Merge branch 'development' into feature/mod_battery_cycle_only

.github/workflows/mpet-code-style.yml

@@ -9,13 +9,13 @@ jobs:
 
     steps:
       - name: Set up python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
           architecture: x64
 
       - name: Checkout MPET
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 1
           path: mpet

.github/workflows/mpet-regression-test.yml

@@ -9,35 +9,27 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7","3.8","3.9","3.10"]
+        python-version: ["3.8","3.9","3.10","3.11"]
     defaults:
       run:
         shell: bash -l {0}
     steps:
 
-    - uses: actions/checkout@v1
-      with:
-        fetch-depth: 1
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 1
         path: mpet
-    - uses: actions/checkout@v2
-      with:
-        fetch-depth: 1
-        path: base-mpet
-        ref: ${{ github.base_ref }}
 
     - uses: conda-incubator/setup-miniconda@v2
       with:
-        auto-update-conda: true
         python-version: ${{ matrix.python-version }}
+        mamba-version: "*"
+        channels: conda-forge,defaults
         activate-environment: mpet-env
 
-    - name: Install daetools via conda
+    - name: Install daetools via mamba
       run: |
-        conda activate mpet-env
-        conda install -c conda-forge daetools python=${{ matrix.python-version }} pip
+        mamba install daetools
 
     - name: Install additional dependencies using mpet's setup.py
       run: |
@@ -57,7 +49,6 @@ jobs:
 
     - name: run tests for modified branch and get coverage
       run: |
-        conda activate mpet-env
         cd mpet/bin/workdir
         coverage run --source=../../mpet/ run_tests.py --test_dir ./tests --output_dir ../../bin/workdir/modified > /dev/null
 

CHANGELOG.md

@@ -4,6 +4,15 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.1.9] - 2023-01-27
+### Added
+- Regression tests for Python 3.10 and 3.11.
+- Additional badges added to README.
+
+### Fixed
+- Code clean up and maintenance updates.
+
+
 ## [0.1.8] - 2022-02-14
 ### Added
 - Online documentation with updated installation instructions: [https://mpet.readthedocs.io/en/latest/](https://mpet.readthedocs.io/en/latest/)

README.md

@@ -1,5 +1,8 @@
-Development: [![Coverage Status](https://coveralls.io/repos/github/TRI-AMDD/mpet/badge.svg?branch=development)](https://coveralls.io/github/TRI-AMDD/mpet?branch=development)
-Master: [![Coverage Status](https://coveralls.io/repos/github/TRI-AMDD/mpet/badge.svg?branch=master)](https://coveralls.io/github/TRI-AMDD/mpet?branch=master)
+[![Build](https://img.shields.io/github/actions/workflow/status/TRI-AMDD/mpet/mpet-regression-test.yml?branch=development)](https://github.com/TRI-AMDD/mpet/actions/workflows/mpet-regression-test.yml)
+[![Coverage Status](https://coveralls.io/repos/github/TRI-AMDD/mpet/badge.svg?branch=development)](https://coveralls.io/github/TRI-AMDD/mpet?branch=development)
+[![readthedocs](https://readthedocs.org/projects/mpet/badge/?version=latest)](https://mpet.readthedocs.io)
+[![release](https://img.shields.io/github/v/release/TRI-AMDD/mpet)](https://github.com/TRI-AMDD/mpet/releases)
+
 # MPET -- Multiphase Porous Electrode Theory
 
 This software is designed to run simulations of batteries with porous electrodes using porous electrode theory, which is a volume-averaged, multiscale approach to capture the coupled behavior of electrolyte and active material within electrodes. As a result, with physical parameter inputs and run protocols (specified current or voltage profiles), it makes predictions about the internal dynamics within a battery (electrolyte concentration and potential, solid phase concentrations, reaction rates, etc.) and also macroscopic, easily measurable electrochemical quantities such as total current and voltage. In this way, it is similar to the [`dualfoil`](http://www.cchem.berkeley.edu/jsngrp/fortran.html) code released by Newman and coworkers from Berkeley. This software has much of the functionality contained in `dualfoil` (it is currently missing, e.g., temperature dependence). However, beyond the standard porous electrode theory simulations, this software can also simulate electrodes in which the active materials phase separate using non-equilibrium thermodynamics within a phase field modeling framework. Such behavior is common in widely used electrode materials, including graphite and LiFePO4.

