diff --git a/docs/6_dust_evolution.html b/docs/6_dust_evolution.html index 9f4d981..aeccc67 100644 --- a/docs/6_dust_evolution.html +++ b/docs/6_dust_evolution.html @@ -195,42 +195,23 @@
fig = plt.figure(dpi=150)
ax = fig.add_subplot(111)
ax.imshow(np.where(sim.dust.Sigma.jacobian().toarray() != 0., 1., 0.), cmap="Blues")
-ax.hlines(np.arange(0., sim.grid.Nr*sim.grid.Nm, sim.grid.Nm)-0.5, -0.5, sim.grid.Nr*sim.grid.Nm-0.5, color="gray", alpha=0.5)
-ax.vlines(np.arange(0., sim.grid.Nr*sim.grid.Nm, sim.grid.Nm)-0.5, -0.5, sim.grid.Nr*sim.grid.Nm-0.5, color="gray", alpha=0.5)
-ax.hlines(np.arange(0., sim.grid.Nr*sim.grid.Nm, 1)-0.5, -0.5, sim.grid.Nr*sim.grid.Nm-0.5, color="gray", alpha=0.25, lw=0.5)
-ax.vlines(np.arange(0., sim.grid.Nr*sim.grid.Nm, 1)-0.5, -0.5, sim.grid.Nr*sim.grid.Nm-0.5, color="gray", alpha=0.25, lw=0.5)
+ax.hlines(np.arange(0., sim.grid.Nr[0]*sim.grid.Nm[0], sim.grid.Nm[0])-0.5, -0.5, sim.grid.Nr[0]*sim.grid.Nm[0]-0.5, color="gray", alpha=0.5)
+ax.vlines(np.arange(0., sim.grid.Nr[0]*sim.grid.Nm[0], sim.grid.Nm[0])-0.5, -0.5, sim.grid.Nr[0]*sim.grid.Nm[0]-0.5, color="gray", alpha=0.5)
+ax.hlines(np.arange(0., sim.grid.Nr[0]*sim.grid.Nm[0], 1)-0.5, -0.5, sim.grid.Nr[0]*sim.grid.Nm[0]-0.5, color="gray", alpha=0.25, lw=0.5)
+ax.vlines(np.arange(0., sim.grid.Nr[0]*sim.grid.Nm[0], 1)-0.5, -0.5, sim.grid.Nr[0]*sim.grid.Nm[0]-0.5, color="gray", alpha=0.25, lw=0.5)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
-ax.set_title("Structure of Jacobian $\mathbb{J}$")
+ax.set_title(r"Structure of Jacobian $\mathbb{J}$")
fig.tight_layout()
plt.show()
-<>:10: SyntaxWarning: invalid escape sequence '\m'
-<>:10: SyntaxWarning: invalid escape sequence '\m'
-/tmp/ipykernel_93912/1018857805.py:10: SyntaxWarning: invalid escape sequence '\m'
- ax.set_title("Structure of Jacobian $\mathbb{J}$")
-/tmp/ipykernel_93912/1018857805.py:4: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
- ax.hlines(np.arange(0., sim.grid.Nr*sim.grid.Nm, sim.grid.Nm)-0.5, -0.5, sim.grid.Nr*sim.grid.Nm-0.5, color="gray", alpha=0.5)
-/tmp/ipykernel_93912/1018857805.py:5: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
- ax.vlines(np.arange(0., sim.grid.Nr*sim.grid.Nm, sim.grid.Nm)-0.5, -0.5, sim.grid.Nr*sim.grid.Nm-0.5, color="gray", alpha=0.5)
-/tmp/ipykernel_93912/1018857805.py:6: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
- ax.hlines(np.arange(0., sim.grid.Nr*sim.grid.Nm, 1)-0.5, -0.5, sim.grid.Nr*sim.grid.Nm-0.5, color="gray", alpha=0.25, lw=0.5)
-/tmp/ipykernel_93912/1018857805.py:7: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
- ax.vlines(np.arange(0., sim.grid.Nr*sim.grid.Nm, 1)-0.5, -0.5, sim.grid.Nr*sim.grid.Nm-0.5, color="gray", alpha=0.25, lw=0.5)
-
This is a the Jacobian for a simulation with 5 radial grid cells and 8 mass bins. This Jacobian acts on the raveled dust surface densities Simulation.dust.Sigma.ravel()
and has a shape of (Simulation.grid.Nr*Simulation.grid.Nm, Simulation.grid.Nr*Simulation.grid.Nm)
fig = plt.figure(dpi=150)
ax = fig.add_subplot(111)
ax.imshow(np.where(sim.gas.Sigma.jacobian().toarray() != 0., 1., 0.), cmap="Blues")
-ax.hlines(np.arange(0., sim.grid.Nr)-0.5, -0.5, sim.grid.Nr-0.5, color="gray", alpha=0.5)
-ax.vlines(np.arange(0., sim.grid.Nr)-0.5, -0.5, sim.grid.Nr-0.5, color="gray", alpha=0.5)
+ax.hlines(np.arange(0., sim.grid.Nr[0])-0.5, -0.5, sim.grid.Nr[0]-0.5, color="gray", alpha=0.5)
+ax.vlines(np.arange(0., sim.grid.Nr[0])-0.5, -0.5, sim.grid.Nr[0]-0.5, color="gray", alpha=0.5)
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
-ax.set_title("Structure of Jacobian $\mathbb{J}$")
+ax.set_title(r"Structure of Jacobian $\mathbb{J}$")
fig.tight_layout()
plt.show()
-<>:8: SyntaxWarning: invalid escape sequence '\m'
-<>:8: SyntaxWarning: invalid escape sequence '\m'
-/tmp/ipykernel_93989/2308441433.py:8: SyntaxWarning: invalid escape sequence '\m'
- ax.set_title("Structure of Jacobian $\mathbb{J}$")
-/tmp/ipykernel_93989/2308441433.py:4: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
- ax.hlines(np.arange(0., sim.grid.Nr)-0.5, -0.5, sim.grid.Nr-0.5, color="gray", alpha=0.5)
-/tmp/ipykernel_93989/2308441433.py:5: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
- ax.vlines(np.arange(0., sim.grid.Nr)-0.5, -0.5, sim.grid.Nr-0.5, color="gray", alpha=0.5)
-
Notable exceptions are the first and the last row, which are used to set the boundary conditions. They require up to three elements to set the gradients if needed.
diff --git a/docs/7_gas_evolution.ipynb b/docs/7_gas_evolution.ipynb index 25cf5f2..366d93a 100644 --- a/docs/7_gas_evolution.ipynb +++ b/docs/7_gas_evolution.ipynb @@ -35,10 +35,10 @@ "execution_count": 1, "metadata": { "execution": { - "iopub.execute_input": "2023-11-30T11:28:23.237559Z", - "iopub.status.busy": "2023-11-30T11:28:23.236864Z", - "iopub.status.idle": "2023-11-30T11:28:24.180435Z", - "shell.execute_reply": "2023-11-30T11:28:24.178773Z" + "iopub.execute_input": "2023-12-01T18:27:33.313774Z", + "iopub.status.busy": "2023-12-01T18:27:33.313154Z", + "iopub.status.idle": "2023-12-01T18:27:34.363317Z", + "shell.execute_reply": "2023-12-01T18:27:34.361722Z" } }, "outputs": [], @@ -78,10 +78,10 @@ "execution_count": 2, "metadata": { "execution": { - "iopub.execute_input": "2023-11-30T11:28:24.187660Z", - "iopub.status.busy": "2023-11-30T11:28:24.186921Z", - "iopub.status.idle": "2023-11-30T11:28:24.193101Z", - "shell.execute_reply": "2023-11-30T11:28:24.192072Z" + "iopub.execute_input": "2023-12-01T18:27:34.371494Z", + "iopub.status.busy": "2023-12-01T18:27:34.370345Z", + "iopub.status.idle": "2023-12-01T18:27:34.377508Z", + "shell.execute_reply": "2023-12-01T18:27:34.376670Z" } }, "outputs": [], @@ -95,27 +95,14 @@ "execution_count": 3, "metadata": { "execution": { - "iopub.execute_input": "2023-11-30T11:28:24.198475Z", - "iopub.status.busy": "2023-11-30T11:28:24.197910Z", - "iopub.status.idle": "2023-11-30T11:28:24.493119Z", - "shell.execute_reply": "2023-11-30T11:28:24.492056Z" - } + "iopub.execute_input": "2023-12-01T18:27:34.382015Z", + "iopub.status.busy": "2023-12-01T18:27:34.381784Z", + "iopub.status.idle": "2023-12-01T18:27:34.664024Z", + "shell.execute_reply": "2023-12-01T18:27:34.663052Z" + }, + "tags": [] }, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "<>:8: SyntaxWarning: invalid escape sequence '\\m'\n", - "<>:8: SyntaxWarning: invalid escape sequence '\\m'\n", - "/tmp/ipykernel_93989/2308441433.py:8: SyntaxWarning: invalid escape sequence '\\m'\n", - " ax.set_title(\"Structure of Jacobian $\\mathbb{J}$\")\n", - "/tmp/ipykernel_93989/2308441433.py:4: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)\n", - " ax.hlines(np.arange(0., sim.grid.Nr)-0.5, -0.5, sim.grid.Nr-0.5, color=\"gray\", alpha=0.5)\n", - "/tmp/ipykernel_93989/2308441433.py:5: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)\n", - " ax.vlines(np.arange(0., sim.grid.Nr)-0.5, -0.5, sim.grid.Nr-0.5, color=\"gray\", alpha=0.5)\n" - ] - }, { "data": { "image/png": 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", @@ -131,11 +118,11 @@ "fig = plt.figure(dpi=150)\n", "ax = fig.add_subplot(111)\n", "ax.imshow(np.where(sim.gas.Sigma.jacobian().toarray() != 0., 1., 0.), cmap=\"Blues\")\n", - "ax.hlines(np.arange(0., sim.grid.Nr)-0.5, -0.5, sim.grid.Nr-0.5, color=\"gray\", alpha=0.5)\n", - "ax.vlines(np.arange(0., sim.grid.Nr)-0.5, -0.5, sim.grid.Nr-0.5, color=\"gray\", alpha=0.5)\n", + "ax.hlines(np.arange(0., sim.grid.Nr[0])-0.5, -0.5, sim.grid.Nr[0]-0.5, color=\"gray\", alpha=0.5)\n", + "ax.vlines(np.arange(0., sim.grid.Nr[0])-0.5, -0.5, sim.grid.Nr[0]-0.5, color=\"gray\", alpha=0.5)\n", "ax.get_xaxis().set_visible(False)\n", "ax.get_yaxis().set_visible(False)\n", - "ax.set_title(\"Structure of Jacobian $\\mathbb{J}$\")\n", + "ax.set_title(r\"Structure of Jacobian $\\mathbb{J}$\")\n", "fig.tight_layout()\n", "plt.show()" ] @@ -191,10 +178,10 @@ "execution_count": 4, "metadata": { "execution": { - "iopub.execute_input": "2023-11-30T11:28:24.497327Z", - "iopub.status.busy": "2023-11-30T11:28:24.497053Z", - "iopub.status.idle": "2023-11-30T11:28:24.505822Z", - "shell.execute_reply": "2023-11-30T11:28:24.504900Z" + "iopub.execute_input": "2023-12-01T18:27:34.720211Z", + "iopub.status.busy": "2023-12-01T18:27:34.718848Z", + "iopub.status.idle": "2023-12-01T18:27:34.732454Z", + "shell.execute_reply": "2023-12-01T18:27:34.731139Z" } }, "outputs": [ @@ -241,10 +228,10 @@ "execution_count": 5, "metadata": { "execution": { - "iopub.execute_input": "2023-11-30T11:28:24.510064Z", - "iopub.status.busy": "2023-11-30T11:28:24.509824Z", - "iopub.status.idle": "2023-11-30T11:28:24.514775Z", - "shell.execute_reply": "2023-11-30T11:28:24.513726Z" + "iopub.execute_input": "2023-12-01T18:27:34.736284Z", + "iopub.status.busy": "2023-12-01T18:27:34.735799Z", + "iopub.status.idle": "2023-12-01T18:27:34.741789Z", + "shell.execute_reply": "2023-12-01T18:27:34.740386Z" } }, "outputs": [], @@ -258,10 +245,10 @@ "execution_count": 6, "metadata": { "execution": { - "iopub.execute_input": "2023-11-30T11:28:24.518863Z", - "iopub.status.busy": "2023-11-30T11:28:24.518590Z", - "iopub.status.idle": "2023-11-30T11:28:24.527562Z", - "shell.execute_reply": "2023-11-30T11:28:24.526435Z" + "iopub.execute_input": "2023-12-01T18:27:34.746216Z", + "iopub.status.busy": "2023-12-01T18:27:34.745619Z", + "iopub.status.idle": "2023-12-01T18:27:34.755321Z", + "shell.execute_reply": "2023-12-01T18:27:34.754195Z" } }, "outputs": [ @@ -312,10 +299,10 @@ "execution_count": 7, "metadata": { "execution": { - "iopub.execute_input": "2023-11-30T11:28:24.533296Z", - "iopub.status.busy": "2023-11-30T11:28:24.532696Z", - "iopub.status.idle": "2023-11-30T11:28:24.539000Z", - "shell.execute_reply": "2023-11-30T11:28:24.537584Z" + "iopub.execute_input": "2023-12-01T18:27:34.760296Z", + "iopub.status.busy": "2023-12-01T18:27:34.759708Z", + "iopub.status.idle": "2023-12-01T18:27:34.765477Z", + "shell.execute_reply": "2023-12-01T18:27:34.764249Z" } }, "outputs": [], @@ -338,10 +325,10 @@ "execution_count": 8, "metadata": { "execution": { - "iopub.execute_input": "2023-11-30T11:28:24.544909Z", - "iopub.status.busy": "2023-11-30T11:28:24.544284Z", - "iopub.status.idle": "2023-11-30T11:28:24.553180Z", - "shell.execute_reply": "2023-11-30T11:28:24.551897Z" + "iopub.execute_input": "2023-12-01T18:27:34.770985Z", + "iopub.status.busy": "2023-12-01T18:27:34.770357Z", + "iopub.status.idle": "2023-12-01T18:27:34.778730Z", + "shell.execute_reply": "2023-12-01T18:27:34.777526Z" } }, "outputs": [ @@ -366,10 +353,10 @@ "execution_count": 9, "metadata": { "execution": { - "iopub.execute_input": "2023-11-30T11:28:24.559812Z", - "iopub.status.busy": "2023-11-30T11:28:24.558316Z", - "iopub.status.idle": "2023-11-30T11:28:24.565185Z", - "shell.execute_reply": "2023-11-30T11:28:24.563771Z" + "iopub.execute_input": "2023-12-01T18:27:34.784596Z", + "iopub.status.busy": "2023-12-01T18:27:34.783885Z", + "iopub.status.idle": "2023-12-01T18:27:34.789985Z", + "shell.execute_reply": "2023-12-01T18:27:34.788520Z" } }, "outputs": [], @@ -382,10 +369,10 @@ "execution_count": 10, "metadata": { "execution": { - "iopub.execute_input": "2023-11-30T11:28:24.571273Z", - "iopub.status.busy": "2023-11-30T11:28:24.570565Z", - "iopub.status.idle": "2023-11-30T11:28:24.580307Z", - "shell.execute_reply": "2023-11-30T11:28:24.578799Z" + "iopub.execute_input": "2023-12-01T18:27:34.795709Z", + "iopub.status.busy": "2023-12-01T18:27:34.795037Z", + "iopub.status.idle": "2023-12-01T18:27:34.803322Z", + "shell.execute_reply": "2023-12-01T18:27:34.802107Z" } }, "outputs": [ @@ -428,7 +415,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.0" + "version": "3.11.5" } }, "nbformat": 4, diff --git a/docs/B_publications.ipynb b/docs/B_publications.ipynb index 321817d..abfb685 100644 --- a/docs/B_publications.ipynb +++ b/docs/B_publications.ipynb @@ -292,7 +292,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.5" + "version": "3.10.13" } }, "nbformat": 4, diff --git a/docs/E_changelog.html b/docs/E_changelog.html index 1437f2b..7a21dea 100644 --- a/docs/E_changelog.html +++ b/docs/E_changelog.html @@ -128,7 +128,7 @@DustPy
since version v1.0.0
including discussions of their influence on the simulations.
Release date: 2nd December 2023
+Release date: 3rd December 2023
Due to the deprecation of numpy.distutils
, DustPy
is now using Meson as build system.
In order to add multiple gas species in future versions, the Jacobian of the gas surface density has been modified. All previous model that have not specifically customized the gas Jacobian should be compatible with this version.
+In order to add multiple gas species in future versions, the Jacobian of the gas surface density has been modified. All previous models that have not specifically customized the gas Jacobian should be compatible with this version.
We can plot our results now.
@@ -615,30 +615,19 @@
-<>:21: SyntaxWarning: invalid escape sequence '\o'
-<>:21: SyntaxWarning: invalid escape sequence '\o'
-/tmp/ipykernel_94249/2126622601.py:21: SyntaxWarning: invalid escape sequence '\o'
- ax10.set_ylabel("Mass [$M_\oplus$]")
-
DustPy
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The Standard Model": [[3, "4.-The-Standard-Model"]], "Dust": [[3, "Dust"]], "Simulation.dust.backreaction": [[3, "Simulation.dust.backreaction"]], "Simulation.dust.boundary": [[3, "Simulation.dust.boundary"]], "Simulation.dust.coagulation": [[3, "Simulation.dust.coagulation"]], "Simulation.dust.delta": [[3, "Simulation.dust.delta"]], "Simulation.dust.delta.rad": [[3, "Simulation.dust.delta.rad"]], "Simulation.dust.delta.turb": [[3, "Simulation.dust.delta.turb"]], "Simulation.dust.delta.vert": [[3, "Simulation.dust.delta.vert"]], "Simulation.dust.Fi": [[3, "Simulation.dust.Fi"]], "Simulation.dust.Fi.adv": [[3, "Simulation.dust.Fi.adv"]], "Simulation.dust.Fi.diff": [[3, "Simulation.dust.Fi.diff"]], "Simulation.dust.Fi.tot": [[3, "Simulation.dust.Fi.tot"]], "Simulation.dust.p": [[3, "Simulation.dust.p"]], "Simulation.dust.p.frag": [[3, "Simulation.dust.p.frag"]], "Simulation.dust.p.stick": [[3, "Simulation.dust.p.stick"]], "Simulation.dust.S": [[3, "Simulation.dust.S"]], "Simulation.dust.S.coag": [[3, "Simulation.dust.S.coag"]], "Simulation.dust.S.ext": [[3, "Simulation.dust.S.ext"]], "Simulation.dust.S.hyd": [[3, "Simulation.dust.S.hyd"]], "Simulation.dust.S.tot": [[3, "Simulation.dust.S.tot"]], "Simulation.dust.v": [[3, "Simulation.dust.v"]], "Simulation.dust.v.rel": [[3, "Simulation.dust.v.rel"]], "Simulation.dust.v.rel.azi": [[3, "Simulation.dust.v.rel.azi"]], "Simulation.dust.v.brown": [[3, "Simulation.dust.v.brown"]], "Simulation.dust.v.rel.rad": [[3, "Simulation.dust.v.rel.rad"]], "Simulation.dust.v.rel.tot": [[3, "Simulation.dust.v.rel.tot"]], "Simulation.dust.v.rel.turb": [[3, "Simulation.dust.v.rel.turb"]], "Simulation.dust.v.rel.vert": [[3, "Simulation.dust.v.rel.vert"]], "Simulation.dust.v.driftmax": [[3, "Simulation.dust.v.driftmax"]], "Simulation.dust.v.frag": [[3, "Simulation.dust.v.frag"]], "Simulation.dust.v.rad": [[3, "Simulation.dust.v.rad"]], "Simulation.dust.a": [[3, "Simulation.dust.a"]], "Simulation.dust.D": [[3, "Simulation.dust.D"]], "Simulation.dust.eps": [[3, "Simulation.dust.eps"]], "Simulation.dust.fill": [[3, "Simulation.dust.fill"]], "Simulation.dust.H": [[3, "Simulation.dust.H"]], "Simulation.dust.kernel": [[3, "Simulation.dust.kernel"]], "Simulation.dust.rho": [[3, "Simulation.dust.rho"]], "Simulation.dust.rhos": [[3, "Simulation.dust.rhos"]], "Simulation.dust.Sigma": [[3, "Simulation.dust.Sigma"]], "Simulation.dust.SigmaFloor": [[3, "Simulation.dust.SigmaFloor"]], "Simulation.dust.St": [[3, "Simulation.dust.St"]], "Update