Include template for simple case

Dockerfile

@@ -1,12 +1,22 @@
-ARG OSP_CORE_IMAGE=simphony/osp-core:latest
-FROM $OSP_CORE_IMAGE
+FROM ubuntu:20.04
 LABEL maintainer="mohsen.shiea@polito.it"
 LABEL dockerfile.version="1.1"
 
+ENV DEBIAN_FRONTEND=noninteractive
+
 # Install requirements
 RUN apt-get update && apt-get -y upgrade && apt-get install -y \
-    git graphviz wget build-essential g++ gfortran libgfortran5 openmpi-bin libopenmpi-dev make libssl-dev libblas-dev liblapack-dev \
-    apt-transport-https software-properties-common openssh-client bash-completion bash-builtins libnss-wrapper vim nano tree curl unzip
+    git graphviz wget build-essential g++ gfortran libgfortran5 openmpi-bin \
+    libopenmpi-dev make libssl-dev libblas-dev liblapack-dev \
+    apt-transport-https software-properties-common openssh-client \
+    bash-completion bash-builtins libnss-wrapper vim nano tree curl unzip \
+    python3-pip
+
+RUN wget -c https://repo.anaconda.com/archive/Anaconda3-2020.02-Linux-x86_64.sh && \
+    /bin/bash Anaconda3-2020.02-Linux-x86_64.sh -bfp /usr/local && \
+    conda update conda && conda create --name wet-synthesis
+
+RUN conda install mkl-service
 
 RUN cd / && mkdir cmake && cd cmake && \
     CMAKE_VERSION=3.20.1 && \
@@ -29,10 +39,9 @@ RUN cd / && mkdir sundials && cd sundials && \
     make install && \
     cd .. && rm -r builddir cvode-${CVODE_VERSION} cvode-${CVODE_VERSION}.tar.gz
 
-RUN cd /usr/bin && rm python3 && ln -s python3.6 python3 && \
-    wget -O - http://dl.openfoam.org/gpg.key | apt-key add - && add-apt-repository http://dl.openfoam.org/ubuntu && \
+RUN wget -O - http://dl.openfoam.org/gpg.key | apt-key add - && add-apt-repository http://dl.openfoam.org/ubuntu && \
     apt-get update && apt-get install -y --no-install-recommends openfoam8 && \
-    cd /usr/bin && rm python3 && ln -s python3.7 python3 && rm -rf /var/lib/apt/lists/*
+    rm -rf /var/lib/apt/lists/*
 
 ENV user=simdomeuser HOME=/home/simdomeuser
 
@@ -52,10 +61,10 @@ RUN mkdir -p $HOME/simdome/wrappers/simdome_wet_synthesis && \
 COPY --chown=$user . $HOME/simdome/wrappers/simdome_wet_synthesis
 WORKDIR $HOME/simdome/wrappers/simdome_wet_synthesis
 
-ENV PATH=$PATH:$HOME/.local/bin
+ENV PATH=$HOME/.local/bin:$PATH
 
-RUN pip install matplotlib scipy \
-    && pico install ontology.wet_synthesis.yml \
-    && python setup.py install --user
+RUN pip install matplotlib scipy numpy sklearn mpi4py
+RUN pip install .
+RUN pico install ontology.wet_synthesis.yml
 
-CMD ["/bin/bash", "-c", "source /opt/openfoam8/etc/bashrc && /bin/bash" ]
+CMD ["/bin/bash", "-c", "source /opt/openfoam8/etc/bashrc && /bin/bash && source activate wet-synthesis" ]

examples/cfd_pbe_precNMC.py

@@ -9,6 +9,7 @@
 from osp.core.utils import pretty_print
 from osp.core.utils import Cuds2dot
 
+print('Hello')
 
 def main(argv):
 