configs/params_NMC532_Colclasure20.cfg

@@ -0,0 +1,23 @@
+#Cathode parameters from A. Colclasure et al., J. Electrochim. Acta 337, 135854 (2020).
+# See params_electrodes.cfg for parameter explanations.
+
+[Particles]
+type = diffn
+discretization = 9.e-8
+shape = sphere
+thickness = 10e-6
+
+[Material]
+muRfunc = NMC532_Colclasure20
+noise = false
+noise_prefac = 1e-6
+numnoise = 200
+rho_s = 2.9869e28
+D = 1
+Dfunc = NMC532_Colclasure20
+
+[Reactions]
+rxnType = BV_Colclasure20
+k0 = 10
+alpha = 0.5
+Rfilm = 0e-0

configs/params_graphite_Colclasure20.cfg

@@ -0,0 +1,23 @@
+#Cathode parameters from A. Colclasure et al., J. Electrochim. Acta 337, 135854 (2020).
+# See params_electrodes.cfg for parameter explanations.
+
+[Particles]
+type = diffn
+discretization = 2.e-7
+shape = sphere
+thickness = 20e-9
+
+[Material]
+muRfunc = LiC6_Colclasure_1506T
+noise = false
+noise_prefac = 1e-6
+numnoise = 200
+rho_s = 1.6862e28
+D = 3.0e-14
+Dfunc = constant
+
+[Reactions]
+rxnType = BV_mod01
+k0 = 11
+alpha = 0.5
+Rfilm = 0.e-0

configs/params_system_Colclasure20.cfg

@@ -0,0 +1,114 @@
+#Parameters for the low loading cell (1.5 mAh/cm^2) from A. Colclasure et al., J. Electrochim. Acta 337, 135854 (2020).
+# See params_system.cfg for parameter explanations.
+
+[Sim Params]
+# Constant voltage or current or segments of one of them
+# Options: CV, CC, CCsegments, CVsegments
+profileType = CC
+# Battery (dis)charge c-rate (only used for CC), number of capacities / hr
+# (positive for discharge, negative for charge)
+Crate=-2
+#Optional nominal 1C current density for the cell, A/m^2
+1C_current_density = 13.475
+# Voltage cutoffs, V
+Vmax = 4.1
+Vmin = 0
+# Continuation directory.
+# Options: false, absolute directory path
+prevDir = false
+# Final time (only used for CV), [s]
+tend = 1.2e4
+# Number disc. in time
+tsteps = 200
+# Numerical Tolerances
+relTol = 1e-6
+absTol = 1e-6
+# Temperature, K
+T = 303.15
+# Random seed. Set to true to give a random seed in the simulation
+randomSeed = false
+# Value of the random seed, must be an integer
+seed = 0
+# Series resistance, [Ohm m^2]
+Rser = 0.
+# Cathode, anode, and separator numer disc. in x direction (volumes in electrodes)
+Nvol_c = 20
+Nvol_s = 10
+Nvol_a = 20
+# Number of particles per volume for cathode and anode
+Npart_c = 1
+Npart_a = 1
+
+[Electrodes]
+cathode = params_NMC532_Colclasure20.cfg
+anode = params_graphite_Colclasure20.cfg
+# Rate constant of the Li foil electrode, A/m^2
+# Used only if Nvol_a = 0
+k0_foil = 1e0
+# Film resistance on the Li foil, Ohm m^2
+Rfilm_foil = 0e-0
+
+[Particles]
+# electrode particle size distribution info, m
+mean_c = 1.8e-6
+stddev_c = 0e-9
+mean_a = 4.0e-6
+stddev_a = 0e-9
+# Initial electrode filling fractions
+cs0_c = 0.91
+cs0_a = 0.05
+
+[Conductivity]
+# Simulate bulk cathode conductivity (Ohm's Law)?
+simBulkCond_c = false
+simBulkCond_a = false
+# Dimensional conductivity (used if simBulkCond = true), S/m
+sigma_s_c = 1e-1
+sigma_s_a = 1e-1
+# Simulate particle connectivity losses (Ohm's Law)?
+# Options: true, false
+simPartCond_c = false
+simPartCond_a = false
+# Conductance between particles, S = 1/Ohm
+G_mean_c = 1e-14
+G_stddev_c = 0
+G_mean_a = 1e-14
+G_stddev_a = 0
+
+[Geometry]
+# Thicknesses, m
+L_c = 42e-6
+L_a = 47e-6
+L_s = 20e-6
+# Volume loading percents of active material (volume fraction of solid
+# that is active material)
+P_L_c = 0.7803
+P_L_a = 0.9026
+# Porosities (liquid volume fraction in each region)
+poros_c = 0.33
+poros_a = 0.37
+poros_s = 0.39
+# Bruggeman exponent (tortuosity = porosity^bruggExp)
+BruggExp_c = -1.0
+BruggExp_a = -1.2
+BruggExp_s = -1.3
+
+[Electrolyte]
+# Initial electrolyte conc., mol/m^3
+c0 = 1200
+# Cation/anion charge number (e.g. 2, -1 for CaCl_2)
+zp = 1
+zm = -1
+# Cation/anion dissociation number (e.g. 1, 2 for CaCl_2)
+nup = 1
+num = 1
+# Electrolyte model,
+# Options: dilute, SM
+elyteModelType = SM
+# Stefan-Maxwell property set, see props_elyte.py file
+SMset = Colclasure20
+# Reference electrode (defining the electrolyte potential) information:
+# number of electrons transfered in the reaction, 1 for Li/Li+
+n = 1
+# Stoichiometric coefficient of cation, -1 for Li/Li+
+sp = -1

