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Update BB figure colour scheme and scaling #6

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1117a30
Update BB figure colour scheme and scaling
ae-foster Mar 30, 2026
12757b4
Remove output
ae-foster Mar 30, 2026
4695dad
save plots default
ae-foster Mar 30, 2026
6011846
Update notebook
ae-foster Apr 1, 2026
18ede4a
cleanup
ae-foster Apr 1, 2026
9f9f13d
move label
ae-foster Apr 1, 2026
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139 changes: 62 additions & 77 deletions notebooks/02_bbmep/create_figures.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -160,12 +160,15 @@
"metadata": {},
"outputs": [],
"source": [
"cost_option = \"hour\" #'wallclock_hour', 'energy', 'hour'\n",
"# {\"Orbformer scratch, single point\": '#74baae', \"Orbformer scratch, all points\": '#4e938d',\n",
"# \"Orbformer finetune LAC (200k), all points\": '#366c6c', \"Orbformer finetune LAC (400k), all points\":'#27474a',\n",
"# \"Orbformer finetune LAC (1000k), all points\":'#1d2429', \"Psiformer scratch, single point\":'#8de971'}\n",
"qmc_colors = [\"#74baae\", \"#4e938d\", \"#27474a\", \"#8de971\"]\n",
"\n",
"# Single color for all non-QMC methods, different markers\n",
"non_qmc_color = \"#E05A33\" # red/orange\n",
"non_qmc_markers = ['s', '^', 'v', 'D', 'p', 'h', '*', 'X', 'P', '<', '>'] # variety of markers\n",
"non_qmc_marker_sizes = {'s': 180, '^': 240, 'v': 240, 'D': 180, 'p': 180, 'h': 180, '*': 300, 'X': 180, 'P': 180, '<': 180, '>': 180}\n",
"\n",
"fig, ax = plt.subplots(3, 2, figsize=(18.5, 19), sharey=True)\n",
"compute_sec = {\n",
Expand All @@ -180,8 +183,7 @@
" \"Ethane\": 296013.404 / 200000 / (4 * 16265.031 / 32000),\n",
" \"Formamide\": 182497.587 / 200000 / (10323.08825 / 32000),\n",
"}\n",
"rcParams[\"axes.spines.top\"] = True\n",
"ax_top = {}\n",
"rcParams[\"axes.spines.top\"] = False\n",
"print(MAE.keys())\n",
"for m, i in enumerate(MAE.keys()):\n",
" for n, j in enumerate(MAE[i].keys()):\n",
Expand All @@ -190,58 +192,44 @@
" x = x * psiformer_factor[i]\n",
" if \"all\" in j.split():\n",
" x = x / 20\n",
" # Convert to GPU hours (x is already in GPU-relative units)\n",
" x_gpu_hr = x * 4 * compute_sec[i] / 3600\n",
" y = 627.5 * MAE[i][j][:, 1]\n",
" h, v = np.divmod(m, 3)\n",
" ax[v][h].scatter(x, y, marker=\"o\", s=140, label=j, color=qmc_colors[n])\n",
" a, b = np.polyfit(np.log(x), np.log(y), 1)\n",
" ax[v][h].plot(x, np.exp(a * np.log(x) + b), color=qmc_colors[n], linewidth=4)\n",
" ax[v][h].set_xscale(\"log\", base=4)\n",
" ax[v][h].scatter(x_gpu_hr, y, marker=\"o\", s=140, label=j, color=qmc_colors[n], zorder=3)\n",
" a, b = np.polyfit(np.log(x_gpu_hr), np.log(y), 1)\n",
" ax[v][h].plot(x_gpu_hr, np.exp(a * np.log(x_gpu_hr) + b), color=qmc_colors[n], linewidth=4, zorder=2)\n",
" ax[v][h].set_xscale(\"log\", base=10)\n",