@@ -108,9 +109,7 @@ def main(argv):
             session.run()
 
             pretty_print(wrapper.get(oclass=wet_synthesis.SizeDistribution)[0])
-
-            plot_size_dist(
-                wrapper.get(oclass=wet_synthesis.SizeDistribution)[0])
+            plot_size_dist(wrapper.get(oclass=wet_synthesis.SizeDistribution)[0])
 
         except Exception as e:
             print(e)

examples/compartment_precNMC.py

@@ -1,59 +1,128 @@
 # Example to use compartment wrapper
+import sys
+import numpy as np
 import traceback
+import argparse
+import matplotlib.pyplot as plt
 
 from osp.wrappers.wet_synthesis_wrappers import CompartmentSession
+from osp.wrappers.wet_synthesis_wrappers.utils import plot_size_dist
 from osp.core.namespaces import wet_synthesis
 from osp.core.utils import pretty_print
 from osp.core.utils import Cuds2dot
 
 
-# create a wrapper session and run it
-with CompartmentSession(
-        engine="fluent", case="precNMC", delete_simulation_files=False,
-        end_time=10) as session:
-    wrapper = wet_synthesis.WetSynthesisWrapper(session=session)
+def main(argv):
 
-    accuracy_level = wet_synthesis.SliderAccuracyLevel(number=1)
-    wrapper.add(accuracy_level)
+    parser = argparse.ArgumentParser(description='Process command-line inputs')
 
-    pressure = wet_synthesis.Pressure(value=101325, unit='Pa')
-    wrapper.add(pressure)
+    parser.add_argument('--delete', action='store_true')
+    parser.add_argument('--dummy', action='store_true')
+    parser.add_argument('-n', '--numproc', type=int, default=1)
+    parser.add_argument('-t', '--endtime', type=float, default=None)
+    parser.add_argument('-w', '--writeinterval', type=int, default=None)
 
-    rotationalSpeed = wet_synthesis.RotationalSpeed(value=-1005, unit='rpm')
-    wrapper.add(rotationalSpeed)
+    args, _ = parser.parse_known_args(argv)
 
-    metal_flowRate = wet_synthesis.FlowRate(value=2.1977, unit='lit/hr')
-    nh3_flowRate = wet_synthesis.FlowRate(value=0.2184, unit='lit/hr')
-    naoh_flowRate = wet_synthesis.FlowRate(value=0.9171, unit='lit/hr')
+    # create a wrapper session and run it
+    with CompartmentSession(
+            engine="pisoPrecNMC", case="precNMC",
+            delete_simulation_files=args.delete, end_time=args.endtime,
+            write_interval=args.writeinterval, num_moments=4,
+            num_proc=args.numproc, dummy=args.dummy) as session:
 
-    metalFeed = wet_synthesis.Feed(name='metals')
-    nh3Feed = wet_synthesis.Feed(name='nh3')
-    naohFeed = wet_synthesis.Feed(name='naoh')
+        wrapper = wet_synthesis.WetSynthesisWrapper(session=session)
 
-    metalFeed.add(metal_flowRate, rel=wet_synthesis.hasPart)
+        accuracy_level = wet_synthesis.SliderAccuracyLevel(number=0)
+        wrapper.add(accuracy_level)
 
-    nh3Feed.add(nh3_flowRate, rel=wet_synthesis.hasPart)
+        pressure = wet_synthesis.Pressure(value=101325, unit='Pa')
+        wrapper.add(pressure)
 
-    naohFeed.add(naoh_flowRate, rel=wet_synthesis.hasPart)
+        temperature = wet_synthesis.Temperature(value=298.15, unit='K')
+        wrapper.add(temperature)
 
-    wrapper.add(metalFeed)
-    wrapper.add(nh3Feed)
-    wrapper.add(naohFeed)
+        rotationalSpeed = wet_synthesis.RotationalSpeed(value=200, unit='rpm')
+        wrapper.add(rotationalSpeed)
 
-    Cuds2dot(wrapper).render()
+        density = wet_synthesis.Density(value=3953, unit='kg/m^3')
+        molecularWeight = wet_synthesis.MolecularWeight(
+            value=92.338, unit='g/mol')
+        shapeFactor = wet_synthesis.ShapeFactor(value=0.523599, unit='')
 
-    compartmentNetwork = wet_synthesis.CompartmentNetwork()
-    wrapper.add(compartmentNetwork)
+        solidParticle = wet_synthesis.SolidParticle()
+        solidParticle.add(density, rel=wet_synthesis.hasProperty)
+        solidParticle.add(molecularWeight, rel=wet_synthesis.hasProperty)
+        solidParticle.add(shapeFactor, rel=wet_synthesis.hasProperty)
+        wrapper.add(solidParticle)
 