dockerfiles/Dockerfile-daetools-2.0.0

@@ -0,0 +1,11 @@
+FROM python:3.10-bullseye
+
+#Install necessary packages for daetools
+RUN apt-get update && \
+    apt-get install --yes libgl1-mesa-glx libgfortran5
+
+#Download and install daetools
+RUN wget https://sourceforge.net/projects/daetools/files/daetools/2.0.0/daetools-2.0.0-gnu_linux-x86_64.zip && \
+    unzip daetools-2.0.0-gnu_linux-x86_64.zip && \
+    pip install ./daetools-2.0.0-gnu_linux-x86_64 && \
+    rm -r ./daetools*

mpet/config/configuration.py

@@ -140,10 +140,6 @@ def _init_from_cfg(self, paramfile):
         if self.D_s['Nvol_a'] > 0:
             trodes.append('a')
         self['trodes'] = trodes
-        # to check for separator, directly access underlying dict of system config;
-        # self['Nvol']['s'] would not work because that requires have_separator to
-        # be defined already
-        self['have_separator'] = self.D_s['Nvol_s'] > 0
 
         # load electrode parameter file(s)
         self.paramfiles = {}
@@ -506,7 +502,7 @@ def _scale_electrode_parameters(self):
                     self[trode, param] = value / kT
 
         # scalings on separator
-        if self['have_separator']:
+        if self['Nvol']['s']:
             self['L']['s'] /= self['L_ref']
 
     def _scale_macroscopic_parameters(self, Vref):
@@ -761,7 +757,7 @@ def _distr_part(self):
             # For homogeneous particles (only one 'volume' per particle)
             elif solidType in ['homog', 'homog_sdn', 'homog2', 'homog2_sdn']:
                 # Each particle is only one volume
-                psd_num = np.ones(raw.shape, dtype=np.int)
+                psd_num = np.ones(raw.shape, dtype=int)
                 # The lengths are given by the original length distr.
                 psd_len = raw
             else:

mpet/config/parameterset.py

@@ -87,7 +87,7 @@ def __getitem__(self, item):
             d = {}
             # some parameters are also defined for the separator
             trodes = self['trodes'][:]  # make a copy here to avoid adding values to the original
-            if item in PARAMS_SEPARATOR and self['have_separator']:
+            if item in PARAMS_SEPARATOR:
                 trodes.append('s')
             for trode in trodes:
                 # get the value for this electrode/separator and store it

mpet/electrode/diffusion/NMC532_Colclasure20.py

@@ -0,0 +1,4 @@
+def NMC532_Colclasure20(y):
+    cm2_s = 20000.*10**(-2319.*y**10 + 6642.*y**9 - 5269.*y**8 - 3319.*y**7 + 10038.*y**6
+                        - 9806.*y**5 + 5817.*y**4 - 2286.*y**3 + 575.3*y**2 - 83.16*y-9.292)
+    return cm2_s/1e4

