Merge branch 'develop' into add-elmer

channel-transport-reaction/chemical-fenics/requirements.txt

@@ -0,0 +1,11 @@
+numpy >1, <2
+fenicsprecice~=2.0
+
+# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/
+# Use --system-site-packages in venv
+fenics-dijitso==2019.2.0.dev0
+fenics-dolfin==2019.2.0.13.dev0
+fenics-ffc==2019.2.0.dev0
+fenics-fiat==2019.2.0.dev0
+fenics-ufl-legacy==2022.3.0
+

channel-transport-reaction/chemical-fenics/run.sh

@@ -4,6 +4,10 @@ set -e -u
 . ../../tools/log.sh
 exec > >(tee --append "$LOGFILE") 2>&1
 
+python3 -m venv --system-site-package .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+
 python3 chemical-reaction-advection-diffusion.py
 
-close_log
+close_log

channel-transport-reaction/fluid-fenics/requirements.txt

@@ -0,0 +1,10 @@
+numpy >1, <2
+fenicsprecice~=2.0
+
+# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/
+# Use --system-site-packages in venv
+fenics-dijitso==2019.2.0.dev0
+fenics-dolfin==2019.2.0.13.dev0
+fenics-ffc==2019.2.0.dev0
+fenics-fiat==2019.2.0.dev0
+fenics-ufl-legacy==2022.3.0

channel-transport-reaction/fluid-fenics/run.sh

@@ -4,6 +4,11 @@ set -e -u
 . ../../tools/log.sh
 exec > >(tee --append "$LOGFILE") 2>&1
 
+python3 -m venv --system-site-package .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+
+
 python3 fluid.py
 
 close_log

elastic-tube-1d/fluid-python/requirements.txt

@@ -1,3 +1,3 @@
 matplotlib
 numpy >1, <2
-pyprecice~=3.0
+pyprecice~=3.0

elastic-tube-3d/solid-fenics/requirements.txt

@@ -0,0 +1,10 @@
+fenicsprecice~=2.0
+numpy  >1, <2
+
+# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/
+# Use --system-site-packages in venv
+fenics-dijitso==2019.2.0.dev0
+fenics-dolfin==2019.2.0.13.dev0
+fenics-ffc==2019.2.0.dev0
+fenics-fiat==2019.2.0.dev0
+fenics-ufl-legacy==2022.3.0

elastic-tube-3d/solid-fenics/run.sh

@@ -1,4 +1,11 @@
 #!/usr/bin/env bash
 set -e -u
 
+. ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
+
+python3 -m venv --system-site-package .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+
 python3 solid.py

flow-around-controlled-moving-cylinder/controller-fmi/requirements.txt

@@ -0,0 +1 @@
+fmiprecice

flow-around-controlled-moving-cylinder/controller-fmi/run.sh

@@ -15,6 +15,10 @@ if [ ! -f PIDcontroller.fmu ]; then
   cd ../../
 fi
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+
 fmiprecice ./fmi-settings.json ./precice-settings.json
 
 close_log

flow-around-controlled-moving-cylinder/solid-python/requirements.txt

@@ -0,0 +1,2 @@
+pyprecice~=3.0
+numpy >1, <2

flow-around-controlled-moving-cylinder/solid-python/run.sh

@@ -4,6 +4,10 @@ set -e -u
 . ../../tools/log.sh
 exec > >(tee --append "$LOGFILE") 2>&1
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+
 python3 solid.py ../precice-config.xml
 
 close_log

flow-over-heated-plate/solid-fenics/requirements.txt

@@ -0,0 +1,10 @@
+fenicsprecice~=2.0
+numpy >1, <2
+
+# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/
+# Use --system-site-packages in venv
+fenics-dijitso==2019.2.0.dev0
+fenics-dolfin==2019.2.0.13.dev0
+fenics-ffc==2019.2.0.dev0
+fenics-fiat==2019.2.0.dev0
+fenics-ufl-legacy==2022.3.0

flow-over-heated-plate/solid-fenics/run.sh

@@ -4,6 +4,10 @@ set -e -u
 . ../../tools/log.sh
 exec > >(tee --append "$LOGFILE") 2>&1
 