" ax[v][h].set_yscale(\"log\", base=4)\n",
" ticks = [10, 50, 250, 1000, 4000, 16000, 64000, 300000]\n",
" ticks = [0.01, 0.1, 1, 10, 100]\n",
" cost_factor = 300 / (280 / 64)\n",
" for k in MAE_es[i].keys():\n",
" for idx, k in enumerate(MAE_es[i].keys()):\n",
" # Convert CPU cost to equivalent GPU hours for plotting\n",
" cpu_hr = MAE_es[i][k][0]\n",
" gpu_hr_equiv = cpu_hr / cost_factor # convert CPU hr to GPU hr equivalent\n",
" ax[v][h].scatter(\n",
" MAE_es[i][k][0] / (4 * compute_sec[i] / 3600 * cost_factor),\n",
" gpu_hr_equiv,\n",
" 627.5 * MAE_es[i][k][1],\n",
" label=k,\n",
" s=180,\n",
" color=colormaps_es[k],\n",
" marker=marker_es[k],\n",
" s=non_qmc_marker_sizes[non_qmc_markers[idx % len(non_qmc_markers)]],\n",
" color=non_qmc_color,\n",
" marker=non_qmc_markers[idx % len(non_qmc_markers)],\n",
" zorder=4,\n",
" edgecolors='white',\n",
" linewidths=1.5,\n",
" )\n",
" ax[v][h].set_xticks(ticks, ticks, fontsize=16)\n",
" ax[v][h].axhspan(0.2, 5, color=\"grey\", alpha=0.2, lw=0)\n",
" ax[v][h].set_xlim([6, 580000])\n",
" ax_top[m] = ax[v][h].twiny()\n",
" ax_top[m].set_xscale(\"log\", base=4)\n",
" ax_top[m].set_xlim([6, 580000])\n",
" if cost_option == \"hour\":\n",
" ax[v][h].set_xticklabels(\n",
" np.round(np.array(ticks) * 4 * compute_sec[i] / 3600 * cost_factor, 1)\n",
" )\n",
" else:\n",
" ax[v][h].set_xticklabels(cost)\n",
" ax[v][h].axhline(1, color=\"k\", ls=\":\", linewidth=4)\n",
" ax[v][h].set_xticks(ticks)\n",
" ax[v][h].set_xticklabels(ticks, fontsize=16)\n",
" ax[v][h].axhspan(0.2, 5, color=\"grey\", alpha=0.2, lw=0, zorder=0)\n",
" ax[v][h].set_xlim([0.0025, 300] if h == 0 else [0.005, 1100])\n",
" ax[v][h].axhline(1, color=\"darkgray\", ls=\":\", linewidth=4, zorder=1)\n",
" ax[v][h].set_yticks(\n",
" [0.5, 1, 2, 5, 10, 20, 50], [0.5, 1, 2, 5, 10, 20, 50], fontsize=16\n",
" [0.5, 1, 2, 5, 10, 20, 50, 100, 200], [0.5, 1, 2, 5, 10, 20, 50, 100, 200], fontsize=16\n",
" )\n",
" ax[v][h].set_ylim([0.2, 99])\n",
" if v == 0:\n",
" if cost_option == \"hour\":\n",
" ax_top[m].set_xlabel(\"Orbformer A100 GPU hr/structure\", fontsize=22)\n",
" else:\n",
" ax_top[m].set_xlabel(\n",
" \"Scratch training or finetuning steps per structure\", fontsize=22\n",
" )\n",
" ax[v][h].minorticks_off()\n",
" ax[v][h].set_ylim([0.25, 850])\n",
" if h == 0:\n",
" ax[v][h].set_ylabel(\"MARE over entire MEP (kcal/mol)\", fontsize=22)\n",
" if cost_option == \"hour\":\n",
" ax_top[m].set_xticks(ticks)\n",
" ax_top[m].set_xticklabels(\n",
" np.round(np.array(ticks) * 4 * compute_sec[i] / 3600, 2), fontsize=16\n",
" )\n",
" else:\n",
" ax_top[m].set_xticks(ticks)\n",
" ax_top[m].set_xticklabels(ticks)\n",
" ax[v][h].set_ylabel(\"MARE over MEP (kcal/mol)\", fontsize=22)\n",
"ax[2][1].set_axis_off()\n",
"\n",
"ax[0][0].legend(\n",
Expand All @@ -251,89 +239,82 @@
" borderpad=0.16,\n",
" labelspacing=0.4,\n",
")\n",