order": [[3, "Update-order"], [3, "id1"], [3, "id2"], [3, "id3"]], "Gas": [[3, "Gas"]], "Simulation.gas.boundary": [[3, "Simulation.gas.boundary"]], "Simulation.gas.S": [[3, "Simulation.gas.S"]], "Simulation.gas.S.ext": [[3, "Simulation.gas.S.ext"]], "Simulation.gas.S.hyd": [[3, "Simulation.gas.S.hyd"]], "Simulation.gas.S.tot": [[3, "Simulation.gas.S.tot"]], "Simulation.gas.v": [[3, "Simulation.gas.v"]], "Simulation.gas.v.rad": [[3, "Simulation.gas.v.rad"]], "Simulation.gas.v.visc": [[3, "Simulation.gas.v.visc"]], "Simulation.gas.alpha": [[3, "Simulation.gas.alpha"]], "Simulation.gas.cs": [[3, "Simulation.gas.cs"]], "Simulation.gas.eta": [[3, "Simulation.gas.eta"]], "Simulation.gas.Fi": [[3, "Simulation.gas.Fi"]], "Simulation.gas.gamma": [[3, "Simulation.gas.gamma"]], "Simulation.gas.Hp": [[3, "Simulation.gas.Hp"]], "Simulation.gas.mfp": [[3, "Simulation.gas.mfp"]], "Simulation.gas.mu": [[3, "Simulation.gas.mu"]], "Simulation.gas.n": [[3, "Simulation.gas.n"]], "Simulation.gas.nu": [[3, "Simulation.gas.nu"]], "Simulation.gas.P": [[3, "Simulation.gas.P"]], "Simulation.gas.rho": [[3, "Simulation.gas.rho"]], "Simulation.gas.Sigma": [[3, "Simulation.gas.Sigma"]], "Simulation.gas.SigmaFloor": [[3, "Simulation.gas.SigmaFloor"]], "Simulation.gas.T": [[3, "Simulation.gas.T"]], "Grid": [[3, "Grid"]], "Simulation.grid.A": [[3, "Simulation.grid.A"]], "Simulation.grid.m": [[3, "Simulation.grid.m"]], "Simulation.grid.Nm": [[3, "Simulation.grid.Nm"]], "Simulation.grid.Nr": [[3, "Simulation.grid.Nr"]], "Simulation.grid.OmegaK": [[3, "Simulation.grid.OmegaK"]], "Simulation.grid.r": [[3, "Simulation.grid.r"]], "Simulation.grid.ri": [[3, "Simulation.grid.ri"]], "Star": [[3, "Star"]], "Simulation.star.L": [[3, "Simulation.star.L"]], "Simulation.star.M": [[3, "Simulation.star.M"]], "Simulation.star.R": [[3, "Simulation.star.R"]], "Simulation.star.T": [[3, "Simulation.star.T"]], "Time": [[3, "Time"]], "Integrator": [[3, "Integrator"]], "Writer": [[3, "Writer"]], "5. Dust Coagulation": [[4, "5.-Dust-Coagulation"]], "Sticking": [[4, "Sticking"]], "Fragmentation & Erosion": [[4, "Fragmentation-&-Erosion"]], "Probabilities": [[4, "Probabilities"]], "Bouncing": [[4, "Bouncing"]], "Collision Rates": [[4, "Collision-Rates"]], "Coagulation Sources": [[4, "Coagulation-Sources"]], "6. Dust Evolution": [[5, "6.-Dust-Evolution"]], "Coagulation": [[5, "Coagulation"]], "Turning off Fragmentation": [[5, "Turning-off-Fragmentation"]], "Turning off Coagulation": [[5, "Turning-off-Coagulation"]], "Hydrodynamics": [[5, "Hydrodynamics"], [6, "Hydrodynamics"]], "Advection": [[5, "Advection"]], "Turning off Advection": [[5, "Turning-off-Advection"]], "Diffusion": [[5, "Diffusion"]], "Turning off Diffusion": [[5, "Turning-off-Diffusion"]], "Turning off Hydrodynamics": [[5, "Turning-off-Hydrodynamics"], [6, "Turning-off-Hydrodynamics"]], "External Sources": [[5, "External-Sources"], [6, "External-Sources"]], "Turning off Dust Evolution": [[5, "Turning-off-Dust-Evolution"], [92, "Turning-off-Dust-Evolution"]], "Changing the Dust Integrator": [[5, "Changing-the-Dust-Integrator"]], "7. Gas Evolution": [[6, "7.-Gas-Evolution"]], "Turning off External Sources": [[6, "Turning-off-External-Sources"]], "Turning off Gas Evolution": [[6, "Turning-off-Gas-Evolution"]], "Appendix A: Citation": [[7, "Appendix-A:-Citation"]], "Appendix B: List of Publications": [[8, "Appendix-B:-List-of-Publications"]], "Appendix C: Contributing/Bugs/Features": [[9, "Appendix-C:-Contributing/Bugs/Features"]], "Contributing": [[9, "Contributing"]], "Bug Reports": [[9, "Bug-Reports"]], "Feature Requests": [[9, "Feature-Requests"]], "Appendix D: DustPy Discussions": [[10, "Appendix-D:-DustPy-Discussions"]], "Appendix E: Changelog": [[11, "Appendix-E:-Changelog"]], "v1.0.5": [[11, "v1.0.5"]], "Using Meson as build system": [[11, "Using-Meson-as-build-system"]], "Bugfix to velocity distribution": [[11, "Bugfix-to-velocity-distribution"]], "Bugfix to plotting script": [[11, "Bugfix-to-plotting-script"]], "Preparation for the addition of multiple gas species": [[11, "Preparation-for-the-addition-of-multiple-gas-species"]], "v1.0.4": [[11, "v1.0.4"]], "Bugfix to boundary conditions": [[11, "Bugfix-to-boundary-conditions"]], "v1.0.3": [[11, "v1.0.3"]], "Correction to inital particle size distribution": [[11, "Correction-to-inital-particle-size-distribution"]], "Removal of non-ASCII characters": [[11, "Removal-of-non-ASCII-characters"]], "v1.0.2": [[11, "v1.0.2"]], "Change in default temperature profile": [[11, "Change-in-default-temperature-profile"]], "v1.0.1": [[11, "v1.0.1"]], "Change to Collision Kernel": [[11, "Change-to-Collision-Kernel"]], "v1.0.0": [[11, "v1.0.0"]], "Module Reference": [[12, "module-reference"]], "dustpy Package": [[12, "module-dustpy"]], "Classes": [[12, "classes"], [12, "id2"], [12, "id4"], [12, "id9"]], "dustpy.constants Package": [[12, "module-dustpy.constants"]], "Constants": [[12, "constants"]], "dustpy.plot Package": [[12, "module-dustpy.plot"]], "Functions": [[12, "functions"], [12, "id1"], [12, "id3"], [12, "id5"], [12, "id6"], [12, "id7"], [12, "id8"]], "dustpy.std Package": [[12, "module-dustpy.std"]], "dustpy.std.dust Module": [[12, "module-dustpy.std.dust"]], "dustpy.std.gas Module": [[12, "module-dustpy.std.gas"]], "dustpy.std.grid Module": [[12, "module-dustpy.std.grid"]], "dustpy.std.sim Module": [[12, "module-dustpy.std.sim"]], "dustpy.std.star Module": [[12, "module-dustpy.std.star"]], "dustpy.utils Package": [[12, "module-dustpy.utils"]], "Simulation": [[13, "simulation"]], "ipanel": [[14, "ipanel"]], "panel": [[15, "panel"]], "D": [[16, "d"]], "F_adv": [[17, "f-adv"]], "F_diff": [[18, "f-diff"]], "F_tot": [[19, "f-tot"]], "H": [[20, "h"]], "MRN_distribution": [[21, "mrn-distribution"]], "S_coag": [[22, "s-coag"]], "S_hyd": [[23, "s-hyd"], [56, "s-hyd"]], "S_tot": [[24, "s-tot"], [57, "s-tot"]], "SigmaFloor": [[25, "sigmafloor"]], "Sigma_deriv": [[26, "sigma-deriv"]], "St_Epstein_StokesI": [[27, "st-epstein-stokesi"]], "a": [[28, "a"]], "boundary": [[29, "boundary"], [59, "boundary"]], "coagulation_parameters": [[30, "coagulation-parameters"]], "dt": [[31, "dt"], [61, "dt"], [77, "dt"]], "dt_adaptive": [[32, "dt-adaptive"], [78, "dt-adaptive"]], "enforce_floor_value": [[33, "enforce-floor-value"], [62, "enforce-floor-value"]], "eps": [[34, "eps"]], "finalize_explicit": [[35, "finalize-explicit"]], "finalize_implicit": [[36, "finalize-implicit"]], "impl_1_direct": [[37, "impl-1-direct"], [65, "impl-1-direct"]], "jacobian": [[38, "jacobian"], [66, "jacobian"]], "kernel": [[39, "kernel"]], "p_frag": [[40, "p-frag"]], "p_stick": [[41, "p-stick"]], "prepare": [[42, "prepare"], [71, "prepare"]], "rho_midplane": [[43, "rho-midplane"], [72, "rho-midplane"]], "set_implicit_boundaries": [[44, "set-implicit-boundaries"], [73, "set-implicit-boundaries"]], "vdriftmax": [[45, "vdriftmax"]], "vrad": [[46, "vrad"], [74, "vrad"]], "vrel_azimuthal_drift": [[47, "vrel-azimuthal-drift"]], "vrel_brownian_motion": [[48, "vrel-brownian-motion"]], "vrel_radial_drift": [[49, "vrel-radial-drift"]], "vrel_tot": [[50, "vrel-tot"]], "vrel_turbulent_motion": [[51, "vrel-turbulent-motion"]], "vrel_vertical_settling": [[52, "vrel-vertical-settling"]], "Fi": [[53, "fi"]], "Hp": [[54, "hp"]], "P_midplane": [[55, "p-midplane"]], "T_passive": [[58, "t-passive"]], "cs_adiabatic": [[60, "cs-adiabatic"]], "eta_midplane": [[63, "eta-midplane"]], "finalize": [[64, "finalize"]], "lyndenbellpringle1974": [[67, "lyndenbellpringle1974"]], "mfp_midplane": [[68, "mfp-midplane"]], "n_midplane": [[69, "n-midplane"]], "nu": [[70, "nu"]], "vvisc": [[75, "vvisc"]], "OmegaK": [[76, "omegak"]], "finalize_explicit_dust": [[79, "finalize-explicit-dust"]], "finalize_implicit_dust": [[80, "finalize-implicit-dust"]], "prepare_explicit_dust": [[81, "prepare-explicit-dust"]], "prepare_implicit_dust": [[82, "prepare-implicit-dust"]], "luminosity": [[83, "luminosity"]], "Boundary": [[84, "boundary"]], "print_version_warning": [[85, "print-version-warning"]], "Library: dustpylib": [[86, "Library:-dustpylib"]], "Example: Ice Lines": [[87, "Example:-Ice-Lines"]], "Example: Planetary Gaps": [[88, "Example:-Planetary-Gaps"]], "Gap Profiles": [[88, "Gap-Profiles"]], "Adding planets": [[88, "Adding-planets"]], "Viscosity pertubation": [[88, "Viscosity-pertubation"]], "Growing planets": [[88, "Growing-planets"]], "Example: Planetesimal Formation": [[89, "Example:-Planetesimal-Formation"]], "Refining the radial grid": [[89, "Refining-the-radial-grid"]], "Adding gap": [[89, "Adding-gap"]], "Adding planetesimals": [[89, "Adding-planetesimals"]], "Adding planetesimal formation": [[89, "Adding-planetesimal-formation"]], "DustPy Documentation": [[90, "dustpy-documentation"]], "Contents:": [[90, null]], "Indices and tables": [[90, "indices-and-tables"]], "Test: Analytical Coagulation Kernels": [[91, "Test:-Analytical-Coagulation-Kernels"]], "The Constant Kernel": [[91, "The-Constant-Kernel"]], "The Linear Kernel": [[91, "The-Linear-Kernel"]], "The Product Kernel": [[91, "The-Product-Kernel"]], "Test: Gas Evolution": [[92, "Test:-Gas-Evolution"]], "Analytical Solution": [[92, "Analytical-Solution"]], "Setting up DustPy": [[92, "Setting-up-DustPy"]], "Modifying Integration Variable": [[92, "Modifying-Integration-Variable"]], "Setting Writer Options": [[92, "Setting-Writer-Options"]], "Reading and Plotting Data": [[92, "Reading-and-Plotting-Data"]], "Modifying the Power Law Index": [[92, "Modifying-the-Power-Law-Index"]]}, "indexentries": {"dustpy": [[12, "module-dustpy"]], "dustpy.constants": [[12, "module-dustpy.constants"]], "dustpy.plot": [[12, "module-dustpy.plot"]], "dustpy.std": [[12, "module-dustpy.std"]], "dustpy.std.dust": [[12, "module-dustpy.std.dust"]], "dustpy.std.gas": [[12, "module-dustpy.std.gas"]], "dustpy.std.grid": [[12, "module-dustpy.std.grid"]], "dustpy.std.sim": [[12, "module-dustpy.std.sim"]], "dustpy.std.star": [[12, "module-dustpy.std.star"]], "dustpy.utils": [[12, "module-dustpy.utils"]], "module": [[12, "module-dustpy"], [12, "module-dustpy.constants"], [12, "module-dustpy.plot"], [12, "module-dustpy.std"], [12, "module-dustpy.std.dust"], [12, "module-dustpy.std.gas"], [12, "module-dustpy.std.grid"], [12, "module-dustpy.std.sim"], [12, "module-dustpy.std.star"], [12, "module-dustpy.utils"]], "simulation (class in dustpy)": [[13, "dustpy.Simulation"]], "checkmassconservation() (dustpy.simulation method)": [[13, "dustpy.Simulation.checkmassconservation"]], "ini (dustpy.simulation attribute)": [[13, "dustpy.Simulation.ini"]], "initialize() (dustpy.simulation method)": [[13, "dustpy.Simulation.initialize"]], "makegrids() (dustpy.simulation method)": [[13, "dustpy.Simulation.makegrids"]], "run() (dustpy.simulation method)": [[13, "dustpy.Simulation.run"]], "setdustintegrator() (dustpy.simulation method)": [[13, "dustpy.Simulation.setdustintegrator"]], "ipanel() (in module dustpy.plot)": [[14, "dustpy.plot.ipanel"]], "panel() (in module dustpy.plot)": [[15, "dustpy.plot.panel"]], "d() (in module dustpy.std.dust)": [[16, "dustpy.std.dust.D"]], "f_adv() (in module dustpy.std.dust)": [[17, "dustpy.std.dust.F_adv"]], "f_diff() (in module dustpy.std.dust)": [[18, "dustpy.std.dust.F_diff"]], "f_tot() (in module dustpy.std.dust)": [[19, "dustpy.std.dust.F_tot"]], "h() (in module dustpy.std.dust)": [[20, "dustpy.std.dust.H"]], "mrn_distribution() (in module dustpy.std.dust)": [[21, "dustpy.std.dust.MRN_distribution"]], "s_coag() (in module dustpy.std.dust)": [[22, "dustpy.std.dust.S_coag"]], "s_hyd() (in module dustpy.std.dust)": [[23, "dustpy.std.dust.S_hyd"]], "s_tot() (in module dustpy.std.dust)": [[24, "dustpy.std.dust.S_tot"]], "sigmafloor() (in module dustpy.std.dust)": [[25, "dustpy.std.dust.SigmaFloor"]], "sigma_deriv() (in module dustpy.std.dust)": [[26, "dustpy.std.dust.Sigma_deriv"]], "st_epstein_stokesi() (in module dustpy.std.dust)": [[27, "dustpy.std.dust.St_Epstein_StokesI"]], "a() (in module dustpy.std.dust)": [[28, "dustpy.std.dust.a"]], "boundary() (in module dustpy.std.dust)": [[29, "dustpy.std.dust.boundary"]], "coagulation_parameters() (in module dustpy.std.dust)": [[30, "dustpy.std.dust.coagulation_parameters"]], "dt() (in module dustpy.std.dust)": [[31, "dustpy.std.dust.dt"]], "dt_adaptive() (in module dustpy.std.dust)": [[32, "dustpy.std.dust.dt_adaptive"]], "enforce_floor_value() (in module dustpy.std.dust)": [[33, "dustpy.std.dust.enforce_floor_value"]], "eps() (in module dustpy.std.dust)": [[34, "dustpy.std.dust.eps"]], "finalize_explicit() (in module dustpy.std.dust)": [[35, "dustpy.std.dust.finalize_explicit"]], "finalize_implicit() (in module dustpy.std.dust)": [[36, "dustpy.std.dust.finalize_implicit"]], "impl_1_direct (class in dustpy.std.dust)": [[37, "dustpy.std.dust.impl_1_direct"]], "jacobian() (in module dustpy.std.dust)": [[38, "dustpy.std.dust.jacobian"]], "kernel() (in module dustpy.std.dust)": [[39, "dustpy.std.dust.kernel"]], "p_frag() (in module dustpy.std.dust)": [[40, "dustpy.std.dust.p_frag"]], "p_stick() (in module dustpy.std.dust)": [[41, "dustpy.std.dust.p_stick"]], "prepare() (in module dustpy.std.dust)": [[42, "dustpy.std.dust.prepare"]], "rho_midplane() (in module dustpy.std.dust)": [[43, "dustpy.std.dust.rho_midplane"]], "set_implicit_boundaries() (in module dustpy.std.dust)": [[44, "dustpy.std.dust.set_implicit_boundaries"]], "vdriftmax() (in module dustpy.std.dust)": [[45, "dustpy.std.dust.vdriftmax"]], "vrad() (in module dustpy.std.dust)": [[46, "dustpy.std.dust.vrad"]], "vrel_azimuthal_drift() (in module dustpy.std.dust)": [[47, "dustpy.std.dust.vrel_azimuthal_drift"]], "vrel_brownian_motion() (in module dustpy.std.dust)": [[48, "dustpy.std.dust.vrel_brownian_motion"]], "vrel_radial_drift() (in module dustpy.std.dust)": [[49, "dustpy.std.dust.vrel_radial_drift"]], "vrel_tot() (in module dustpy.std.dust)": [[50, "dustpy.std.dust.vrel_tot"]], "vrel_turbulent_motion() (in module dustpy.std.dust)": [[51, "dustpy.std.dust.vrel_turbulent_motion"]], "vrel_vertical_settling() (in module dustpy.std.dust)": [[52, "dustpy.std.dust.vrel_vertical_settling"]], "fi() (in module dustpy.std.gas)": [[53, "dustpy.std.gas.Fi"]], "hp() (in module dustpy.std.gas)": [[54, "dustpy.std.gas.Hp"]], "p_midplane() (in module dustpy.std.gas)": [[55, "dustpy.std.gas.P_midplane"]], "s_hyd() (in module dustpy.std.gas)": [[56, "dustpy.std.gas.S_hyd"]], "s_tot() (in module dustpy.std.gas)": [[57, "dustpy.std.gas.S_tot"]], "t_passive() (in module dustpy.std.gas)": [[58, "dustpy.std.gas.T_passive"]], "boundary() (in module dustpy.std.gas)": [[59, "dustpy.std.gas.boundary"]], "cs_adiabatic() (in module dustpy.std.gas)": [[60, "dustpy.std.gas.cs_adiabatic"]], "dt() (in module dustpy.std.gas)": [[61, "dustpy.std.gas.dt"]], "enforce_floor_value() (in module dustpy.std.gas)": [[62, "dustpy.std.gas.enforce_floor_value"]], "eta_midplane() (in module dustpy.std.gas)": [[63, "dustpy.std.gas.eta_midplane"]], "finalize() (in module dustpy.std.gas)": [[64, "dustpy.std.gas.finalize"]], "impl_1_direct (class in dustpy.std.gas)": [[65, "dustpy.std.gas.impl_1_direct"]], "jacobian() (in module dustpy.std.gas)": [[66, "dustpy.std.gas.jacobian"]], "lyndenbellpringle1974() (in module dustpy.std.gas)": [[67, "dustpy.std.gas.lyndenbellpringle1974"]], "mfp_midplane() (in