakkos@protonmail.com
+            # "git checkout master" is unnecessary, already here by default
+            git pull --unshallow  # this option is very important, you would get
+                                  # complains about unrelated histories without it.
+                                  # (but actions/checkout@v2 can also be instructed
+                                  # to fetch all git depth right from the start)
+            git remote add upstream https://github.com/nufeb/NUFEB
+            git fetch upstream
+            git merge --no-edit upstream/master
+            git push origin master
+  merge-cyano:
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v2
+        - name: Merge master
+          run: |
+            git checkout -b cyano
+            git fetch origin
+            git merge origin/master
+            git push origin cyano

.gitignore

@@ -33,3 +33,9 @@
 .project
 .cproject
 .settings/
+# Simulation outputs
+*.vtu
+*.vti
+*.vtr
+\Sucrose*
+*.csv

Dockerfile

@@ -0,0 +1,34 @@
+FROM ubuntu:20.04
+RUN useradd --create-home --shell /bin/bash admin
+
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    g++ \
+    cmake \
+    git \
+    openmpi-bin \
+    openmpi-common \
+    libopenmpi-dev \
+    libpng-dev \
+    python3-pip \
+    bash \
+    nano
+
+USER admin
+WORKDIR /home/admin
+RUN git clone https://github.com/Jsakkos/NUFEB nufeb --recursive
+
+WORKDIR /home/admin/nufeb
+RUN git checkout cyano
+
+WORKDIR /home/admin/nufeb/thirdparty
+RUN chmod +x ./install-hdf5.sh
+RUN ./install-hdf5.sh
+
+WORKDIR /home/admin/nufeb
+RUN chmod +x ./install.sh
+RUN ./install.sh --enable-hdf5
+RUN pip install nufeb-tools -U --user
+ENV PATH $HOME/.local/bin:$PATH
+

README.md

@@ -1,65 +1,70 @@
+Fork of [NUFEB](https://github.com/nufeb/NUFEB) to simulation sucrose-secreting cyanobacteria with heterotrophic partners.
 
-NUFEB is an open source tool for modelling and simulating microbial communities.
-The tool is based on the Individual-based Modelling (IbM) approach, 
-where microbes are represented as discrete units and their
-behaviour changes over time due to a variety of processes. 
+# Instructions for compiling and testing NUFEB phototroph on CADES
 
-NUFEB is built on top of the molecular dynamics simulator
-LAMMPS (as a LAMMPS' user package), extended with IbM features. 
-A wide range of biological, physical and
-chemical processes are implemented to explicitly model microbial systems. 
+## To login to CADES remotely
+[See CADES Documentation](https://docs.cades.ornl.gov/#external-access-ucams/)
+```shell
+ssh userID@login1.ornl.gov
+ssh userID@or-slurm-login.ornl.gov
+```
 
-NUFEB is a freely-available open-source code, distributed under the terms
-of the GNU Public License.
+## clone repo into your home directory
+```shell
+git clone https://github.com/Jsakkos/NUFEB --recursive
+git checkout cyano
+git pull
+```
+## To build
 
-NUFEB development has been funded by the UK’s EPSRC EP/K039083/1 
-Newcastle University Frontiers in Engineering Biology (NUFEB) project.
+### With Ansible
+Install Ansible
+#### On CADES
+```
+module load python/3.6.3
+pip3 install ansible --user
+```
+#### On Ubuntu
+```
+sudo apt update
+sudo apt install software-properties-common
+sudo apt-add-repository --yes --update ppa:ansible/ansible
+sudo apt install ansible
+```
+Run the playbook
+```
+ansible-playbook playbook.yml
+```
+### Manually
+```shell
+module purge
+module load PE-gnu/3.0
+module load cmake
+cd ~/NUFEB/thirdparty/
+./install-hdf5.sh
+./install-vtk.sh
+cd ~/NUFEB/
+./install.sh --enable-hdf5 --enable-vtk
+```
+## To test
 