-    pretty_print(wrapper.get(oclass=wet_synthesis.CompartmentNetwork)[0])
+        ni_conc = wet_synthesis.MolarConcentration(value=1.6, unit='mol/lit')
+        mn_conc = wet_synthesis.MolarConcentration(value=0.2, unit='mol/lit')
+        co_conc = wet_synthesis.MolarConcentration(value=0.2, unit='mol/lit')
+        so4_conc = wet_synthesis.MolarConcentration(value=2.0, unit='mol/lit')
+        nh3_conc = wet_synthesis.MolarConcentration(value=10, unit='mol/lit')
+        na_conc = wet_synthesis.MolarConcentration(value=5, unit='mol/lit')
 
-    try:
-        # run the session
-        session.run()
+        ni = wet_synthesis.Component(name='nickel')
+        mn = wet_synthesis.Component(name='manganese')
+        co = wet_synthesis.Component(name='cobalt')
+        so4 = wet_synthesis.Component(name='so4')
+        nh3 = wet_synthesis.Component(name='nh3')
+        na = wet_synthesis.Component(name='na')
 
+        ni.add(ni_conc, rel=wet_synthesis.hasPart)
+        mn.add(mn_conc, rel=wet_synthesis.hasPart)
+        co.add(co_conc, rel=wet_synthesis.hasPart)
+        so4.add(so4_conc, rel=wet_synthesis.hasPart)
+        nh3.add(nh3_conc, rel=wet_synthesis.hasPart)
+        na.add(na_conc, rel=wet_synthesis.hasPart)
+
+        metal_flowRate = wet_synthesis.FlowRate(value=1.5330924, unit='lit/hr')
+        nh3_flowRate = wet_synthesis.FlowRate(value=0.30666132, unit='lit/hr')
+        naoh_flowRate = wet_synthesis.FlowRate(value=1.226646, unit='lit/hr')
+
+        metalFeed = wet_synthesis.Feed(name='metals')
+        nh3Feed = wet_synthesis.Feed(name='nh3')
+        naohFeed = wet_synthesis.Feed(name='naoh')
+
+        metalFeed.add(ni, mn, co, so4, rel=wet_synthesis.hasPart)
+        metalFeed.add(metal_flowRate, rel=wet_synthesis.hasPart)
+
+        nh3Feed.add(nh3, rel=wet_synthesis.hasPart)
+        nh3Feed.add(nh3_flowRate, rel=wet_synthesis.hasPart)
+
+        naohFeed.add(na, rel=wet_synthesis.hasPart)
+        naohFeed.add(naoh_flowRate, rel=wet_synthesis.hasPart)
+
+        wrapper.add(metalFeed)
+        wrapper.add(nh3Feed)
+        wrapper.add(naohFeed)
+
+        Cuds2dot(wrapper).render()
+
+        sizeDistribution = wet_synthesis.SizeDistribution()
+        wrapper.add(sizeDistribution)
+        compartmentNetwork = wet_synthesis.CompartmentNetwork()
+        wrapper.add(compartmentNetwork)
+
+        pretty_print(wrapper.get(oclass=wet_synthesis.SizeDistribution)[0])
         pretty_print(wrapper.get(oclass=wet_synthesis.CompartmentNetwork)[0])
 
-    except Exception as e:
-        print(e)
-        traceback.print_exc()
-        # session._delete_simulation_files = True
+        try:
+            # run the session
+            session.run()
+
+            pretty_print(wrapper.get(oclass=wet_synthesis.SizeDistribution)[0])
+            plot_size_dist(wrapper.get(oclass=wet_synthesis.SizeDistribution)[0])
+
+            pretty_print(wrapper.get(oclass=wet_synthesis.CompartmentNetwork)[0])
+
+        except Exception as e:
+            print(e)
+            traceback.print_exc()
+            # session._delete_simulation_files = True
+
+
+if __name__ == "__main__":
+
+    main(sys.argv[1:])