module dustpy.std.gas)": [[68, "dustpy.std.gas.mfp_midplane"]], "n_midplane() (in module dustpy.std.gas)": [[69, "dustpy.std.gas.n_midplane"]], "nu() (in module dustpy.std.gas)": [[70, "dustpy.std.gas.nu"]], "prepare() (in module dustpy.std.gas)": [[71, "dustpy.std.gas.prepare"]], "rho_midplane() (in module dustpy.std.gas)": [[72, "dustpy.std.gas.rho_midplane"]], "set_implicit_boundaries() (in module dustpy.std.gas)": [[73, "dustpy.std.gas.set_implicit_boundaries"]], "vrad() (in module dustpy.std.gas)": [[74, "dustpy.std.gas.vrad"]], "vvisc() (in module dustpy.std.gas)": [[75, "dustpy.std.gas.vvisc"]], "omegak() (in module dustpy.std.grid)": [[76, "dustpy.std.grid.OmegaK"]], "dt() (in module dustpy.std.sim)": [[77, "dustpy.std.sim.dt"]], "dt_adaptive() (in module dustpy.std.sim)": [[78, "dustpy.std.sim.dt_adaptive"]], "finalize_explicit_dust() (in module dustpy.std.sim)": [[79, "dustpy.std.sim.finalize_explicit_dust"]], "finalize_implicit_dust() (in module dustpy.std.sim)": [[80, "dustpy.std.sim.finalize_implicit_dust"]], "prepare_explicit_dust() (in module dustpy.std.sim)": [[81, "dustpy.std.sim.prepare_explicit_dust"]], "prepare_implicit_dust() (in module dustpy.std.sim)": [[82, "dustpy.std.sim.prepare_implicit_dust"]], "luminosity() (in module dustpy.std.star)": [[83, "dustpy.std.star.luminosity"]], "boundary (class in dustpy.utils)": [[84, "dustpy.utils.Boundary"]], "condition (dustpy.utils.boundary attribute)": [[84, "dustpy.utils.Boundary.condition"]], "setboundary() (dustpy.utils.boundary method)": [[84, "dustpy.utils.Boundary.setboundary"]], "setcondition() (dustpy.utils.boundary method)": [[84, "dustpy.utils.Boundary.setcondition"]], "value (dustpy.utils.boundary attribute)": [[84, 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\ No newline at end of file
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Basic usage": [[0, "1.-Basic-usage"]], "The Simulation Frame": [[0, "The-Simulation-Frame"]], "Initializing": [[0, "Initializing"]], "Running a Simulation": [[0, "Running-a-Simulation"]], "Plotting": [[0, "Plotting"]], "Code Units": [[0, "Code-Units"]], "Reading data files": [[0, "Reading-data-files"]], "Reading Dump Files": [[0, "Reading-Dump-Files"]], "2. Simple Customization": [[1, "2.-Simple-Customization"]], "Stellar parameters": [[1, "Stellar-parameters"]], "Grid parameters": [[1, "Grid-parameters"]], "Gas Parameters": [[1, "Gas-Parameters"]], "Dust Parameters": [[1, "Dust-Parameters"]], "Changing the Initial Conditions": [[1, "Changing-the-Initial-Conditions"]], "Changing the Snapshots": [[1, "Changing-the-Snapshots"]], "Changing the Output Directory": [[1, "Changing-the-Output-Directory"]], "3. Advanced Customization": [[2, "3.-Advanced-Customization"]], "Customizing the Grids": [[2, "Customizing-the-Grids"]], "The Radial Grid": [[2, "The-Radial-Grid"]], "The Mass Grid": [[2, "The-Mass-Grid"]], "Customizing the Physics of a Field": [[2, "Customizing-the-Physics-of-a-Field"]], "Adding Custom Fields": [[2, "Adding-Custom-Fields"]], "Modifying the Update Order": [[2, "Modifying-the-Update-Order"]], "Systoles and Diastoles": [[2, "Systoles-and-Diastoles"]], "Customizing the Snapshots": [[2, "Customizing-the-Snapshots"]], "4. The Standard Model": [[3, "4.-The-Standard-Model"]], "Dust": [[3, "Dust"]], "Simulation.dust.backreaction": [[3, "Simulation.dust.backreaction"]], "Simulation.dust.boundary": [[3, "Simulation.dust.boundary"]], "Simulation.dust.coagulation": [[3, "Simulation.dust.coagulation"]], "Simulation.dust.delta": [[3, "Simulation.dust.delta"]], "Simulation.dust.delta.rad": [[3, "Simulation.dust.delta.rad"]], "Simulation.dust.delta.turb": [[3, "Simulation.dust.delta.turb"]], "Simulation.dust.delta.vert": [[3, "Simulation.dust.delta.vert"]], "Simulation.dust.Fi": [[3, "Simulation.dust.Fi"]], "Simulation.dust.Fi.adv": [[3, "Simulation.dust.Fi.adv"]], "Simulation.dust.Fi.diff": [[3, "Simulation.dust.Fi.diff"]], "Simulation.dust.Fi.tot": [[3, "Simulation.dust.Fi.tot"]], "Simulation.dust.p": [[3, "Simulation.dust.p"]], "Simulation.dust.p.frag": [[3, "Simulation.dust.p.frag"]], "Simulation.dust.p.stick": [[3, "Simulation.dust.p.stick"]], "Simulation.dust.S": [[3, "Simulation.dust.S"]], "Simulation.dust.S.coag": [[3, "Simulation.dust.S.coag"]], "Simulation.dust.S.ext": [[3, "Simulation.dust.S.ext"]], "Simulation.dust.S.hyd": [[3, "Simulation.dust.S.hyd"]], "Simulation.dust.S.tot": [[3, "Simulation.dust.S.tot"]], "Simulation.dust.v": [[3, "Simulation.dust.v"]], "Simulation.dust.v.rel": [[3, "Simulation.dust.v.rel"]], "Simulation.dust.v.rel.azi": [[3, "Simulation.dust.v.rel.azi"]], "Simulation.dust.v.brown": [[3, "Simulation.dust.v.brown"]], "Simulation.dust.v.rel.rad": [[3, "Simulation.dust.v.rel.rad"]], "Simulation.dust.v.rel.tot": [[3, "Simulation.dust.v.rel.tot"]], "Simulation.dust.v.rel.turb": [[3, "Simulation.dust.v.rel.turb"]], "Simulation.dust.v.rel.vert": [[3, "Simulation.dust.v.rel.vert"]], "Simulation.dust.v.driftmax": [[3, "Simulation.dust.v.driftmax"]], "Simulation.dust.v.frag": [[3, "Simulation.dust.v.frag"]], "Simulation.dust.v.rad": [[3, "Simulation.dust.v.rad"]], "Simulation.dust.a": [[3, "Simulation.dust.a"]], "Simulation.dust.D": [[3, "Simulation.dust.D"]], "Simulation.dust.eps": [[3, "Simulation.dust.eps"]], "Simulation.dust.fill": [[3, "Simulation.dust.fill"]], "Simulation.dust.H": [[3, "Simulation.dust.H"]], "Simulation.dust.kernel": [[3, "Simulation.dust.kernel"]], "Simulation.dust.rho": [[3, "Simulation.dust.rho"]], "Simulation.dust.rhos": [[3, "Simulation.dust.rhos"]], "Simulation.dust.Sigma": [[3, "Simulation.dust.Sigma"]], "Simulation.dust.SigmaFloor": [[3, "Simulation.dust.SigmaFloor"]], "Simulation.dust.St": [[3, "Simulation.dust.St"]], "Update order": [[3, "Update-order"], [3, "id1"], [3, "id2"], [3, "id3"]], "Gas": [[3, "Gas"]], "Simulation.gas.boundary": [[3, "Simulation.gas.boundary"]], "Simulation.gas.S": [[3, "Simulation.gas.S"]], "Simulation.gas.S.ext": [[3, "Simulation.gas.S.ext"]], "Simulation.gas.S.hyd": [[3, "Simulation.gas.S.hyd"]], "Simulation.gas.S.tot": [[3, "Simulation.gas.S.tot"]], "Simulation.gas.v": [[3, "Simulation.gas.v"]], "Simulation.gas.v.rad": [[3, "Simulation.gas.v.rad"]], "Simulation.gas.v.visc": [[3, "Simulation.gas.v.visc"]], "Simulation.gas.alpha": [[3, "Simulation.gas.alpha"]], "Simulation.gas.cs": [[3, "Simulation.gas.cs"]], "Simulation.gas.eta": [[3, "Simulation.gas.eta"]], "Simulation.gas.Fi": [[3, "Simulation.gas.Fi"]], "Simulation.gas.gamma": [[3, "Simulation.gas.gamma"]], "Simulation.gas.Hp": [[3, "Simulation.gas.Hp"]], "Simulation.gas.mfp": [[3, "Simulation.gas.mfp"]], "Simulation.gas.mu": [[3, "Simulation.gas.mu"]], "Simulation.gas.n": [[3, "Simulation.gas.n"]], "Simulation.gas.nu": [[3, "Simulation.gas.nu"]], "Simulation.gas.P": [[3, "Simulation.gas.P"]], "Simulation.gas.rho": [[3, "Simulation.gas.rho"]], "Simulation.gas.Sigma": [[3, "Simulation.gas.Sigma"]], "Simulation.gas.SigmaFloor": [[3, "Simulation.gas.SigmaFloor"]], "Simulation.gas.T": [[3, "Simulation.gas.T"]], "Grid": [[3, "Grid"]], "Simulation.grid.A": [[3, "Simulation.grid.A"]], "Simulation.grid.m": [[3, "Simulation.grid.m"]], "Simulation.grid.Nm": [[3, "Simulation.grid.Nm"]], "Simulation.grid.Nr": [[3, "Simulation.grid.Nr"]], "Simulation.grid.OmegaK": [[3, "Simulation.grid.OmegaK"]], "Simulation.grid.r": [[3, "Simulation.grid.r"]], "Simulation.grid.ri": [[3, "Simulation.grid.ri"]], "Star": [[3, "Star"]], "Simulation.star.L": [[3, "Simulation.star.L"]], "Simulation.star.M": [[3, "Simulation.star.M"]], "Simulation.star.R": [[3, "Simulation.star.R"]], "Simulation.star.T": [[3, "Simulation.star.T"]], "Time": [[3, "Time"]], "Integrator": [[3, "Integrator"]], "Writer": [[3, "Writer"]], "5. Dust Coagulation": [[4, "5.