mpet/electrode/materials/LiC6_Colclasure_1506T.py

@@ -0,0 +1,29 @@
+import numpy as np
+
+
+def LiC6_Colclasure_1506T(self, y, ybar, muR_ref, ISfuncs=None):
+    """Taken from Colclasure 2020, but only for lithiating. The range of\
+    confidence is 0.01 to 0.97 for voltages of ~0.6V and \
+    0.0435V. Don’t calculate U2 for intercalation fractions below 0.8, \
+    it will cause numeric issues just use U1."""
+    x = y
+    U1 = \
+        - 1.059423355572770E-02*np.tanh((x - 1.453708425609560E-02) / 9.089868397988610E-05) \
+        + 2.443615203087110E-02*np.tanh((x - 5.464261369950400E-01) / 6.270508166379020E-01) \
+        - 1.637520788053810E-02*np.tanh((x - 5.639025014475490E-01) / 7.053886409518520E-02) \
+        - 6.542365622896410E-02*np.tanh((x - 5.960370524233590E-01) / 1.409966536648620E+00) \
+        - 4.173226059293490E-02*np.tanh((x - 1.787670587868640E-01) / 7.693844911793470E-02) \
+        - 4.792178163846890E-01*np.tanh((x + 3.845707852011820E-03) / 4.112633446959460E-02) \
+        + 6.594735004847470E-01 \
+        - 4.364293924074990E-02*np.tanh((x - 9.449231893318330E-02) / -2.046776012570780E-02) \
+        - 8.241166396760410E-02*np.tanh((x - 7.746685789572230E-02) / 3.593817905677970E-02)
+    U2 = \
+        -1.731504647676420E+02*np.power(x, 8.0) + 8.252008712749000E+01*np.power(x, 7.0) \
+        + 1.233160814852810E+02*np.power(x, 6.0) + 5.913206621637760E+01*np.power(x, 5.0) \
+        + 3.322960033709470E+01*np.power(x, 4.0) + 3.437968012320620E+00*np.power(x, 3.0) \
+        - 6.906367679257650E+01*np.power(x, 2.0) - \
+        1.228217254296760E+01*x - 5.037944982759270E+01
+    U = U1 + (U2 - U1) / (1.0 + np.exp(-1.0e2*(x - 1.02956203215198)))
+    muR = self.get_muR_from_OCV(U, muR_ref)
+    actR = None
+    return muR, actR

mpet/electrode/materials/NMC532_Colclasure20.py

@@ -0,0 +1,18 @@
+import numpy as np
+
+
+def NMC532_Colclasure20(self, y, ybar, muR_ref, ISfuncs=None):
+    x = y
+    OCV = (5.314735633000300E+00 +
+           -3.640117692001490E+03*x**14.0 + 1.317657544484270E+04*x**13.0
+           - 1.455742062291360E+04*x**12.0 - 1.571094264365090E+03*x**11.0
+           + 1.265630978512400E+04*x**10.0 - 2.057808873526350E+03*x**9.0
+           - 1.074374333186190E+04*x**8.0 + 8.698112755348720E+03*x**7.0
+           - 8.297904604107030E+02*x**6.0 - 2.073765547574810E+03*x**5.0
+           + 1.190223421193310E+03*x**4.0 - 2.724851668445780E+02*x**3.0
+           + 2.723409218042130E+01*x**2.0 - 4.158276603609060E+00*x +
+           -5.573191762723310E-04*np.exp(6.560240842659690E+00*x**4.148209275061330E+01)
+           )
+    muR = self.get_muR_from_OCV(OCV, muR_ref)
+    actR = None
+    return muR, actR

mpet/electrode/reactions/BV_Colclasure20.py

@@ -0,0 +1,11 @@
+import numpy as np
+
+
+def BV_Colclasure20(eta, c_sld, c_lyte, k0, E_A, T, act_R=None,
+                    act_lyte=None, lmbda=None, alpha=None):
+    """Implemented for the Finegan 2020/Colclasure 2020 model comparison
+    for the NMC electrode"""
+    ecd = k0 * (165*c_sld**5 - 752.4*c_sld**4 + 1241*c_sld**3
+                - 941.7*c_sld**2 + 325*c_sld - 35.85) * (c_lyte/1.2)**0.5
+    Rate = ecd * (np.exp(-alpha*eta/T) - np.exp((1-alpha)*eta/T))
+    return Rate