Include all analysis (#260)

* include notebooks and figures for main project * include all plotting notebooks for mdmc * add remaining notebooks * also include pdf generated
mosdef-hub · Mar 6, 2024 · 65daf88 · 65daf88
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commit 65daf88
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Showing 22 changed files with 2,953 additions and 442 deletions.
diff --git a/..._project/aggregate_summary/FinalFig.ipynb → ..._project/aggregate_summary/Plotting.ipynb b/..._project/aggregate_summary/FinalFig.ipynb → ..._project/aggregate_summary/Plotting.ipynb
@@ -679,7 +679,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/reproducibility_project/aggregate_summary/figures/benzeneUA_stacked_deviation_density.pdf b/reproducibility_project/aggregate_summary/figures/benzeneUA_stacked_deviation_density.pdf
diff --git a/reproducibility_project/aggregate_summary/figures/ethanolAA_stacked_deviation_density.pdf b/reproducibility_project/aggregate_summary/figures/ethanolAA_stacked_deviation_density.pdf
diff --git a/reproducibility_project/aggregate_summary/figures/methaneUA_stacked_deviation_density.pdf b/reproducibility_project/aggregate_summary/figures/methaneUA_stacked_deviation_density.pdf
diff --git a/...project/aggregate_summary/figures/pentaneUA-constrain_bonds_stacked_deviation_density.pdf b/...project/aggregate_summary/figures/pentaneUA-constrain_bonds_stacked_deviation_density.pdf
diff --git a/reproducibility_project/aggregate_summary/figures/waterSPCE_stacked_deviation_density.pdf b/reproducibility_project/aggregate_summary/figures/waterSPCE_stacked_deviation_density.pdf
diff --git a/reproducibility_project/lrc_shift_subproject/aggregate_summary/Densities.ipynb b/reproducibility_project/lrc_shift_subproject/aggregate_summary/Densities.ipynb
@@ -364,7 +364,6 @@
     "        ax[0].set_xticklabels([\n",
     "            pretty_states[sp] for sp in statepoints]\n",
     "        )\n",
-    "        ax[0].set_xlim(sps_positions[0]-1, sps_positions[-1]+1)\n",
     "        ax[1].set_xlim(sps_positions[0]-1, sps_positions[-1]+1)\n",
     "        ax[1].axhline(y = 0, color = 'black', alpha=0.5, linestyle = '--')\n",
     "\n",
@@ -492,14 +491,6 @@
    "metadata": {},
    "outputs": [],
    "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "14b9b961-d1c4-4fbf-b6f7-353881d359a5",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -518,7 +509,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/...rc_shift_subproject/aggregate_summary/figures/methaneUA_lrc_stacked_deviation_density.pdf b/...rc_shift_subproject/aggregate_summary/figures/methaneUA_lrc_stacked_deviation_density.pdf
diff --git a/...rc_shift_subproject/aggregate_summary/figures/waterSPCE_lrc_stacked_deviation_density.pdf b/...rc_shift_subproject/aggregate_summary/figures/waterSPCE_lrc_stacked_deviation_density.pdf
diff --git a/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/CombinedPlots.ipynb b/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/CombinedPlots.ipynb
diff --git a/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/EtOHDensities.ipynb b/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/EtOHDensities.ipynb
@@ -384,11 +384,6 @@
     "\n",
     "ax[0].set_xticks([pos for pos in sps_positions])    \n",
     "if len(statepoints) != 1:\n",
-    "    # ax[0].set_xticklabels([\n",
-    "    #     f'{sp}\\n' +r'$\\rho_{\\mathrm{ave}}$'+'$ = {:.3f}$'.format(sp_omean) \n",
-    "    #     for sp_omean, sp in zip(statepoints_overall_means, statepoints)\n",
-    "    #     ]\n",
-    "    # )\n",
     "    ax[0].set_xticklabels([statepoint for statepoint in statepoints])\n",
     "\n",
     "    ax[0].set_xlim(sps_positions[0]-1, sps_positions[-1]+1)\n",
@@ -418,16 +413,6 @@
     "sorted_labels = [pretty_names[engine+bcond] \n",
     "                 for engine, bcond in itertools.product(engines, [\"flex\", \"fix\"])]\n",
     "\n",
-    "# plt.legend(sorted_handles, \n",
-    "#            sorted_labels,\n",
-    "#            bbox_to_anchor=(1.05, 0.4),\n",
-    "#            bbox_transform=fig.transFigure,\n",
-    "#            labelspacing=2,\n",
-    "#            facecolor='white', \n",
-    "#            loc='lower right',\n",
-    "#            prop={'size': 12},\n",
-    "#            ncol=1)\n",
-    "\n",
     "\n",
     "ax[0].legend(\n",
     "           sorted_handles, \n",
@@ -472,22 +457,6 @@
     "plt.show()\n",
     "plt.close()\n"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7e2ab3c2-2a35-4f48-89bd-0012d5b5c729",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "93c60f24-f421-4e25-99a6-81ed27c9f1ac",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -506,7 +475,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/RDF-CDF.ipynb b/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/RDF-CDF.ipynb
diff --git a/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/Reference.ipynb b/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/Reference.ipynb
diff --git a/...ducibility_project/mdmc_ethanol_subproject/aggregate_summary/figures/combined_ethanol.pdf b/...ducibility_project/mdmc_ethanol_subproject/aggregate_summary/figures/combined_ethanol.pdf
diff --git a/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/hBonds.ipynb b/reproducibility_project/mdmc_ethanol_subproject/aggregate_summary/hBonds.ipynb
@@ -298,7 +298,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,