-Dust-Coagulation"]], "Sticking": [[4, "Sticking"]], "Fragmentation & Erosion": [[4, "Fragmentation-&-Erosion"]], "Probabilities": [[4, "Probabilities"]], "Bouncing": [[4, "Bouncing"]], "Collision Rates": [[4, "Collision-Rates"]], "Coagulation Sources": [[4, "Coagulation-Sources"]], "6. Dust Evolution": [[5, "6.-Dust-Evolution"]], "Coagulation": [[5, "Coagulation"]], "Turning off Fragmentation": [[5, "Turning-off-Fragmentation"]], "Turning off Coagulation": [[5, "Turning-off-Coagulation"]], "Hydrodynamics": [[5, "Hydrodynamics"], [6, "Hydrodynamics"]], "Advection": [[5, "Advection"]], "Turning off Advection": [[5, "Turning-off-Advection"]], "Diffusion": [[5, "Diffusion"]], "Turning off Diffusion": [[5, "Turning-off-Diffusion"]], "Turning off Hydrodynamics": [[5, "Turning-off-Hydrodynamics"], [6, "Turning-off-Hydrodynamics"]], "External Sources": [[5, "External-Sources"], [6, "External-Sources"]], "Turning off Dust Evolution": [[5, "Turning-off-Dust-Evolution"], [92, "Turning-off-Dust-Evolution"]], "Changing the Dust Integrator": [[5, "Changing-the-Dust-Integrator"]], "7. Gas Evolution": [[6, "7.-Gas-Evolution"]], "Turning off External Sources": [[6, "Turning-off-External-Sources"]], "Turning off Gas Evolution": [[6, "Turning-off-Gas-Evolution"]], "Appendix A: Citation": [[7, "Appendix-A:-Citation"]], "Appendix B: List of Publications": [[8, "Appendix-B:-List-of-Publications"]], "Appendix C: Contributing/Bugs/Features": [[9, "Appendix-C:-Contributing/Bugs/Features"]], "Contributing": [[9, "Contributing"]], "Bug Reports": [[9, "Bug-Reports"]], "Feature Requests": [[9, "Feature-Requests"]], "Appendix D: DustPy Discussions": [[10, "Appendix-D:-DustPy-Discussions"]], "Appendix E: Changelog": [[11, "Appendix-E:-Changelog"]], "v1.0.5": [[11, "v1.0.5"]], "Using Meson as build system": [[11, "Using-Meson-as-build-system"]], "Bugfix to velocity distribution": [[11, "Bugfix-to-velocity-distribution"]], "Bugfix to plotting script": [[11, "Bugfix-to-plotting-script"]], "Preparation for the addition of multiple gas species": [[11, "Preparation-for-the-addition-of-multiple-gas-species"]], "v1.0.4": [[11, "v1.0.4"]], "Bugfix to boundary conditions": [[11, "Bugfix-to-boundary-conditions"]], "v1.0.3": [[11, "v1.0.3"]], "Correction to inital particle size distribution": [[11, "Correction-to-inital-particle-size-distribution"]], "Removal of non-ASCII characters": [[11, "Removal-of-non-ASCII-characters"]], "v1.0.2": [[11, "v1.0.2"]], "Change in default temperature profile": [[11, "Change-in-default-temperature-profile"]], "v1.0.1": [[11, "v1.0.1"]], "Change to Collision Kernel": [[11, "Change-to-Collision-Kernel"]], "v1.0.0": [[11, "v1.0.0"]], "Module Reference": [[12, "module-reference"]], "dustpy Package": [[12, "module-dustpy"]], "Classes": [[12, "classes"], [12, "id2"], [12, "id4"], [12, "id9"]], "dustpy.constants Package": [[12, "module-dustpy.constants"]], "Constants": [[12, "constants"]], "dustpy.plot Package": [[12, "module-dustpy.plot"]], "Functions": [[12, "functions"], [12, "id1"], [12, "id3"], [12, "id5"], [12, "id6"], [12, "id7"], [12, "id8"]], "dustpy.std Package": [[12, "module-dustpy.std"]], "dustpy.std.dust Module": [[12, "module-dustpy.std.dust"]], "dustpy.std.gas Module": [[12, "module-dustpy.std.gas"]], "dustpy.std.grid Module": [[12, "module-dustpy.std.grid"]], "dustpy.std.sim Module": [[12, "module-dustpy.std.sim"]], "dustpy.std.star Module": [[12, "module-dustpy.std.star"]], "dustpy.utils Package": [[12, "module-dustpy.utils"]], "Simulation": [[13, "simulation"]], "ipanel": [[14, "ipanel"]], "panel": [[15, "panel"]], "D": [[16, "d"]], "F_adv": [[17, "f-adv"]], "F_diff": [[18, "f-diff"]], "F_tot": [[19, "f-tot"]], "H": [[20, "h"]], "MRN_distribution": [[21, "mrn-distribution"]], "S_coag": [[22, "s-coag"]], "S_hyd": [[23, "s-hyd"], [56, "s-hyd"]], "S_tot": [[24, "s-tot"], [57, "s-tot"]], "SigmaFloor": [[25, "sigmafloor"]], "Sigma_deriv": [[26, "sigma-deriv"]], "St_Epstein_StokesI": [[27, "st-epstein-stokesi"]], "a": [[28, "a"]], "boundary": [[29, "boundary"], [59, "boundary"]], "coagulation_parameters": [[30, "coagulation-parameters"]], "dt": [[31, "dt"], [61, "dt"], [77, "dt"]], "dt_adaptive": [[32, "dt-adaptive"], [78, "dt-adaptive"]], "enforce_floor_value": [[33, "enforce-floor-value"], [62, "enforce-floor-value"]], "eps": [[34, "eps"]], "finalize_explicit": [[35, "finalize-explicit"]], "finalize_implicit": [[36, "finalize-implicit"]], "impl_1_direct": [[37, "impl-1-direct"], [65, "impl-1-direct"]], "jacobian": [[38, "jacobian"], [66, "jacobian"]], "kernel": [[39, "kernel"]], "p_frag": [[40, "p-frag"]], "p_stick": [[41, "p-stick"]], "prepare": [[42, "prepare"], [71, "prepare"]], "rho_midplane": [[43, "rho-midplane"], [72, "rho-midplane"]], "set_implicit_boundaries": [[44, "set-implicit-boundaries"], [73, "set-implicit-boundaries"]], "vdriftmax": [[45, "vdriftmax"]], "vrad": [[46, "vrad"], [74, "vrad"]], "vrel_azimuthal_drift": [[47, "vrel-azimuthal-drift"]], "vrel_brownian_motion": [[48, "vrel-brownian-motion"]], "vrel_radial_drift": [[49, "vrel-radial-drift"]], "vrel_tot": [[50, "vrel-tot"]], "vrel_turbulent_motion": [[51, "vrel-turbulent-motion"]], "vrel_vertical_settling": [[52, "vrel-vertical-settling"]], "Fi": [[53, "fi"]], "Hp": [[54, "hp"]], "P_midplane": [[55, "p-midplane"]], "T_passive": [[58, "t-passive"]], "cs_adiabatic": [[60, "cs-adiabatic"]], "eta_midplane": [[63, "eta-midplane"]], "finalize": [[64, "finalize"]], "lyndenbellpringle1974": [[67, "lyndenbellpringle1974"]], "mfp_midplane": [[68, "mfp-midplane"]], "n_midplane": [[69, "n-midplane"]], "nu": [[70, "nu"]], "vvisc": [[75, "vvisc"]], "OmegaK": [[76, "omegak"]], "finalize_explicit_dust": [[79, "finalize-explicit-dust"]], "finalize_implicit_dust": [[80, "finalize-implicit-dust"]], "prepare_explicit_dust": [[81, "prepare-explicit-dust"]], "prepare_implicit_dust": [[82, "prepare-implicit-dust"]], "luminosity": [[83, "luminosity"]], "Boundary": [[84, "boundary"]], "print_version_warning": [[85, "print-version-warning"]], "Library: dustpylib": [[86, "Library:-dustpylib"]], "Example: Ice Lines": [[87, "Example:-Ice-Lines"]], "Example: Planetary Gaps": [[88, "Example:-Planetary-Gaps"]], "Gap Profiles": [[88, "Gap-Profiles"]], "Adding planets": [[88, "Adding-planets"]], "Viscosity pertubation": [[88, "Viscosity-pertubation"]], "Growing planets": [[88, "Growing-planets"]], "Example: Planetesimal Formation": [[89, "Example:-Planetesimal-Formation"]], "Refining the radial grid": [[89, "Refining-the-radial-grid"]], "Adding gap": [[89, "Adding-gap"]], "Adding planetesimals": [[89, "Adding-planetesimals"]], "Adding planetesimal formation": [[89, "Adding-planetesimal-formation"]], "DustPy Documentation": [[90, "dustpy-documentation"]], "Contents:": [[90, null]], "Indices and tables": [[90, "indices-and-tables"]], "Test: Analytical Coagulation Kernels": [[91, "Test:-Analytical-Coagulation-Kernels"]], "The Constant Kernel": [[91, "The-Constant-Kernel"]], "The Linear Kernel": [[91, "The-Linear-Kernel"]], "The Product Kernel": [[91, "The-Product-Kernel"]], "Test: Gas Evolution": [[92, "Test:-Gas-Evolution"]], "Analytical Solution": [[92, "Analytical-Solution"]], "Setting up DustPy": [[92, "Setting-up-DustPy"]], "Modifying Integration Variable": [[92, "Modifying-Integration-Variable"]], "Setting Writer Options": [[92, "Setting-Writer-Options"]], "Reading and Plotting Data": [[92, "Reading-and-Plotting-Data"]], "Modifying the Power Law