+python3 -m venv --system-site-packages .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+
 python3 solid.py
 
 close_log

oscillator-overlap/mass-left-python/run.sh

@@ -1,13 +1,13 @@
 #!/usr/bin/env bash
 set -e -u
 
-python3 -m venv .venv
-. .venv/bin/activate
-pip install -r requirements.txt
-
 . ../../tools/log.sh
 exec > >(tee --append "$LOGFILE") 2>&1
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r ../solver-python/requirements.txt
+
 python3 ../solver-python/oscillator.py Mass-Left
 
 close_log

oscillator-overlap/mass-right-python/run.sh

@@ -1,13 +1,13 @@
 #!/usr/bin/env bash
 set -e -u
 
-python3 -m venv .venv
-. .venv/bin/activate
-pip install -r requirements.txt
-
 . ../../tools/log.sh
 exec > >(tee --append "$LOGFILE") 2>&1
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r ../solver-python/requirements.txt
+
 python3 ../solver-python/oscillator.py Mass-Right
 
 close_log

oscillator/mass-left-fmi/requirements.txt

@@ -0,0 +1 @@
+fmiprecice

oscillator/mass-left-fmi/run.sh

@@ -16,6 +16,10 @@ if [ ! -f ../solver-fmi/Oscillator.fmu ]; then
   cd ../../../mass-left-fmi
 fi
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+
 fmiprecice fmi-settings.json precice-settings.json
 python3 ../solver-fmi/calculate-error.py ../mass-left-fmi/fmi-settings.json ../mass-left-fmi/precice-settings.json ../mass-right-fmi/fmi-settings.json ../mass-right-fmi/precice-settings.json Mass-Left
 

oscillator/mass-left-python/run.sh

@@ -1,13 +1,13 @@
 #!/usr/bin/env bash
 set -e -u
 
-python3 -m venv .venv
-. .venv/bin/activate
-pip install -r requirements.txt
-
 . ../../tools/log.sh
 exec > >(tee --append "$LOGFILE") 2>&1
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r ../solver-python/requirements.txt
+
 python3 ../solver-python/oscillator.py Mass-Left
 
 close_log

oscillator/mass-right-fmi/requirements.txt

@@ -0,0 +1 @@
+fmiprecice

oscillator/mass-right-fmi/run.sh

@@ -16,6 +16,10 @@ if [ ! -f ../solver-fmi/Oscillator.fmu ]; then
   cd ../../../mass-right-fmi
 fi
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+
 fmiprecice fmi-settings.json precice-settings.json
 python3 ../solver-fmi/calculate-error.py ../mass-left-fmi/fmi-settings.json ../mass-left-fmi/precice-settings.json ../mass-right-fmi/fmi-settings.json ../mass-right-fmi/precice-settings.json Mass-Right
 

oscillator/mass-right-python/run.sh

@@ -1,13 +1,13 @@
 #!/usr/bin/env bash
 set -e -u
 
-python3 -m venv .venv
-. .venv/bin/activate
-pip install -r requirements.txt
-
 . ../../tools/log.sh
 exec > >(tee --append "$LOGFILE") 2>&1
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r ../solver-python/requirements.txt
+
 python3 ../solver-python/oscillator.py Mass-Right
 
 close_log

oscillator/solver-fmi/requirements.txt

@@ -0,0 +1 @@
+fmiprecice

oscillator/solver-python/mypy.ini

@@ -0,0 +1,7 @@
+[mypy]
+
+[mypy-scipy.*]
+ignore_missing_imports = True
+
+[mypy-precice.*]
+ignore_missing_imports = True

oscillator/solver-python/oscillator.py

@@ -7,9 +7,10 @@
 from enum import Enum
 import csv
 import os
+from typing import Type
 
 import problemDefinition
-import timeSteppers
+from timeSteppers import TimeStepper, TimeSteppingSchemes, GeneralizedAlpha, RungeKutta4, RadauIIA
 
 
 class Participant(Enum):
@@ -25,20 +26,24 @@ class Participant(Enum):
     help="Time stepping scheme being used.",
     type=str,
     choices=[
-        s.value for s in timeSteppers.TimeSteppingSchemes],
-    default=timeSteppers.TimeSteppingSchemes.NEWMARK_BETA.value)
+        s.value for s in TimeSteppingSchemes],
+    default=TimeSteppingSchemes.NEWMARK_BETA.value)
 args = parser.parse_args()
 
 participant_name = args.participantName
 
+this_mass: Type[problemDefinition.Mass]
+other_mass: Type[problemDefinition.Mass]
+this_spring: Type[problemDefinition.Spring]
+connecting_spring = problemDefinition.SpringMiddle
+
 if participant_name == Participant.MASS_LEFT.value:
     write_data_name = 'Force-Left'
     read_data_name = 'Force-Right'
     mesh_name = 'Mass-Left-Mesh'
 
     this_mass = problemDefinition.MassLeft
     this_spring = problemDefinition.SpringLeft
-    connecting_spring = problemDefinition.SpringMiddle
     other_mass = problemDefinition.MassRight
 
 elif participant_name == Participant.MASS_RIGHT.value:
@@ -48,7 +53,6 @@ class Participant(Enum):
 
     this_mass = problemDefinition.MassRight
     this_spring = problemDefinition.SpringRight
-    connecting_spring = problemDefinition.SpringMiddle
     other_mass = problemDefinition.MassLeft
 
