Convert ecm to jellybamm

.gitignore

@@ -1,12 +1,12 @@
 .ipynb_checkpoints/
-ecm/__pycache__/
-ecm.egg-info/
+jellybamm/__pycache__/
+jellybamm.egg-info/
 *.pyc
 .coverage
-ecm/output/1d/
-ecm/output/spiral/1.5A/
-ecm/output/spiral_tesla/
-ecm/output/tomography/3.0A/
+jellybamm/output/1d/
+jellybamm/output/spiral/1.5A/
+jellybamm/output/spiral_tesla/
+jellybamm/output/tomography/3.0A/
 build/
 dist/
 .virtual_documents/

docs/reference.md

@@ -1 +1 @@
-::: ecm
+::: jellybamm

ecm.egg-info/PKG-INFO

@@ -0,0 +1,21 @@
+Metadata-Version: 2.1
+Name: ecm
+Version: 0.0.2
+Summary: Equivalent Circuit Model for battery modelling using PyBaMM
+Home-page: https://ecm.readthedocs.io/en/latest/
+Author: Tom Tranter
+Author-email: t.g.tranter@gmail.com
+Project-URL: Documentation, https://ecm.readthedocs.io/en/latest/
+Project-URL: Source, https://github.com/TomTranter/pybamm_pnm
+Project-URL: Tracker, https://github.com/TomTranter/pybamm_pnm/issues
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Physics
+License-File: LICENSE
+Requires-Dist: numba
+Requires-Dist: pybamm
+Requires-Dist: liionpack
+Requires-Dist: openpnm==2.8.2
+Requires-Dist: ffmpeg-python

ecm.egg-info/SOURCES.txt

@@ -0,0 +1,18 @@
+LICENSE
+README.md
+setup.cfg
+setup.py
+ecm/__battery__.py
+ecm/__definitions__.py
+ecm/__funcs__.py
+ecm/__init__.py
+ecm/__liionsolve__.py
+ecm/__postprocess__.py
+ecm/__segment_jellyroll__.py
+ecm/__topology__.py
+ecm/__utilities__.py
+ecm.egg-info/PKG-INFO
+ecm.egg-info/SOURCES.txt
+ecm.egg-info/dependency_links.txt
+ecm.egg-info/requires.txt
+ecm.egg-info/top_level.txt

ecm.egg-info/requires.txt

@@ -0,0 +1,5 @@
+numba
+pybamm
+liionpack
+openpnm==2.8.2
+ffmpeg-python

ecm.egg-info/top_level.txt

@@ -0,0 +1 @@
+ecm

ecm/__definitions__.py → jellybamm/__definitions__.py

@@ -5,10 +5,10 @@
 @author: tom
 """
 
-import ecm
+import jellybamm
 import os
 
-ROOT_DIR = os.path.dirname(os.path.abspath(ecm.__file__))
+ROOT_DIR = os.path.dirname(os.path.abspath(jellybamm.__file__))
 PARENT_DIR = os.path.dirname(ROOT_DIR)
 TESTS_DIR = os.path.join(PARENT_DIR, 'tests')
 FIXTURES_DIR = os.path.join(TESTS_DIR, 'fixtures')

ecm/__funcs__.py → jellybamm/__funcs__.py

@@ -131,7 +131,7 @@ def get_cc_heat(net, alg, V_terminal):
     )
 