-Installation guide, tutorial, example videos, and more details can be found in [NUFEB Wiki page](https://github.com/nufeb/NUFEB/wiki) and
-[User Manual](https://github.com/nufeb/NUFEB/tree/master/doc)
-
----------------------------------------------------------------------------
-
-The NUFEB distribution includes the following files and directories:
-<pre>
-README                  this file 
-LICENSE                 the GNU General Public License (GPL)
-install.sh              script for building NUFEB 
-uninstall.sh            script for uninstalling NUFEB 
-doc                     user manual and other documentation 
-examples                test problems and cases used in publications 
-lib                     libraries NUFEB can be linked with 
-lammps                  LAMMPS source code
-post-processing         Povray visualisation routine 
-src                     source files 
-thirdparty              thirdparty tools
-</pre>
-
-### Getting source
-Get NUFEB source code and submodules for its thirdparty libraries:
-<pre>
-git clone https://github.com/nufeb/NUFEB --recursive
-</pre>
-
-### Building
-NUFEB requires gcc/g++ and openmpi for a successful build.
-
-Build NUFEB:
-<pre>
-./install.sh
-</pre>
-
-### Running
-Run a case in /examples after building NUFEB, for example:
-<pre>
-cd examples/biofilm-het
-mpirun -np 4 lmp_mpi -in Inputscript.lammps
-</pre>
-
----------------------------------------------------------------------------
-Developers:
-
-Bowen Li: bowen.li2@newcastle.ac.uk
-
-Denis Taniguchi: denis.taniguchi@newcastle.ac.uk
+### interactively
+```shell
 
+module load env/cades-cnms
+module load anaconda3
+cd $SCRATCH
+python3 ./tools/GenerateAtom.py --u your_user_name
+module purge
+module load PE-gnu/3.0
+salloc -A cnms -p batch --nodes=1 --mem=80G --exclusive -t 00:30:00
+cd runs
+srun --ntasks-per-node 32 -n 32 ~/NUFEB/lammps/src/lmp_png -in ~/NUFEB/runs/Inputscript*.lammps
+```
+### batches
+```shell
+module load anaconda3
+cd $SCRATCH
+python3 ./tools/GenerateAtom.py --u your_user_name
+./tools/slurmRun.sh
+```

examples/Cyanobacteria-E. coli/Inputscript.lammps

@@ -0,0 +1,99 @@
+# NUFEB simulation
+
+atom_style	bio
+atom_modify	map array sort 1000 5.0e-7
+boundary	ff ff ff
+newton		off
+processors  * * 1
+
+comm_modify	vel yes
+read_data_bio D:\runs\Run_50_50_1.00e+00_1_2022-12-30_602200\atom.in
+##############Define initial particle distribution##############
+
+lattice sc 1e-6 origin 0 0 0
+#region reg block 0 1000 0 1000 0 100
+
+group CYANO type 1
+group ECW type 2
+
+neighbor	5e-7 bin
+neigh_modify	delay 0 one 5000
+
+##############Define DEM Variables&Commands##############
+
+pair_style  gran/hooke/history 1.e-4 NULL 1.e-5 NULL 0.0 1
+pair_coeff  * *
+
+timestep 10
+
+fix 1 all nve/limit 1e-8
+fix fv all viscous 1e-5
+
+fix zw all wall/gran hooke/history 2000 NULL 500.0 NULL 1.5 0 zplane  0.0  1e-05
+
+variable kanc equal 50
+
+variable ke equal 5e+10
+
+
+##############Define IBm Variables##############
+
+#variables used in fix eps_extract
+variable EPSdens equal 30
+variable EPSratio equal 1.3
+
+#variables used in fix division
+variable divDia1 equal 1.96e-6
+variable divDia2 equal 1.04e-6
+
+#variables used in fix kinetics
+variable diffT equal 1e-4
+variable tol equal 1e-11
+variable etaHET equal 0.6
+variable layer equal -1
+
+#variables used in fix death
+#variable deadDia equal 9e-7
+
+
+##############Define IBm Commands##############
+
+fix k1 all kinetics 100 50 50 5 v_diffT v_layer niter 1000000
+fix kgm all kinetics/growth/monod sucexp 1.0
+fix g1 all kinetics/diffusion v_tol
+fix d1 CYANO divide 100 v_EPSdens v_divDia1 859152
+fix d2 ECW divide 100 v_EPSdens v_divDia2 976082
+#fix d2 all death 1 v_deadDia demflag 0
+
+
+##############Define IBm Computes##############
+
+compute myNtypes all ntypes
+compute myMass all biomass
+compute myCon all avg_con
+
+##############Simulation exit condition##############
+variable co2 equal c_myCon[4]
+fix 10 all halt 1000 v_co2 <= 1e-19
+
+variable suc equal c_myCon[3]
+
+
+variable light equal c_myCon[1]
+fix hl all halt 1000 v_light <= 1e-19
+
+variable mass equal c_myMass[1]+c_myMass[2]
+fix my_halt all halt 1 v_mass >= 1.50e-11
+##############Simulation Output##############
+
+
+
+dump    du3 all bio 100 ntypes biomass avg_con
+dump    traj all bio/hdf5 100 trajectory.h5 id type radius x y z con
+thermo_style    custom step cpu atoms c_myNtypes[*] c_myMass[*] c_myCon[*]
+thermo		100
+thermo_modify	lost ignore
+
+
+run 35000
+