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Merge pull request #1206 from pybamm-team/issue-1203-save-to-matlab
Issue 1203 save to matlab
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‎CHANGELOG.md

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@@ -2,6 +2,7 @@
22

33
## Features
44

5+
- Added variables related to equivalent circuit models ([#1204](https://github.com/pybamm-team/PyBaMM/pull/1204))
56
- Added an example script to check conservation of lithium ([#1186](https://github.com/pybamm-team/PyBaMM/pull/1186))
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- Added `erf` and `erfc` functions ([#1184](https://github.com/pybamm-team/PyBaMM/pull/1184))
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@@ -10,6 +11,7 @@
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## Bug fixes
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14+
- Raise error if saving to matlab with variable names that matlab can't read, and give option of providing alternative variable names ([#1206](https://github.com/pybamm-team/PyBaMM/pull/1206))
1315
- Raise error if the boundary condition at the origin in a spherical domain is other than no-flux ([#1175](https://github.com/pybamm-team/PyBaMM/pull/1175))
1416
- Fix boundary conditions at r = 0 for Creating Models notebooks ([#1173](https://github.com/pybamm-team/PyBaMM/pull/1173))
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‎examples/notebooks/Getting Started/Tutorial 6 - Managing simulation outputs.ipynb

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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"name": "stdout",
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"text": [
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"\u001b[33mWARNING: You are using pip version 20.2.1; however, version 20.2.4 is available.\n",
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"You should consider upgrading via the '/Users/vsulzer/Documents/Energy_storage/PyBaMM/.tox/dev/bin/python -m pip install --upgrade pip' command.\u001b[0m\n",
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"Note: you may need to restart the kernel to use updated packages.\n"
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]
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},
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{
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"output_type": "execute_result",
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"data": {
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"text/plain": [
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"<pybamm.solvers.solution.Solution at 0x7f39e107d1d0>"
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"<pybamm.solvers.solution.Solution at 0x1467c6820>"
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]
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},
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"execution_count": 1,
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"metadata": {},
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"output_type": "execute_result"
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"execution_count": 1
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}
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],
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"source": [
@@ -100,6 +102,7 @@
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"metadata": {},
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"outputs": [
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{
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"output_type": "execute_result",
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"data": {
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"text/plain": [
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"array([3.77047806, 3.75305163, 3.74567013, 3.74038819, 3.73581198,\n",
@@ -124,9 +127,8 @@
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" 3.45439366, 3.41299183, 3.35578872, 3.27680073, 3.16842637])"
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]
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},
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"execution_count": 4,
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"metadata": {},
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"output_type": "execute_result"
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"execution_count": 4
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}
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],
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"source": [
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"metadata": {},
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"outputs": [
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{
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"output_type": "execute_result",
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"data": {
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"text/plain": [
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"array([ 0. , 36.36363636, 72.72727273, 109.09090909,\n",
@@ -175,9 +178,8 @@
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" 3490.90909091, 3527.27272727, 3563.63636364, 3600. ])"
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]
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},
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"execution_count": 5,
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"metadata": {},
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"output_type": "execute_result"
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"execution_count": 5
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}
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],
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"source": [
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"metadata": {},
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"outputs": [
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{
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"output_type": "execute_result",
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"data": {
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"text/plain": [
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"array([3.72947891, 3.70860034, 3.67810702, 3.65400558])"
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]
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},
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"execution_count": 6,
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"metadata": {},
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"output_type": "execute_result"
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"execution_count": 6
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}
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],
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"source": [
@@ -263,18 +265,16 @@
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"metadata": {},
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"outputs": [
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{
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"output_type": "display_data",
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"data": {
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"text/plain": "interactive(children=(FloatSlider(value=0.0, description='t', max=1.0, step=0.01), Output()), _dom_classes=('w…",
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "7e116fdff90e40b28b3f13b79f3e7347",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"interactive(children=(FloatSlider(value=0.0, description='t', max=1.0, step=0.01), Output()), _dom_classes=('w…"
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]
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"version_minor": 0,
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"model_id": "0b4ebac3fdd947218f9444b2b381cf04"
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}
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},
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"metadata": {},
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"output_type": "display_data"
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"metadata": {}
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}
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],
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"source": [
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"metadata": {},
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"outputs": [
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{
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"output_type": "display_data",
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"data": {
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"text/plain": "interactive(children=(FloatSlider(value=0.0, description='t', max=1.0, step=0.01), Output()), _dom_classes=('w…",
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "cb9640519af3475b9b921b8523c01020",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"interactive(children=(FloatSlider(value=0.0, description='t', max=1.0, step=0.01), Output()), _dom_classes=('w…"
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]
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"version_minor": 0,
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"model_id": "f4a1b65b2bf945099197135c5598084b"
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}
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},
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"metadata": {},
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"output_type": "display_data"
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"metadata": {}
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},
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{
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"output_type": "execute_result",
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"data": {
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"text/plain": [
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"<pybamm.plotting.quick_plot.QuickPlot at 0x7f39dc81a0b8>"
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"<pybamm.plotting.quick_plot.QuickPlot at 0x14be13b80>"
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]
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},
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"execution_count": 11,
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"metadata": {},
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"output_type": "execute_result"
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"execution_count": 11
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}
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],
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"source": [
@@ -370,7 +368,9 @@
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"outputs": [],
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"source": [
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"sol.save_data(\"sol_data.csv\", [\"Current [A]\", \"Terminal voltage [V]\"], to_format=\"csv\")\n",
373-
"sol.save_data(\"sol_data.mat\", [\"Current [A]\", \"Terminal voltage [V]\"], to_format=\"matlab\")"
371+
"# matlab needs names without spaces\n",
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"sol.save_data(\"sol_data.mat\", [\"Current [A]\", \"Terminal voltage [V]\"], to_format=\"matlab\",\n",
373+
" short_names={\"Current [A]\": \"I\", \"Terminal voltage [V]\": \"V\"})"
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]
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},
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{
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.9"
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"version": "3.8.5-final"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}
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}