"ax[0][0].text(0.03, 0.9, \"(g) Ethane\", transform=ax[0][0].transAxes, fontsize=24)\n",
"ax[0][0].text(0.03, 1.02, \"(g) Ethane\", transform=ax[0][0].transAxes, fontsize=24)\n",
"arrimg = mpimg.imread(f\"{data_dir}/molecule_images/bbmep/Ethane/Ethane_0.png\")\n",
"imagebox = OffsetImage(arrimg, zoom=0.12)\n",
"ab = AnnotationBbox(imagebox, (2500, 20), frameon=False)\n",
"ab = AnnotationBbox(imagebox, (0.62, 0.88), xycoords='axes fraction', frameon=False, clip_on=False)\n",
"ax[0][0].add_artist(ab)\n",
"arrimg = mpimg.imread(f\"{data_dir}/molecule_images/bbmep/Ethane/Ethane_19.png\")\n",
"imagebox = OffsetImage(arrimg, zoom=0.2)\n",
"ab = AnnotationBbox(imagebox, (35000, 15), frameon=False)\n",
"ab = AnnotationBbox(imagebox, (0.88, 0.82), xycoords='axes fraction', frameon=False, clip_on=False)\n",
"ax[0][0].add_artist(ab)\n",
"ax[0][0].annotate(\n",
" \"\", xytext=(5500, 20), xy=(12000, 20), arrowprops=dict(arrowstyle=\"->\")\n",
" \"\", xytext=(0.72, 0.88), xy=(0.78, 0.88), xycoords='axes fraction', arrowprops=dict(arrowstyle=\"->\")\n",
")\n",
"\n",
"ax[1][0].text(0.03, 0.9, \"(h) Formamide\", transform=ax[1][0].transAxes, fontsize=24)\n",
"arrimg = mpimg.imread(f\"{data_dir}/molecule_images/bbmep/Formamide/Formamide_0.png\")\n",
"imagebox = OffsetImage(arrimg, zoom=0.12)\n",
"ab = AnnotationBbox(imagebox, (10000, 30), frameon=False)\n",
"ab = AnnotationBbox(imagebox, (0.68, 0.88), xycoords='axes fraction', frameon=False, clip_on=False)\n",
"ax[1][0].add_artist(ab)\n",
"arrimg = mpimg.imread(f\"{data_dir}/molecule_images/bbmep/Formamide/Formamide_19.png\")\n",
"imagebox = OffsetImage(arrimg, zoom=0.2)\n",
"ab = AnnotationBbox(imagebox, (100000, 25), frameon=False)\n",
"ab = AnnotationBbox(imagebox, (0.92, 0.82), xycoords='axes fraction', frameon=False, clip_on=False)\n",
"ax[1][0].add_artist(ab)\n",
"ax[1][0].annotate(\n",
" \"\", xytext=(22000, 30), xy=(45000, 30), arrowprops=dict(arrowstyle=\"->\")\n",
" \"\", xytext=(0.78, 0.88), xy=(0.84, 0.88), xycoords='axes fraction', arrowprops=dict(arrowstyle=\"->\")\n",
")\n",
"\n",
"ax[2][0].text(0.03, 0.9, \"(i) 1-Propanol\", transform=ax[2][0].transAxes, fontsize=24)\n",
"arrimg = mpimg.imread(f\"{data_dir}/molecule_images/bbmep/1-Propanol/1-Propanol_0.png\")\n",
"imagebox = OffsetImage(arrimg, zoom=0.17)\n",
"ab = AnnotationBbox(imagebox, (12000, 38), frameon=False)\n",
"ab = AnnotationBbox(imagebox, (0.68, 0.88), xycoords='axes fraction', frameon=False, clip_on=False)\n",
"ax[2][0].add_artist(ab)\n",
"arrimg = mpimg.imread(f\"{data_dir}/molecule_images/bbmep/1-Propanol/1-Propanol_19.png\")\n",
"arrimg = np.rot90(arrimg)\n",
"imagebox = OffsetImage(arrimg, zoom=0.25)\n",
"ab = AnnotationBbox(imagebox, (120000, 28), frameon=False)\n",
"ab = AnnotationBbox(imagebox, (0.92, 0.82), xycoords='axes fraction', frameon=False, clip_on=False)\n",
"ax[2][0].add_artist(ab)\n",