 
-def run_ecm(net, alg, V_terminal, plot=False):
+def run_jellybamm(net, alg, V_terminal, plot=False):
     potential_pairs = net["throat.conns"][net.throats("spm_resistor")]
     P1 = potential_pairs[:, 0]
     P2 = potential_pairs[:, 1]

ecm/__init__.py → jellybamm/__init__.py

@@ -1,8 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
-jellysim: a package for simulating Li-ion electrochemistry
-          on jellyroll structures
+JellyBaMM: a package for simulating Li-ion electrochemistry on jellyroll structures with PyBaMM
 """
 
 from .__funcs__ import *

ecm/__liionsolve__.py → jellybamm/__liionsolve__.py

@@ -3,7 +3,7 @@
 #
 import os
 import numpy as np
-import ecm
+import jellybamm
 import pybamm
 import time as ticker
 import openpnm as op
@@ -74,7 +74,7 @@ def run_simulation_lp(parameter_values, experiment, initial_soc, project):
     ###########################################################################
     # Make the pybamm simulation - should be moved to a simfunc               #
     ###########################################################################
-    parameter_values = ecm.adjust_parameters(parameter_values, I_typical)
+    parameter_values = jellybamm.adjust_parameters(parameter_values, I_typical)
     # width = parameter_values["Electrode width [m]"]
     # t1 = parameter_values["Negative electrode thickness [m]"]
     # t2 = parameter_values["Positive electrode thickness [m]"]
@@ -89,12 +89,12 @@ def run_simulation_lp(parameter_values, experiment, initial_soc, project):
     ###########################################################################
     # Output variables                                                        #
     ###########################################################################
-    output_variables = ecm.output_variables()
+    output_variables = jellybamm.output_variables()
     ###########################################################################
     # Thermal parameters                                                      #
     ###########################################################################
     T0 = parameter_values["Initial temperature [K]"]
-    lumpy_therm = ecm.lump_thermal_props(parameter_values)
+    lumpy_therm = jellybamm.lump_thermal_props(parameter_values)
     cp = lumpy_therm["lump_Cp"]
     rho = lumpy_therm["lump_rho"]
     ###########################################################################
@@ -103,7 +103,7 @@ def run_simulation_lp(parameter_values, experiment, initial_soc, project):
     # outer_step = 0
     # if config.getboolean("PHYSICS", "do_thermal"):
     # Always do thermal
-    ecm.setup_thermal(project, parameter_values)
+    jellybamm.setup_thermal(project, parameter_values)
     # try:
     #     thermal_third = config.getboolean("RUN", "third")
     # except KeyError:
@@ -112,12 +112,12 @@ def run_simulation_lp(parameter_values, experiment, initial_soc, project):
     # New Liionpack code                                                      #
     ###########################################################################
     dim_time_step = 10
-    neg_econd, pos_econd = ecm.cc_cond(project, parameter_values)
+    neg_econd, pos_econd = jellybamm.cc_cond(project, parameter_values)
     Rs = 1e-2  # series resistance
     Ri = 90  # initial guess for internal resistance
     V = 3.6  # initial guess for cell voltage
     # I_app = 0.5
-    netlist = ecm.network_to_netlist(net, Rs, Ri, V, I_app)
+    netlist = jellybamm.network_to_netlist(net, Rs, Ri, V, I_app)
     T0 = parameter_values["Initial temperature [K]"]
     e_heights = net["throat.electrode_height"][net.throats("throat.spm_resistor")]
     spm_temperature = np.ones(Nspm) * T0
@@ -171,9 +171,9 @@ def run_simulation_lp(parameter_values, experiment, initial_soc, project):
             # key = "Volume-averaged Ohmic heating CC [W.m-3]"
             # vh[key][outer_step, :] = Q_ohm_cc[sorted_res_Ts]
             Q[res_Ts] += Q_tot
-            ecm.apply_heat_source_lp(project, Q)
+            jellybamm.apply_heat_source_lp(project, Q)
             # Calculate Global Temperature
-            ecm.run_step_transient(project, dim_time_step, T0, cp, rho, thermal_third)
+            jellybamm.run_step_transient(project, dim_time_step, T0, cp, rho, thermal_third)
             # Interpolate the node temperatures for the SPMs
             spm_temperature = phase.interpolate_data("pore.temperature")[res_Ts]
             # T_non_dim_spm = fT_non_dim(parameter_values, spm_temperature)
@@ -231,9 +231,9 @@ def run_simulation_lp(parameter_values, experiment, initial_soc, project):
             # key = "Volume-averaged Ohmic heating CC [W.m-3]"
             # vh[key][outer_step, :] = Q_ohm_cc[sorted_res_Ts]
             Q[res_Ts] += Q_tot
-            ecm.apply_heat_source_lp(project, Q)
+            jellybamm.apply_heat_source_lp(project, Q)
             # Calculate Global Temperature
-            ecm.run_step_transient(project, dim_time_step, T0, cp, rho, thermal_third)
+            jellybamm.run_step_transient(project, dim_time_step, T0, cp, rho, thermal_third)
             # Interpolate the node temperatures for the SPMs
             spm_temperature = phase.interpolate_data("pore.temperature")[res_Ts]
             ###################################################################

