Add micro-dumux-surrogate participant to two-scale heat conduction

changelog-entries/684.md

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+- Added PCE-base surrogate for micro-dumux in two-scale heat conduction [#684](https://github.com/precice/tutorials/pull/684)

two-scale-heat-conduction/micro-dumux-mada/mada_switcher.py

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+import numpy as np
+
+
+def switching_function(resolution, location, t, input, prev_output):
+    result = 0
+    # in the beginning we only want FOM
+    if t == 0.0:
+        if resolution > 0:
+            result = -1
+        else:
+            result = 0
+    # after small init phase, we want dynamic model selection
+    # for test purposes we say ROM is accurate in range
+    else:
+        concentration = input['concentration']
+        is_valid_range = 0.45 < concentration < 0.55
+        is_fom = resolution == 0
+
+        if is_fom and is_valid_range:
+            result = 1
+        if not is_fom and not is_valid_range:
+            result = -1
+
+    return result

two-scale-heat-conduction/micro-dumux-mada/micro-manager-mada-config.json

@@ -0,0 +1,35 @@
+{
+    "micro_file_name": "micro_sim",
+    "coupling_params": {
+            "participant_name": "Micro-Manager",
+            "precice_config_file_name": "../precice-config.xml",
+            "macro_mesh_name": "macro-mesh",
+            "write_data_names": ["k_00", "k_01", "k_10", "k_11", "porosity"],
+            "read_data_names": ["concentration"]
+    },
+    "simulation_params": {
+      "micro_dt": 0.01,
+      "macro_domain_bounds": [0.0, 1.0, 0.0, 0.5],
+      "decomposition": [1, 1],
+      "adaptivity": "True",
+      "adaptivity_settings": {
+            "type": "global",
+            "data": ["k_00", "k_11", "porosity", "concentration"],
+            "history_param": 0.1,
+            "coarsening_constant": 0.2,
+            "refining_constant": 0.05,
+            "every_implicit_iteration": "False",
+            "similarity_measure": "L2rel"
+        },
+      "model_adaptivity": true,
+      "model_adaptivity_settings": {
+            "micro_file_names": ["micro_sim", "micro_sim_sur"],
+            "data": [],
+            "thresholds": [1.0, 1.0],
+            "switching_function": "mada_switcher"
+        }
+    },
+    "diagnostics": {
+      "data_from_micro_sims": ["grain_size"]
+    }
+}

two-scale-heat-conduction/micro-dumux-mada/micro_sim.pc.in

@@ -0,0 +1,15 @@
+prefix=@prefix@
+exec_prefix=@exec_prefix@
+libdir=@libdir@
+includedir=@includedir@
+CXX=@CXX@
+CC=@CC@
+DEPENDENCIES=@REQUIRES@
+
+Name: @PACKAGE_NAME@
+Version: @VERSION@
+Description: micro_sim module
+URL: http://dune-project.org/
+Requires: dumux-phasefield dumux-precice
+Libs: -L${libdir}
+Cflags: -I${includedir}

two-scale-heat-conduction/micro-dumux-mada/micro_sim_sur.py

@@ -0,0 +1,56 @@
+"""
+Micro simulation Surrogate, requrie previous computation of surrogate model
+"""
+import os
+import subprocess
+from bayesvalidrox import PyLinkForwardModel, Input, PCE, ExpDesigns, Engine
+import h5py
+import joblib
+import numpy as np
+import math
+
+
+class MicroSimulation:
+
+    def __init__(self, sim_id):
+        """
+        Constructor of MicroSimulation class.
+        """
+        self._sim_id = sim_id
+        self._state = None
+
+        self._model = None
+        with open('micro-dumux-surrogate.pkl', 'rb') as input:
+            self._model = joblib.load(input)
+        if self._model is None:
+            raise RuntimeError("Failed to load model.")
+
+    def initialize(self):
+        output_data = dict()
+        output_data["k_00"] = 0.4912490635619572
+        output_data["k_11"] = 0.4912490635989945
+        output_data["porosity"] = 0.4933482661391027
+
+        if self._sim_id == 0:
+            output_data["k_00"] = 0.4912490640081466
+            output_data["k_11"] = 0.4912490640081367
+
+        return output_data
+
+    def get_state(self):
+        return self._state
+
+    def set_state(self, state):
+        self._state = state
+
+    def solve(self, macro_data, dt):
+        model_eval, _ = self._model.eval_metamodel(np.array([macro_data["concentration"]])[:, np.newaxis])
+        output_data = dict()
+        output_data["k_00"] = model_eval["k_00"][0][0]
+        output_data["k_01"] = model_eval["k_01"][0][0]
+        output_data["k_10"] = model_eval["k_10"][0][0]
+        output_data["k_11"] = model_eval["k_11"][0][0]
+        output_data["porosity"] = model_eval["porosity"][0][0]
+        output_data["grain_size"] = math.sqrt((1 - model_eval["porosity"][0][0]) / math.pi)
+
+        return output_data