"ax[2][0].annotate(\n",
" \"\", xytext=(30000, 38), xy=(55000, 38), arrowprops=dict(arrowstyle=\"->\")\n",
" \"\", xytext=(0.78, 0.88), xy=(0.84, 0.88), xycoords='axes fraction', arrowprops=dict(arrowstyle=\"->\")\n",
")\n",
"\n",
"ax[0][1].text(\n",
" 0.03, 0.9, \"(j) 2-Aminopropan-2-ol\", transform=ax[0][1].transAxes, fontsize=24\n",
" 0.03, 1.02, \"(j) 2-Aminopropan-2-ol\", transform=ax[0][1].transAxes, fontsize=24\n",
")\n",
"arrimg = mpimg.imread(\n",
" f\"{data_dir}/molecule_images/bbmep/2-Aminopropan-2-ol/2-Aminopropan-2-ol_0.png\"\n",
")\n",
"imagebox = OffsetImage(arrimg, zoom=0.18)\n",
"ab = AnnotationBbox(imagebox, (14000, 35), frameon=False)\n",
"ab = AnnotationBbox(imagebox, (0.68, 0.88), xycoords='axes fraction', frameon=False, clip_on=False)\n",
"ax[0][1].add_artist(ab)\n",
"arrimg = mpimg.imread(\n",
" f\"{data_dir}/molecule_images/bbmep/2-Aminopropan-2-ol/2-Aminopropan-2-ol_19.png\"\n",
")\n",
"arrimg = remove_black_edge(rotate(arrimg, angle=60, reshape=True))\n",
"imagebox = OffsetImage(arrimg, zoom=0.23)\n",
"ab = AnnotationBbox(imagebox, (120000, 28), frameon=False)\n",
"ab = AnnotationBbox(imagebox, (0.92, 0.82), xycoords='axes fraction', frameon=False, clip_on=False)\n",
"ax[0][1].add_artist(ab)\n",
"ax[0][1].annotate(\n",
" \"\", xytext=(28000, 30), xy=(60000, 30), arrowprops=dict(arrowstyle=\"->\")\n",
" \"\", xytext=(0.78, 0.88), xy=(0.84, 0.88), xycoords='axes fraction', arrowprops=dict(arrowstyle=\"->\")\n",
")\n",
"\n",
"ax[1][1].text(0.03, 0.9, \"(k) L-Alanine\", transform=ax[1][1].transAxes, fontsize=24)\n",
"arrimg = mpimg.imread(f\"{data_dir}/molecule_images/bbmep/L-Alanine/L-Alanine_0.png\")\n",
"imagebox = OffsetImage(arrimg, zoom=0.18)\n",
"ab = AnnotationBbox(imagebox, (28000, 40), frameon=False)\n",
"ab = AnnotationBbox(imagebox, (0.7, 0.88), xycoords='axes fraction', frameon=False, clip_on=False)\n",
"ax[1][1].add_artist(ab)\n",
"arrimg = mpimg.imread(f\"{data_dir}/molecule_images/bbmep/L-Alanine/L-Alanine_19.png\")\n",
"arrimg = remove_black_edge(rotate(arrimg, angle=60))\n",
"imagebox = OffsetImage(arrimg, zoom=0.16)\n",
"ab = AnnotationBbox(imagebox, (140000, 25), frameon=False)\n",
"ab = AnnotationBbox(imagebox, (0.92, 0.82), xycoords='axes fraction', frameon=False, clip_on=False)\n",
"ax[1][1].add_artist(ab)\n",
"ax[1][1].annotate(\n",
" \"\", xytext=(44000, 30), xy=(85000, 30), arrowprops=dict(arrowstyle=\"->\")\n",
" \"\", xytext=(0.8, 0.88), xy=(0.86, 0.88), xycoords='axes fraction', arrowprops=dict(arrowstyle=\"->\")\n",
")\n",
"\n",
"if cost_option == \"wallclock_hour\":\n",
" ax[2][0].set_xlabel(\"GPU or CPU hr/structure\", fontsize=22)\n",
" ax[1][1].set_xlabel(\"GPU or CPU hr/structure\", fontsize=22)\n",
"elif cost_option == \"energy\":\n",
" ax[2][0].set_xlabel(\"Energy cost/structure (KWh)\", fontsize=22)\n",