ecm/__postprocess__.py → jellybamm/__postprocess__.py

@@ -16,7 +16,7 @@
 from matplotlib import gridspec
 import matplotlib.ticker as mtick
 from string import ascii_lowercase as abc
-import ecm
+import jellybamm
 
 
 prop_cycle = plt.rcParams["axes.prop_cycle"]
@@ -188,7 +188,7 @@ def load_data(filepath):
 
 def get_net(filepath=None, filename="spider_net.pnm"):
     if filepath is None:
-        filepath = ecm.INPUT_DIR
+        filepath = jellybamm.INPUT_DIR
     wrk.load_project(os.path.join(filepath, filename))
     sim_name = list(wrk.keys())[-1]
     project = wrk[sim_name]
@@ -592,7 +592,7 @@ def animate_data4(data, case, amp, variables=None, filename=None):
     net = data[case]["network"]
     weights = get_weights(net)
     project = net.project
-    im_spm_map = np.load(os.path.join(ecm.INPUT_DIR, "im_spm_map.npz"))["arr_0"]
+    im_spm_map = np.load(os.path.join(jellybamm.INPUT_DIR, "im_spm_map.npz"))["arr_0"]
     title = filename.split("\\")
     if len(title) == 1:
         title = title[0]
@@ -744,7 +744,7 @@ def jellyroll_subplot(
     soc_arr = np.asarray(soc_list)
     (nrows, ncols) = soc_arr.shape
     fig, axes = plt.subplots(nrows, ncols, figsize=(12, 12), sharex=True, sharey=True)
-    spm_map = np.load(os.path.join(ecm.INPUT_DIR, "im_spm_map.npz"))["arr_0"]
+    spm_map = np.load(os.path.join(jellybamm.INPUT_DIR, "im_spm_map.npz"))["arr_0"]
     spm_map_copy = spm_map.copy()
     spm_map_copy[np.isnan(spm_map_copy)] = -1
     spm_map_copy = spm_map_copy.astype(int)

ecm/__segment_jellyroll__.py → jellybamm/__segment_jellyroll__.py

@@ -17,15 +17,15 @@
 import os
 import openpnm as op
 import openpnm.topotools as tt
-import ecm
+import jellybamm
 
 
 wrk = op.Workspace()
 
 
 def average_images(path=None):
     if path is None:
-        path = ecm.INPUT_DIR
+        path = jellybamm.INPUT_DIR
     # Get File list
     files = []
     for file in os.listdir(path):
@@ -117,9 +117,9 @@ def adjust_radial_average(im, step, deg, dt):
 