‎examples/notebooks/solution-data-and-processed-variables.ipynb

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Large diffs are not rendered by default.

‎examples/scripts/experimental_protocols/cccv.py

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Original file line numberDiff line numberDiff line change
@@ -34,8 +34,8 @@
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ax.set_xlim([0, 13])
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ax.legend()
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37-
# Save time, voltage, current, discharge capacity and temperature to csv and matlab
38-
# formats
37+
# Save time, voltage, current, discharge capacity, temperature, and electrolyte
38+
# concentration to csv and matlab formats
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sim.solution.save_data(
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"output.mat",
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[
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"Terminal voltage [V]",
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"Discharge capacity [A.h]",
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"X-averaged cell temperature [K]",
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"Electrolyte concentration [mol.m-3]",
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],
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to_format="matlab",
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short_names={
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"Time [h]": "t",
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"Current [A]": "I",
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"Terminal voltage [V]": "V",
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"Discharge capacity [A.h]": "Q",
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"X-averaged cell temperature [K]": "T",
56+
"Electrolyte concentration [mol.m-3]": "c_e",
57+
},
4958
)
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# We can only save 0D variables to csv
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sim.solution.save_data(
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"output.csv",
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[

‎pybamm/simulation.py

+4-1
Original file line numberDiff line numberDiff line change
@@ -350,7 +350,10 @@ def solve(
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"list [t0, tf] where t0 is the initial time and tf is the "
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"final time. "
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"For a constant current (dis)charge the suggested 't_eval' "
353-
"is [0, 3700/C] where C is the C-rate."
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"is [0, 3700/C] where C is the C-rate. "
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"For example, run\n\n"
355+
"\tsim.solve([0, 3700])\n\n"
356+
"for a 1C discharge."
354357
)
355358

356359
elif self.operating_mode == "drive cycle":

‎pybamm/solvers/solution.py

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Original file line numberDiff line numberDiff line change
@@ -201,14 +201,31 @@ def __getitem__(self, key):
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self.update(key)
202202
return self._variables[key]
203203