" ax[1][1].set_xlabel(\"Energy cost/structure (KWh)\", fontsize=22)\n",
"else:\n",
" ax[2][0].set_xlabel(\"Other methods AMD EPYC 7763 CPU hr/structure\", fontsize=22)\n",
" ax[1][1].set_xlabel(\"Other methods AMD EPYC 7763 CPU hr/structure\", fontsize=22)\n",
"ax[2][0].set_xlabel(\"A100 GPU hr/structure\", fontsize=22)\n",
"ax[1][1].set_xlabel(\"A100 GPU hr/structure\", fontsize=22)\n",
"\n",
"ax[0][0].text(\n",
" 0.55,\n",
Expand All @@ -347,7 +328,7 @@
"# plt.draw()\n",
"if save_figures:\n",
" plt.savefig(f\"{data_dir}/BBMEP_result_fig_hours.pdf\", dpi=600, bbox_inches='tight')\n",
"# plt.show()"
"plt.show()\n"
]
},
{
Expand All @@ -359,7 +340,7 @@
"source": [
"## Get reaction profile figure\n",
"\n",
"fig, ax = plt.subplots(3, 2, figsize=(13, 17.5), sharex=True)\n",
"fig, ax = plt.subplots(3, 2, figsize=(13, 19), sharex=True)\n",
"\n",
"for m, j in enumerate([\"Ethane\", \"Formamide\", \"2-Aminopropan-2-ol\"]):\n",
" step = int(MAE[j][\"Orbformer fine-tune LAC (400k), all structures\"][-1, 0])\n",
Expand Down Expand Up @@ -464,8 +445,8 @@
" )\n",
" ax[m][0].set_ylabel(\"Relative E (kcal/mol)\", fontsize=22)\n",
" ax[m][1].set_ylabel(\"Relative E Error (kcal/mol)\", fontsize=22)\n",
"ax[0][0].text(0.03, 0.9, \"(a) Ethane\", transform=ax[0][0].transAxes, fontsize=24)\n",
"ax[0][1].text(0.03, 0.9, \"(d) Ethane\", transform=ax[0][1].transAxes, fontsize=24)\n",
"ax[0][0].text(0.03, 1.02, \"(a) Ethane\", transform=ax[0][0].transAxes, fontsize=24)\n",
"ax[0][1].text(0.03, 1.02, \"(d) Ethane\", transform=ax[0][1].transAxes, fontsize=24)\n",
"ax[1][0].text(0.03, 0.9, \"(b) Formamide\", transform=ax[1][0].transAxes, fontsize=24)\n",
"ax[1][1].text(0.03, 0.9, \"(e) Formamide\", transform=ax[1][1].transAxes, fontsize=24)\n",
"ax[2][0].text(\n",
Expand Down Expand Up @@ -532,14 +513,18 @@
"ax[0][1].text(\n",
" 0.18, 1.1, \"Relative Energy Error\", transform=ax[0][1].transAxes, fontsize=26\n",
")\n",
"ax[0][0].set_ylim([-100, 55])\n",
"ax[2][0].set_ylim([-65, 58])\n",
"plt.subplots_adjust(wspace=0.2, hspace=0.02)\n",
"fig.align_ylabels(ax[:, 0])\n",
"fig.align_ylabels(ax[:, 1])\n",
"plt.subplots_adjust(wspace=0.2, hspace=0.15)\n",
"ax[2][0].set_xticks(2 * np.arange(11))\n",
"ax[2][0].set_xlim([-0.5, 19.5])\n",
"ax[2][0].set_xticklabels(2 * np.arange(11))\n",
"ax[2][0].set_xlabel(\"Image ID on MEP\", fontsize=22)\n",
"ax[2][1].set_xlabel(\"Image ID on MEP\", fontsize=22)\n",
"plt.draw()\n",
"\n",
"if save_figures:\n",
" plt.savefig(f\"{data_dir}/BBMEP_energy_profile.pdf\", dpi=600, bbox_inches='tight')\n",
"plt.show()"
Expand All @@ -556,7 +541,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "oneqmc",
"language": "python",
"name": "python3"
},
Expand All @@ -570,7 +555,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.10"
"version": "3.11.14"
}
},
"nbformat": 4,
Expand Down
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