Index": [[92, "Modifying-the-Power-Law-Index"]]}, "indexentries": {"dustpy": [[12, "module-dustpy"]], "dustpy.constants": [[12, "module-dustpy.constants"]], "dustpy.plot": [[12, "module-dustpy.plot"]], "dustpy.std": [[12, "module-dustpy.std"]], "dustpy.std.dust": [[12, "module-dustpy.std.dust"]], "dustpy.std.gas": [[12, "module-dustpy.std.gas"]], "dustpy.std.grid": [[12, "module-dustpy.std.grid"]], "dustpy.std.sim": [[12, "module-dustpy.std.sim"]], "dustpy.std.star": [[12, "module-dustpy.std.star"]], "dustpy.utils": [[12, "module-dustpy.utils"]], "module": [[12, "module-dustpy"], [12, "module-dustpy.constants"], [12, "module-dustpy.plot"], [12, "module-dustpy.std"], [12, "module-dustpy.std.dust"], [12, "module-dustpy.std.gas"], [12, "module-dustpy.std.grid"], [12, "module-dustpy.std.sim"], [12, "module-dustpy.std.star"], [12, "module-dustpy.utils"]], "simulation (class in dustpy)": [[13, "dustpy.Simulation"]], "checkmassconservation() (dustpy.simulation method)": [[13, "dustpy.Simulation.checkmassconservation"]], "ini (dustpy.simulation attribute)": [[13, "dustpy.Simulation.ini"]], "initialize() (dustpy.simulation method)": [[13, "dustpy.Simulation.initialize"]], "makegrids() (dustpy.simulation method)": [[13, "dustpy.Simulation.makegrids"]], "run() (dustpy.simulation method)": [[13, "dustpy.Simulation.run"]], "setdustintegrator() (dustpy.simulation method)": [[13, "dustpy.Simulation.setdustintegrator"]], "ipanel() (in module dustpy.plot)": [[14, "dustpy.plot.ipanel"]], "panel() (in module dustpy.plot)": [[15, "dustpy.plot.panel"]], "d() (in module dustpy.std.dust)": [[16, "dustpy.std.dust.D"]], "f_adv() (in module dustpy.std.dust)": [[17, "dustpy.std.dust.F_adv"]], "f_diff() (in module dustpy.std.dust)": [[18, "dustpy.std.dust.F_diff"]], "f_tot() (in module dustpy.std.dust)": [[19, "dustpy.std.dust.F_tot"]], "h() (in module dustpy.std.dust)": [[20, "dustpy.std.dust.H"]], "mrn_distribution() (in module dustpy.std.dust)": [[21, "dustpy.std.dust.MRN_distribution"]], "s_coag() (in module dustpy.std.dust)": [[22, "dustpy.std.dust.S_coag"]], "s_hyd() (in module dustpy.std.dust)": [[23, "dustpy.std.dust.S_hyd"]], "s_tot() (in module dustpy.std.dust)": [[24, "dustpy.std.dust.S_tot"]], "sigmafloor() (in module dustpy.std.dust)": [[25, "dustpy.std.dust.SigmaFloor"]], "sigma_deriv() (in module dustpy.std.dust)": [[26, "dustpy.std.dust.Sigma_deriv"]], "st_epstein_stokesi() (in module dustpy.std.dust)": [[27, "dustpy.std.dust.St_Epstein_StokesI"]], "a() (in module dustpy.std.dust)": [[28, "dustpy.std.dust.a"]], "boundary() (in module dustpy.std.dust)": [[29, "dustpy.std.dust.boundary"]], "coagulation_parameters() (in module dustpy.std.dust)": [[30, "dustpy.std.dust.coagulation_parameters"]], "dt() (in module dustpy.std.dust)": [[31, "dustpy.std.dust.dt"]], "dt_adaptive() (in module dustpy.std.dust)": [[32, "dustpy.std.dust.dt_adaptive"]], "enforce_floor_value() (in module dustpy.std.dust)": [[33, "dustpy.std.dust.enforce_floor_value"]], "eps() (in module dustpy.std.dust)": [[34, "dustpy.std.dust.eps"]], "finalize_explicit() (in module dustpy.std.dust)": [[35, "dustpy.std.dust.finalize_explicit"]], "finalize_implicit() (in module dustpy.std.dust)": [[36, "dustpy.std.dust.finalize_implicit"]], "impl_1_direct (class in dustpy.std.dust)": [[37, "dustpy.std.dust.impl_1_direct"]], "jacobian() (in module dustpy.std.dust)": [[38, "dustpy.std.dust.jacobian"]], "kernel() (in module dustpy.std.dust)": [[39, "dustpy.std.dust.kernel"]], "p_frag() (in module dustpy.std.dust)": [[40, "dustpy.std.dust.p_frag"]], "p_stick() (in module dustpy.std.dust)": [[41, "dustpy.std.dust.p_stick"]], "prepare() (in module dustpy.std.dust)": [[42, "dustpy.std.dust.prepare"]], "rho_midplane() (in module dustpy.std.dust)": [[43, "dustpy.std.dust.rho_midplane"]], "set_implicit_boundaries() (in module dustpy.std.dust)": [[44, "dustpy.std.dust.set_implicit_boundaries"]], "vdriftmax() (in module dustpy.std.dust)": [[45, "dustpy.std.dust.vdriftmax"]], "vrad() (in module dustpy.std.dust)": [[46, "dustpy.std.dust.vrad"]], "vrel_azimuthal_drift() (in module dustpy.std.dust)": [[47, "dustpy.std.dust.vrel_azimuthal_drift"]], "vrel_brownian_motion() (in module dustpy.std.dust)": [[48, "dustpy.std.dust.vrel_brownian_motion"]], "vrel_radial_drift() (in module dustpy.std.dust)": [[49, "dustpy.std.dust.vrel_radial_drift"]], "vrel_tot() (in module dustpy.std.dust)": [[50, "dustpy.std.dust.vrel_tot"]], "vrel_turbulent_motion() (in module dustpy.std.dust)": [[51, "dustpy.std.dust.vrel_turbulent_motion"]], "vrel_vertical_settling() (in module dustpy.std.dust)": [[52, "dustpy.std.dust.vrel_vertical_settling"]], "fi() (in module dustpy.std.gas)": [[53, "dustpy.std.gas.Fi"]], "hp() (in module dustpy.std.gas)": [[54, "dustpy.std.gas.Hp"]], "p_midplane() (in module dustpy.std.gas)": [[55, "dustpy.std.gas.P_midplane"]], "s_hyd() (in module dustpy.std.gas)": [[56, "dustpy.std.gas.S_hyd"]], "s_tot() (in module dustpy.std.gas)": [[57, "dustpy.std.gas.S_tot"]], "t_passive() (in module dustpy.std.gas)": [[58, "dustpy.std.gas.T_passive"]], "boundary() (in module dustpy.std.gas)": [[59, "dustpy.std.gas.boundary"]], "cs_adiabatic() (in module dustpy.std.gas)": [[60, "dustpy.std.gas.cs_adiabatic"]], "dt() (in module dustpy.std.gas)": [[61, "dustpy.std.gas.dt"]], "enforce_floor_value() (in module dustpy.std.gas)": [[62, "dustpy.std.gas.enforce_floor_value"]], "eta_midplane() (in module dustpy.std.gas)": [[63, "dustpy.std.gas.eta_midplane"]], "finalize() (in module dustpy.std.gas)": [[64, "dustpy.std.gas.finalize"]], "impl_1_direct (class in dustpy.std.gas)": [[65, "dustpy.std.gas.impl_1_direct"]], "jacobian() (in module dustpy.std.gas)": [[66, "dustpy.std.gas.jacobian"]], "lyndenbellpringle1974() (in module dustpy.std.gas)": [[67, "dustpy.std.gas.lyndenbellpringle1974"]], "mfp_midplane() (in module dustpy.std.gas)": [[68, "dustpy.std.gas.mfp_midplane"]], "n_midplane() (in module dustpy.std.gas)": [[69, "dustpy.std.gas.n_midplane"]], "nu() (in module dustpy.std.gas)": [[70, "dustpy.std.gas.nu"]], "prepare() (in module dustpy.std.gas)": [[71, "dustpy.std.gas.prepare"]], "rho_midplane() (in module dustpy.std.gas)": [[72, "dustpy.std.gas.rho_midplane"]], "set_implicit_boundaries() (in module dustpy.std.gas)": [[73, "dustpy.std.gas.set_implicit_boundaries"]], "vrad() (in module dustpy.std.gas)": [[74, "dustpy.std.gas.vrad"]], "vvisc() (in module dustpy.std.gas)": [[75, "dustpy.std.gas.vvisc"]], "omegak() (in module dustpy.std.grid)": [[76, "dustpy.std.grid.OmegaK"]], "dt() (in module dustpy.std.sim)": [[77, "dustpy.std.sim.dt"]], "dt_adaptive() (in module dustpy.std.sim)": [[78, "dustpy.std.sim.dt_adaptive"]], "finalize_explicit_dust() (in module dustpy.std.sim)": [[79, "dustpy.std.sim.finalize_explicit_dust"]], "finalize_implicit_dust() (in module dustpy.std.sim)": [[80, "dustpy.std.sim.finalize_implicit_dust"]], "prepare_explicit_dust() (in module dustpy.std.sim)": [[81, "dustpy.std.sim.prepare_explicit_dust"]], "prepare_implicit_dust() (in module dustpy.std.sim)": [[82, "dustpy.std.sim.prepare_implicit_dust"]], "luminosity() (in module dustpy.std.star)": [[83, "dustpy.std.star.luminosity"]], "boundary (class in dustpy.utils)": [[84, "dustpy.utils.Boundary"]], "condition (dustpy.utils.boundary attribute)": [[84, "dustpy.utils.Boundary.condition"]], "setboundary() (dustpy.utils.boundary method)": [[84, "dustpy.utils.Boundary.setboundary"]], "setcondition() (dustpy.utils.boundary method)": [[84, "dustpy.utils.Boundary.setcondition"]], "value (dustpy.utils.boundary attribute)": [[84, "dustpy.utils.Boundary.value"]], "print_version_warning() (in module dustpy.utils)": [[85, "dustpy.utils.print_version_warning"]]}})
\ No newline at end of file
diff --git a/docs/test_analytical_coagulation_kernels.html b/docs/test_analytical_coagulation_kernels.html
index 51a02f3..08b88c5 100644
--- a/docs/test_analytical_coagulation_kernels.html
+++ b/docs/test_analytical_coagulation_kernels.html
@@ -367,7 +367,7 @@ We now read the necessary data and plot it.