 def remove_beam_hardening(im, dt, step, deg):
     # Compute radial averages and adjustments for beam hardening - soften image
-    dat_im = ecm.get_radial_average(im, step, dt)
-    im_soft = ecm.adjust_radial_average(im, step, deg, dt)
-    dat_soft = ecm.get_radial_average(im_soft, step, dt)
+    dat_im = jellybamm.get_radial_average(im, step, dt)
+    im_soft = jellybamm.adjust_radial_average(im, step, deg, dt)
+    dat_soft = jellybamm.get_radial_average(im_soft, step, dt)
     fig, axes = plt.subplots(2, 1, figsize=(10, 10))
     axes[0].imshow(im_soft - im.astype(float))
     axes[1].plot(dat_im[:, 0], dat_im[:, 1])
@@ -375,9 +375,9 @@ def spider_web_network(im_soft, mhs, cc_im, dtheta=10, pixel_size=10.4e-6,
     outer_pos = net['pore.coords'][net.pores('outer')]
     x = outer_pos[:, 0] - mhs
     y = outer_pos[:, 1] - mhs
-    r, t = ecm.polar_transform(x, y)
+    r, t = jellybamm.polar_transform(x, y)
     r_new = np.ones(num_free) * (r + 25)
-    new_x, new_y = ecm.cartesian_transform(r_new, t)
+    new_x, new_y = jellybamm.cartesian_transform(r_new, t)
     free_coords = outer_pos.copy()
     free_coords[:, 0] = new_x + mhs
     free_coords[:, 1] = new_y + mhs
@@ -395,9 +395,9 @@ def spider_web_network(im_soft, mhs, cc_im, dtheta=10, pixel_size=10.4e-6,
     inner_pos = net['pore.coords'][net.pores('inner')]
     x = inner_pos[:, 0] - mhs
     y = inner_pos[:, 1] - mhs
-    r, t = ecm.polar_transform(x, y)
+    r, t = jellybamm.polar_transform(x, y)
     r_new = np.ones(num_inner) * (r - 25)
-    new_x, new_y = ecm.cartesian_transform(r_new, t)
+    new_x, new_y = jellybamm.cartesian_transform(r_new, t)
     inner_coords = inner_pos.copy()
     inner_coords[:, 0] = new_x + mhs
     inner_coords[:, 1] = new_y + mhs
@@ -421,6 +421,6 @@ def spider_web_network(im_soft, mhs, cc_im, dtheta=10, pixel_size=10.4e-6,
     net['throat.arc_length'] = net['throat.radial_position'] * np.deg2rad(dtheta)
 
     if path is None:
-        path = ecm.INPUT_DIR
+        path = jellybamm.INPUT_DIR
     wrk.save_project(project=prj, filename=os.path.join(path, filename))
     return net

ecm/__topology__.py → jellybamm/__topology__.py

@@ -9,7 +9,7 @@
 from openpnm.topotools import plot_coordinates as pcoord
 import os
 import matplotlib.pyplot as plt
-import ecm
+import jellybamm
 import pandas as pd
 
 
@@ -23,8 +23,8 @@ def plot_topology(net, ax=None):
     c3 = np.array([[100 / 255, 100 / 255, 100 / 255, 1]])  # Granite Gray
     if ax is None:
         fig, ax = plt.subplots(1, 1, figsize=(10, 10))
-    ax = ecm.plot_resistors(net, throats=net.throats("throat.neg_cc"), color=c1, ax=ax)
-    ax = ecm.plot_resistors(net, throats=net.throats("throat.pos_cc"), color=c2, ax=ax)
+    ax = jellybamm.plot_resistors(net, throats=net.throats("throat.neg_cc"), color=c1, ax=ax)
+    ax = jellybamm.plot_resistors(net, throats=net.throats("throat.pos_cc"), color=c2, ax=ax)
     ax = pcoord(net, pores=net.pores("neg_cc"), color=c1, s=25, ax=ax)
     ax = pcoord(net, pores=net.pores("pos_cc"), color=c2, s=25, ax=ax)
     ax = pcoord(net, pores=net["pore.neg_tab"], color=c1, s=75, ax=ax)
@@ -253,7 +253,7 @@ def make_spiral_net(
     op.topotools.trim(network=net, throats=net.throats("trimmers"))
 