two-scale-heat-conduction/micro-dumux-mada/params.input

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+[Assembly]
+Multithreading = false
+
+[TimeLoop]
+TEnd = 0.25                 # end time of the simulation
+DtInitial = 0.01            # initial time step size
+MaxTimeStepSize = 0.01      # maximal time step size
+
+[Grid]
+LowerLeft = 0.0 0.0         # lower left (front) corner of the domain (keep this fixed at 0 0!)
+UpperRight = 1.0 1.0        # upper right (back) corner of the domain
+Cells = 80 80               # grid resolution in each coordinate direction
+Periodic = 1 1              # Periodic Boundary conditions in both dimensions
+
+[Problem]
+xi = 0.08                   # phasefield parameter (lambda, set to around 4/Ncells) 
+omega = 0.01                # phasefield diffusivity/surface tension parameter (gamma)
+kt = 1.0                    # constant deciding speed of expansion/contraction
+eqconc = 0.5                # equilibrium concentration 
+ks = 1.0                    # conductivity of sand material
+kg = 0.0                    # conductivity of void material
+Name = cell_phase           # base name for VTK output files
+Radius = 0.4                # initial radius of the grain
+PhasefieldICScaling = 4.0   # factor in initial phasefield function
+MaxPorosity = 0.9686        # porosity cap

two-scale-heat-conduction/micro-dumux-surrogate/clean.sh

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+#!/usr/bin/env sh
+set -e -u
+
+. ../../tools/cleaning-tools.sh
+
+clean_dumux .

two-scale-heat-conduction/micro-dumux-surrogate/create-snapshots.sh

@@ -0,0 +1,29 @@
+#!/usr/bin/env bash
+set -e -u
+
+. ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
+
+usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; }
+
+# Check if no input argument was provided
+if [ -z "$*" ] ; then
+  echo "No input argument provided. Micro Manager for snapshot computation is launched in serial"
+  micro-manager-precice --snapshot micro-manager-snapshot-config.json
+fi
+
+while getopts ":sp" opt; do
+  case ${opt} in
+  s)
+    micro-manager-precice --snapshot micro-manager-snapshot-config.json
+    ;;
+  p)
+    mpiexec -n "$2" micro-manager-precice --snapshot micro-manager-snapshot-config.json
+    ;;
+  *)
+    usage
+    ;;
+  esac
+done
+
+close_log

two-scale-heat-conduction/micro-dumux-surrogate/micro-manager-snapshot-config.json

@@ -0,0 +1,15 @@
+{
+    "micro_file_name": "micro_sim",
+    "coupling_params": {
+            "parameter_file_name": "input_samples.hdf5",
+            "read_data_names": ["concentration"],
+            "write_data_names": ["k_00", "k_01", "k_10", "k_11", "porosity"]
+    },
+    "simulation_params": {
+      "micro_dt": 0.01
+    },
+    "snapshot_params": {
+      "initialize_once": false
+    }, 
+    "output_directory": "output"
+}

two-scale-heat-conduction/micro-dumux-surrogate/micro-manager-surrogate-config.json

@@ -0,0 +1,28 @@
+{
+    "micro_file_name": "micro_sim_sur",
+    "coupling_params": {
+            "participant_name": "Micro-Manager",
+            "precice_config_file_name": "../precice-config.xml",
+            "macro_mesh_name": "macro-mesh",
+            "write_data_names": ["k_00", "k_01", "k_10", "k_11", "porosity"],
+            "read_data_names": ["concentration"]
+    },
+    "simulation_params": {
+      "micro_dt": 0.01,
+      "macro_domain_bounds": [0.0, 1.0, 0.0, 0.5],
+      "decomposition": [1, 1],
+      "adaptivity": "True",
+      "adaptivity_settings": {
+            "type": "global",
+            "data": ["k_00", "k_11", "porosity", "concentration"],
+            "history_param": 0.1,
+            "coarsening_constant": 0.2,
+            "refining_constant": 0.05,
+            "every_implicit_iteration": "False",
+            "similarity_measure": "L2rel"
+        }
+    },
+    "diagnostics": {
+      "data_from_micro_sims": ["grain_size"]
+    }
+}

two-scale-heat-conduction/micro-dumux-surrogate/micro_sim.pc.in

@@ -0,0 +1,15 @@
+prefix=@prefix@
+exec_prefix=@exec_prefix@
+libdir=@libdir@
+includedir=@includedir@
+CXX=@CXX@
+CC=@CC@
+DEPENDENCIES=@REQUIRES@
+
+Name: @PACKAGE_NAME@
+Version: @VERSION@
+Description: micro_sim module
+URL: http://dune-project.org/
+Requires: dumux-phasefield dumux-precice
+Libs: -L${libdir}
+Cflags: -I${includedir}

