Modifications to publications and changelog notebooks

Author: stammler

examples/B_publications.ipynb

@@ -21,10 +21,10 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "* **Introducing CUDISC: a 2D code for protoplanetary disc structure and evolution calculations**  \n",
-    "Robinson, Alfie; Booth, Richard A.; Owen, James E. (2024)  \n",
-    "_Monthly Notices of the Royal Astronomical Society, Volume 529, Issue 2, pp.1524-1541_  \n",
-    "[doi: 10.1093/mnras/stae624](https://doi.org/10.1093/mnras/stae624)"
+    "* **Sequential giant planet formation initiated by disc substructure**  \n",
+    "Lau, Tommy Chi Ho; Birnstiel, Til; Drążkowska, Joanna; Stammler, Sebastian (2024)  \n",
+    "_eprint arXiv:2406.12340_  \n",
+    "[doi: 10.48550/arXiv.2406.12340](https://doi.org/10.48550/arXiv.2406.12340])"
    ]
   },
   {
@@ -33,8 +33,18 @@
    "source": [
     "* **Survival of the long-lived inner disk of PDS 70**  \n",
     "Pinilla, Paola; Benisty, Myriam; Waters, Rens; Bae, Jaehan; Facchini, Stefano (2024)  \n",
-    "_eprint arXiv:2403.07057_  \n",
-    "[doi: 10.48550/arXiv.2403.07057](https://doi.org/10.48550/arXiv.2403.07057)"
+    "_Astronomy & Astrophysics, Volume 686, id.A135, 10 pp._  \n",
+    "[doi: 10.1051/0004-6361/202348707](https://doi.org/10.1051/0004-6361/202348707)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "* **Introducing CUDISC: a 2D code for protoplanetary disc structure and evolution calculations**  \n",
+    "Robinson, Alfie; Booth, Richard A.; Owen, James E. (2024)  \n",
+    "_Monthly Notices of the Royal Astronomical Society, Volume 529, Issue 2, pp.1524-1541_  \n",
+    "[doi: 10.1093/mnras/stae624](https://doi.org/10.1093/mnras/stae624)"
    ]
   },
   {

examples/E_changelog.ipynb

@@ -26,8 +26,22 @@
     "\n",
     "#### Simframe compatibility\n",
     "\n",
-    "The necessary modifications have been made to make `DustPy` compatible to the latest `Simframe v1.0.5`.\n",
-    "\n"
+    "The necessary modifications have been made to make `DustPy` compatible to the latest `Simframe v1.0.5`.  \n",
+    "`Simframe` has to be updated to at least version `1.0.5`.\n",
+    "\n",
+    "Due to the changes in `Simframe`, the snapshots stored in `sim.t.snapshots` now need to additionally contain the time, at which the initial conditions are written. By default this is for `t=0`.\n",
+    "\n",
+    "#### Bugfix to initial fluxes and source terms\n",
+    "\n",
+    "A bug was writing false gas and dust fluxes and source terms into the output files. The results of previous simulations were not affected by this issue.\n",
+    "\n",
+    "#### Bugfix to implicit fluxes and source terms\n",
+    "\n",
+    "When using implicit integration, the gas and dust fluxes and source terms are computed after the integration step from the new surface density. A bug in referencing to the old values of the surface densities caused fluxes and source terms to be computed incorrectly. The simulations are not affected, since these quantities are only computed for convenience and post-simulation analysis, but values written to the output files may have been incorrect.\n",
+    "\n",
+    "#### Modification to total dust flux function\n",
+    "\n",
+    "The default function to compute the total dust flux has been modified to be downstream compatible to other software packages using `DustPy`. Simulations that are not customizing this function are not affected by this change."
    ]
   },
   {