     # print("N SPM", net.num_throats("spm_resistor"))
-    geo = ecm.setup_geometry(net, dtheta, spacing, length_3d=length_3d)
+    geo = jellybamm.setup_geometry(net, dtheta, spacing, length_3d=length_3d)
     net["throat.arc_length"] = np.deg2rad(dtheta) * net["throat.radial_position"]
     phase = op.phases.GenericPhase(network=net)
     op.physics.GenericPhysics(network=net, phase=phase, geometry=geo)
@@ -262,7 +262,7 @@ def make_spiral_net(
 
 def make_tomo_net(tomo_pnm, dtheta, spacing, length_3d, pos_tabs, neg_tabs):
     wrk = op.Workspace()
-    input_dir = ecm.INPUT_DIR
+    input_dir = jellybamm.INPUT_DIR
     wrk.load_project(os.path.join(input_dir, tomo_pnm))
     sim_name = list(wrk.keys())[-1]
     project = wrk[sim_name]
@@ -291,7 +291,7 @@ def make_tomo_net(tomo_pnm, dtheta, spacing, length_3d, pos_tabs, neg_tabs):
     # Add 1 more
     arc_edges.append(arc_edges[-1] + d)
     arc_edges = np.asarray(arc_edges)
-    geo = ecm.setup_geometry(net, dtheta, spacing, length_3d=length_3d)
+    geo = jellybamm.setup_geometry(net, dtheta, spacing, length_3d=length_3d)
     phase = op.phases.GenericPhase(network=net)
     op.physics.GenericPhysics(network=net, phase=phase, geometry=geo)
     return project, arc_edges

ecm/__utilities__.py → jellybamm/__utilities__.py

@@ -2,14 +2,14 @@
 # Utilities
 #
 
-import ecm
+import jellybamm
 import os
 import numpy as np
 from scipy.interpolate import NearestNDInterpolator
 
 
 def interpolate_timeseries(project, data):
-    im_soft = np.load(os.path.join(ecm.INPUT_DIR, 'im_soft.npz'))['arr_0']
+    im_soft = np.load(os.path.join(jellybamm.INPUT_DIR, 'im_soft.npz'))['arr_0']
     x_len, y_len = im_soft.shape
     net = project.network
     res_Ts = net.throats('spm_resistor')

jellybamm/output/__init__.py

@@ -0,0 +1 @@
+

post_scripts/animate_saved_data.py

@@ -8,7 +8,7 @@
 import pybamm
 import openpnm as op
 import matplotlib.pyplot as plt
-import ecm
+import jellybamm
 import os
 from scipy import io
 import numpy as np
@@ -64,5 +64,5 @@
             variables[plot_time] = time_amalg
 
             save_path = os.path.join(save_root, 'Current collector current density')
-            ecm.animate_data4(project, variables, plot_left, plot_right, weights,
+            jellybamm.animate_data4(project, variables, plot_left, plot_right, weights,
                               filename=save_path)

post_scripts/compare_jelly_stats.py

@@ -5,16 +5,16 @@
 @author: Tom
 """
 
-import ecm
+import jellybamm
 import os
 from scipy import io
 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib import cm
 
 root = 'D:\\pybamm_pnm_results\\Chen2020_v3'
-cases = ecm.get_cases()
-amps = ecm.get_amp_cases()
+cases = jellybamm.get_cases()
+amps = jellybamm.get_amp_cases()
 data_suff = ['mean', 'std', 'chi']
 d = {}
 for case in cases.keys():
@@ -66,7 +66,7 @@ def jellyroll_multiplot(data, cases=[0, 1, 2], amps=[1.75, 3.5, 5.25], var='std'
                 im = ax.imshow(arr, cmap=cm.inferno)
             ax.set_axis_off()
             plt.colorbar(im, ax=ax, format='%.' + str(dp) + 'f')
-            ax.set_title(ecm.format_case(case, amp, expanded=False))
+            ax.set_title(jellybamm.format_case(case, amp, expanded=False))
 
     return fig