two-scale-heat-conduction/micro-dumux-surrogate/micro_sim_sur.py

@@ -0,0 +1,56 @@
+"""
+Micro simulation Surrogate, requrie previous computation of surrogate model
+"""
+import os
+import subprocess
+from bayesvalidrox import PyLinkForwardModel, Input, PCE, ExpDesigns, Engine
+import h5py
+import joblib
+import numpy as np
+import math
+
+
+class MicroSimulation:
+
+    def __init__(self, sim_id):
+        """
+        Constructor of MicroSimulation class.
+        """
+        self._sim_id = sim_id
+        self._state = None
+
+        self._model = None
+        with open('micro-dumux-surrogate.pkl', 'rb') as input:
+            self._model = joblib.load(input)
+        if self._model is None:
+            raise RuntimeError("Failed to load model.")
+
+    def initialize(self):
+        output_data = dict()
+        output_data["k_00"] = 0.4912490635619572
+        output_data["k_11"] = 0.4912490635989945
+        output_data["porosity"] = 0.4933482661391027
+
+        if self._sim_id == 0:
+            output_data["k_00"] = 0.4912490640081466
+            output_data["k_11"] = 0.4912490640081367
+
+        return output_data
+
+    def get_state(self):
+        return self._state
+
+    def set_state(self, state):
+        self._state = state
+
+    def solve(self, macro_data, dt):
+        model_eval, _ = self._model.eval_metamodel(np.array([macro_data["concentration"]])[:, np.newaxis])
+        output_data = dict()
+        output_data["k_00"] = model_eval["k_00"][0][0]
+        output_data["k_01"] = model_eval["k_01"][0][0]
+        output_data["k_10"] = model_eval["k_10"][0][0]
+        output_data["k_11"] = model_eval["k_11"][0][0]
+        output_data["porosity"] = model_eval["porosity"][0][0]
+        output_data["grain_size"] = math.sqrt((1 - model_eval["porosity"][0][0]) / math.pi)
+
+        return output_data

two-scale-heat-conduction/micro-dumux-surrogate/model.py

@@ -0,0 +1,5 @@
+# Dummy model function for the micro-dumux surrogate.
+# We do not wrap the original DuMuX model because we will directly provide
+# snapshots (computed by the Micro Manager) to BayesValidRox.
+def model(samples):
+    return None

two-scale-heat-conduction/micro-dumux-surrogate/params.input

@@ -0,0 +1,25 @@
+[Assembly]
+Multithreading = false
+
+[TimeLoop]
+TEnd = 0.25                 # end time of the simulation
+DtInitial = 0.01            # initial time step size
+MaxTimeStepSize = 0.01      # maximal time step size
+
+[Grid]
+LowerLeft = 0.0 0.0         # lower left (front) corner of the domain (keep this fixed at 0 0!)
+UpperRight = 1.0 1.0        # upper right (back) corner of the domain
+Cells = 80 80               # grid resolution in each coordinate direction
+Periodic = 1 1              # Periodic Boundary conditions in both dimensions
+
+[Problem]
+xi = 0.08                   # phasefield parameter (lambda, set to around 4/Ncells) 
+omega = 0.01                # phasefield diffusivity/surface tension parameter (gamma)
+kt = 1.0                    # constant deciding speed of expansion/contraction
+eqconc = 0.5                # equilibrium concentration 
+ks = 1.0                    # conductivity of sand material
+kg = 0.0                    # conductivity of void material
+Name = cell_phase           # base name for VTK output files
+Radius = 0.4                # initial radius of the grain
+PhasefieldICScaling = 4.0   # factor in initial phasefield function
+MaxPorosity = 0.9686        # porosity cap

two-scale-heat-conduction/micro-dumux-surrogate/requirements.txt

@@ -0,0 +1,3 @@
+numpy
+bayesvalidrox
+micro-manager-precice

two-scale-heat-conduction/micro-dumux-surrogate/run-surrogate-workflow.sh

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+set -e -u
+
+python3 -m venv .venv
+. .venv/bin/activate
+
+pip install -r requirements.txt
+
+python surrogate_workflow.py

two-scale-heat-conduction/micro-dumux-surrogate/run.sh

@@ -0,0 +1,29 @@
+#!/usr/bin/env bash
+set -e -u
+
+. ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
+
+usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; }
+
+# Check if no input argument was provided
+if [ -z "$*" ] ; then
+  echo "No input argument provided. Micro Manager is launched in serial"
+  micro-manager-precice micro-manager-surrogate-config.json
+fi
+
+while getopts ":sp" opt; do
+  case ${opt} in
+  s)
+    micro-manager-precice micro-manager-surrogate-config.json
+    ;;
+  p)
+    mpiexec -n "$2" micro-manager-precice micro-manager-surrogate-config.json
+    ;;
+  *)
+    usage
+    ;;
+  esac
+done
+
+close_log