204+
def plot(self, output_variables=None, **kwargs):
205+
"""
206+
A method to quickly plot the outputs of the solution. Creates a
207+
:class:`pybamm.QuickPlot` object (with keyword arguments 'kwargs') and
208+
then calls :meth:`pybamm.QuickPlot.dynamic_plot`.
209+
210+
Parameters
211+
----------
212+
output_variables: list, optional
213+
A list of the variables to plot.
214+
**kwargs
215+
Additional keyword arguments passed to
216+
:meth:`pybamm.QuickPlot.dynamic_plot`.
217+
For a list of all possible keyword arguments see :class:`pybamm.QuickPlot`.
218+
"""
219+
return pybamm.dynamic_plot(self, output_variables=output_variables, **kwargs)
220+
204221
def save(self, filename):
205222
"""Save the whole solution using pickle"""
206223
# No warning here if len(self.data)==0 as solution can be loaded
207224
# and used to process new variables
208225
with open(filename, "wb") as f:
209226
pickle.dump(self, f, pickle.HIGHEST_PROTOCOL)
210227

211-
def save_data(self, filename, variables=None, to_format="pickle"):
228+
def save_data(self, filename, variables=None, to_format="pickle", short_names=None):
212229
"""
213230
Save solution data only (raw arrays)
214231
@@ -224,7 +241,12 @@ def save_data(self, filename, variables=None, to_format="pickle"):
224241
225242
- 'pickle' (default): creates a pickle file with the data dictionary
226243
- 'matlab': creates a .mat file, for loading in matlab
227-
- 'csv': creates a csv file (1D variables only)
244+
- 'csv': creates a csv file (0D variables only)
245+
short_names : dict, optional
246+
Dictionary of shortened names to use when saving. This may be necessary when
247+
saving to MATLAB, since no spaces or special characters are allowed in
248+
MATLAB variable names. Note that not all the variables need to be given
249+
a short name.
228250
229251
"""
230252
if variables is None:
@@ -243,20 +265,55 @@ def save_data(self, filename, variables=None, to_format="pickle"):
243265
to save.
244266
"""
245267
)
268+
269+
# Use any short names if provided
270+
data_short_names = {}
271+
short_names = short_names or {}
272+
for name, var in data.items():
273+
# change to short name if it exists
274+
if name in short_names:
275+
data_short_names[short_names[name]] = var
276+
else:
277+
data_short_names[name] = var
278+
246279
if to_format == "pickle":
247280
with open(filename, "wb") as f:
248-
pickle.dump(data, f, pickle.HIGHEST_PROTOCOL)
281+
pickle.dump(data_short_names, f, pickle.HIGHEST_PROTOCOL)
249282
elif to_format == "matlab":
250-
savemat(filename, data)
283+
# Check all the variable names only contain a-z, A-Z or _ or numbers
284+
for name in data_short_names.keys():
285+
# Check the string only contains the following ASCII:
286+
# a-z (97-122)
287+
# A-Z (65-90)
288+
# _ (95)
289+
# 0-9 (48-57) but not in the first position
290+
for i, s in enumerate(name):
291+
if not (
292+
97 <= ord(s) <= 122
293+
or 65 <= ord(s) <= 90
294+
or ord(s) == 95
295+
or (i > 0 and 48 <= ord(s) <= 57)
296+
):
297+
raise ValueError(
298+
"Invalid character '{}' found in '{}'. ".format(s, name)
299+
+ "MATLAB variable names must only contain a-z, A-Z, _, "
300+
"or 0-9 (except the first position). "
301+
"Use the 'short_names' argument to pass an alternative "
302+
"variable name, e.g. \n\n"
303+
"\tsolution.save_data(filename, "
304+
"['Electrolyte concentration'], to_format='matlab, "
305+
"short_names={'Electrolyte concentration': 'c_e'})"
306+
)
307+
savemat(filename, data_short_names)
251308
elif to_format == "csv":
252-
for name, var in data.items():
309+
for name, var in data_short_names.items():
253310
if var.ndim >= 2:
254311
raise ValueError(
255312
"only 0D variables can be saved to csv, but '{}' is {}D".format(
256313
name, var.ndim - 1
257314
)
258315
)
259-
df = pd.DataFrame(data)
316+
df = pd.DataFrame(data_short_names)
260317
df.to_csv(filename, index=False)
261318
else:
262319
raise ValueError("format '{}' not recognised".format(to_format))

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