 else:
@@ -89,25 +93,19 @@ class Participant(Enum):
 a = a0
 t = 0
 
-if args.time_stepping == timeSteppers.TimeSteppingSchemes.GENERALIZED_ALPHA.value:
-    time_stepper = timeSteppers.GeneralizedAlpha(stiffness=stiffness, mass=mass, alpha_f=0.4, alpha_m=0.2)
-elif args.time_stepping == timeSteppers.TimeSteppingSchemes.NEWMARK_BETA.value:
-    time_stepper = timeSteppers.GeneralizedAlpha(stiffness=stiffness, mass=mass, alpha_f=0.0, alpha_m=0.0)
-elif args.time_stepping == timeSteppers.TimeSteppingSchemes.RUNGE_KUTTA_4.value:
-    ode_system = np.array([
-        [0, 1],  # du
-        [-stiffness / mass, 0],  # dv
-    ])
-    time_stepper = timeSteppers.RungeKutta4(ode_system=ode_system)
-elif args.time_stepping == timeSteppers.TimeSteppingSchemes.Radau_IIA.value:
-    ode_system = np.array([
-        [0, 1],  # du
-        [-stiffness / mass, 0],  # dv
-    ])
-    time_stepper = timeSteppers.RadauIIA(ode_system=ode_system)
+time_stepper: TimeStepper
+
+if args.time_stepping == TimeSteppingSchemes.GENERALIZED_ALPHA.value:
+    time_stepper = GeneralizedAlpha(stiffness=stiffness, mass=mass, alpha_f=0.4, alpha_m=0.2)
+elif args.time_stepping == TimeSteppingSchemes.NEWMARK_BETA.value:
+    time_stepper = GeneralizedAlpha(stiffness=stiffness, mass=mass, alpha_f=0.0, alpha_m=0.0)
+elif args.time_stepping == TimeSteppingSchemes.RUNGE_KUTTA_4.value:
+    time_stepper = RungeKutta4(stiffness=stiffness, mass=mass)
+elif args.time_stepping == TimeSteppingSchemes.Radau_IIA.value:
+    time_stepper = RadauIIA(stiffness=stiffness, mass=mass)
 else:
     raise Exception(
-        f"Invalid time stepping scheme {args.time_stepping}. Please use one of {[ts.value for ts in timeSteppers.TimeSteppingSchemes]}")
+        f"Invalid time stepping scheme {args.time_stepping}. Please use one of {[ts.value for ts in TimeSteppingSchemes]}")
 
 
 positions = []
@@ -133,34 +131,32 @@ class Participant(Enum):
     precice_dt = participant.get_max_time_step_size()
     dt = np.min([precice_dt, my_dt])
 
-    def f(t): return participant.read_data(mesh_name, read_data_name, vertex_ids, t)[0]
+    def f(t: float) -> float: return participant.read_data(mesh_name, read_data_name, vertex_ids, t)[0]
 
     # do time step, write data, and advance
-    # performs adaptive time stepping with dense output; multiple write calls per time step
-    if args.time_stepping == timeSteppers.TimeSteppingSchemes.Radau_IIA.value:
-        u_new, v_new, a_new, sol = time_stepper.do_step(u, v, a, f, dt)
-        t_new = t + dt
+    u_new, v_new, a_new = time_stepper.do_step(u, v, a, f, dt)
+
+    t_new = t + dt
+
+    # RadauIIA time stepper provides dense output. Do multiple write calls per time step.
+    if isinstance(time_stepper, RadauIIA):
         # create n samples_per_step of time stepping scheme. Degree of dense
         # interpolating function is usually larger 1 and, therefore, we need
         # multiple samples per step.
         samples_per_step = 5
-        n_time_steps = len(sol.ts)  # number of time steps performed by adaptive time stepper
+        n_time_steps = len(time_stepper.dense_output.ts)  # number of time steps performed by adaptive time stepper
         n_pseudo = samples_per_step * n_time_steps  # samples_per_step times no. time steps per window.
-
         t_pseudo = 0
         for i in range(n_pseudo):
             # perform n_pseudo pseudosteps
             dt_pseudo = dt / n_pseudo
             t_pseudo += dt_pseudo
-            write_data = [connecting_spring.k * sol(t_pseudo)[0]]
+            write_data = np.array([connecting_spring.k * time_stepper.dense_output(t_pseudo)[0]])
             participant.write_data(mesh_name, write_data_name, vertex_ids, write_data)
             participant.advance(dt_pseudo)
 
     else:  # simple time stepping without dense output; only a single write call per time step
-        u_new, v_new, a_new = time_stepper.do_step(u, v, a, f, dt)
-        t_new = t + dt
-
-        write_data = [connecting_spring.k * u_new]
+        write_data = np.array([connecting_spring.k * u_new])
         participant.write_data(mesh_name, write_data_name, vertex_ids, write_data)
         participant.advance(dt)