@@ -401,7 +401,7 @@
----------------------------------------------------------------------------
-TypeError Traceback (most recent call last)
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/IPython/core/formatters.py:340, in BaseFormatter.__call__(self, obj)
- 338 pass
- 339 else:
---> 340 return printer(obj)
- 341 # Finally look for special method names
- 342 method = get_real_method(obj, self.print_method)
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/IPython/core/pylabtools.py:152, in print_figure(fig, fmt, bbox_inches, base64, **kwargs)
- 149 from matplotlib.backend_bases import FigureCanvasBase
- 150 FigureCanvasBase(fig)
---> 152 fig.canvas.print_figure(bytes_io, **kw)
- 153 data = bytes_io.getvalue()
- 154 if fmt == 'svg':
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/backend_bases.py:2193, in FigureCanvasBase.print_figure(self, filename, dpi, facecolor, edgecolor, orientation, format, bbox_inches, pad_inches, bbox_extra_artists, backend, **kwargs)
- 2189 try:
- 2190 # _get_renderer may change the figure dpi (as vector formats
- 2191 # force the figure dpi to 72), so we need to set it again here.
- 2192 with cbook._setattr_cm(self.figure, dpi=dpi):
--> 2193 result = print_method(
- 2194 filename,
- 2195 facecolor=facecolor,
- 2196 edgecolor=edgecolor,
- 2197 orientation=orientation,
- 2198 bbox_inches_restore=_bbox_inches_restore,
- 2199 **kwargs)
- 2200 finally:
- 2201 if bbox_inches and restore_bbox:
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/backend_bases.py:2043, in FigureCanvasBase._switch_canvas_and_return_print_method.<locals>.<lambda>(*args, **kwargs)
- 2039 optional_kws = { # Passed by print_figure for other renderers.
- 2040 "dpi", "facecolor", "edgecolor", "orientation",
- 2041 "bbox_inches_restore"}
- 2042 skip = optional_kws - {*inspect.signature(meth).parameters}
--> 2043 print_method = functools.wraps(meth)(lambda *args, **kwargs: meth(
- 2044 *args, **{k: v for k, v in kwargs.items() if k not in skip}))
- 2045 else: # Let third-parties do as they see fit.
- 2046 print_method = meth
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/backends/backend_agg.py:497, in FigureCanvasAgg.print_png(self, filename_or_obj, metadata, pil_kwargs)
- 450 def print_png(self, filename_or_obj, *, metadata=None, pil_kwargs=None):
- 451 """
- 452 Write the figure to a PNG file.
- 453
- (...)
- 495 *metadata*, including the default 'Software' key.
- 496 """
---> 497 self._print_pil(filename_or_obj, "png", pil_kwargs, metadata)
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/backends/backend_agg.py:445, in FigureCanvasAgg._print_pil(self, filename_or_obj, fmt, pil_kwargs, metadata)
- 440 def _print_pil(self, filename_or_obj, fmt, pil_kwargs, metadata=None):
- 441 """
- 442 Draw the canvas, then save it using `.image.imsave` (to which
- 443 *pil_kwargs* and *metadata* are forwarded).
- 444 """
---> 445 FigureCanvasAgg.draw(self)
- 446 mpl.image.imsave(
- 447 filename_or_obj, self.buffer_rgba(), format=fmt, origin="upper",
- 448 dpi=self.figure.dpi, metadata=metadata, pil_kwargs=pil_kwargs)
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/backends/backend_agg.py:388, in FigureCanvasAgg.draw(self)
- 385 # Acquire a lock on the shared font cache.
- 386 with (self.toolbar._wait_cursor_for_draw_cm() if self.toolbar
- 387 else nullcontext()):
---> 388 self.figure.draw(self.renderer)
- 389 # A GUI class may be need to update a window using this draw, so
- 390 # don't forget to call the superclass.
- 391 super().draw()
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/artist.py:95, in _finalize_rasterization.<locals>.draw_wrapper(artist, renderer, *args, **kwargs)
- 93 @wraps(draw)
- 94 def draw_wrapper(artist, renderer, *args, **kwargs):
----> 95 result = draw(artist, renderer, *args, **kwargs)
- 96 if renderer._rasterizing:
- 97 renderer.stop_rasterizing()
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/artist.py:72, in allow_rasterization.<locals>.draw_wrapper(artist, renderer)
- 69 if artist.get_agg_filter() is not None:
- 70 renderer.start_filter()
----> 72 return draw(artist, renderer)
- 73 finally:
- 74 if artist.get_agg_filter() is not None:
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/figure.py:3154, in Figure.draw(self, renderer)
- 3151 # ValueError can occur when resizing a window.
- 3153 self.patch.draw(renderer)
--> 3154 mimage._draw_list_compositing_images(
- 3155 renderer, self, artists, self.suppressComposite)
- 3157 for sfig in self.subfigs:
- 3158 sfig.draw(renderer)
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/image.py:132, in _draw_list_compositing_images(renderer, parent, artists, suppress_composite)
- 130 if not_composite or not has_images:
- 131 for a in artists:
---> 132 a.draw(renderer)
- 133 else:
- 134 # Composite any adjacent images together
- 135 image_group = []
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/artist.py:72, in allow_rasterization.<locals>.draw_wrapper(artist, renderer)
- 69 if artist.get_agg_filter() is not None:
- 70 renderer.start_filter()
----> 72 return draw(artist, renderer)
- 73 finally:
- 74 if artist.get_agg_filter() is not None:
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/axes/_base.py:3070, in _AxesBase.draw(self, renderer)
- 3067 if artists_rasterized:
- 3068 _draw_rasterized(self.figure, artists_rasterized, renderer)
--> 3070 mimage._draw_list_compositing_images(
- 3071 renderer, self, artists, self.figure.suppressComposite)
- 3073 renderer.close_group('axes')
- 3074 self.stale = False
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/image.py:132, in _draw_list_compositing_images(renderer, parent, artists, suppress_composite)
- 130 if not_composite or not has_images:
- 131 for a in artists:
---> 132 a.draw(renderer)
- 133 else:
- 134 # Composite any adjacent images together
- 135 image_group = []
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/artist.py:72, in allow_rasterization.<locals>.draw_wrapper(artist, renderer)
- 69 if artist.get_agg_filter() is not None:
- 70 renderer.start_filter()
----> 72 return draw(artist, renderer)
- 73 finally:
- 74 if artist.get_agg_filter() is not None:
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/text.py:1988, in Annotation.draw(self, renderer)
- 1986 if self.arrow_patch.figure is None and self.figure is not None:
- 1987 self.arrow_patch.figure = self.figure
--> 1988 self.arrow_patch.draw(renderer)
- 1989 # Draw text, including FancyBboxPatch, after FancyArrowPatch.
- 1990 # Otherwise, a wedge arrowstyle can land partly on top of the Bbox.
- 1991 Text.draw(self, renderer)
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/artist.py:39, in _prevent_rasterization.<locals>.draw_wrapper(artist, renderer, *args, **kwargs)
- 36 renderer.stop_rasterizing()
- 37 renderer._rasterizing = False
----> 39 return draw(artist, renderer, *args, **kwargs)
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/patches.py:4388, in FancyArrowPatch.draw(self, renderer)
- 4384 fillable = [fillable]
- 4386 affine = transforms.IdentityTransform()
--> 4388 self._draw_paths_with_artist_properties(
- 4389 renderer,
- 4390 [(p, affine, self._facecolor if f and self._facecolor[3] else None)
- 4391 for p, f in zip(path, fillable)])
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/patches.py:573, in Patch._draw_paths_with_artist_properties(self, renderer, draw_path_args_list)
- 570 renderer = PathEffectRenderer(self.get_path_effects(), renderer)
- 572 for draw_path_args in draw_path_args_list:
---> 573 renderer.draw_path(gc, *draw_path_args)
- 575 gc.restore()
- 576 renderer.close_group('patch')
-
-File ~/anaconda3/envs/dustpy_docs/lib/python3.12/site-packages/matplotlib/backends/backend_agg.py:132, in RendererAgg.draw_path(self, gc, path, transform, rgbFace)
- 130 else:
- 131 try:
---> 132 self._renderer.draw_path(gc, path, transform, rgbFace)
- 133 except OverflowError:
- 134 cant_chunk = ''
-
-TypeError: must be real number, not str
-
-<Figure size 960x720 with 1 Axes>
-
As marked by the red arrow, the upper end of the mass distribution is a bit off from the analytical solution. The reason for that is, that on a logarithmic mass grid the sum of two colliding masses will lie between two mass bins and has to be distributed between them. That means that a mass bin will be filled that is larger than the combined mass of both collision partners. This leads to accelerated particles growth.
To counteract this, the mass resolution can be increased. In the following example we are running the same simulation again but with 28 mass bins per mass decade. Default is 7.
@@ -709,7 +534,7 @@