update ai2cat notebook

chenggroup · Nov 3, 2023 · 55c2055 · 55c2055
1 parent 48a313e
commit 55c2055
Showing 1 changed file with 10 additions and 13 deletions.
diff --git a/notebook/ai2cat.ipynb b/notebook/ai2cat.ipynb
@@ -70,6 +70,12 @@
     "LAMMPS_BATCH_TEMPLATE  = f'{AI4EC_DIR}/slurm/ai2cat-lammps.sbatch'\n",
     "AI2KIT_EXECUTOR_CONFIG = f'{AI4EC_DIR}/ai2-kit/executor.yml'\n",
     "\n",
+    "CP2K_DEFAULTS = dict(\n",
+    "    basic_set_file = os.path.join(CP2K_DATA, 'BASIS_MOLOPT'),\n",
+    "    potential_file = os.path.join(CP2K_DATA, 'GTH_POTENTIALS'),\n",
+    "    parameter_file = os.path.join(CP2K_DATA, 'dftd3.dat'),\n",
+    ")\n",
+    "\n",
     "ui_helper = ui.get_the_ui_helper()\n",
     "print(\"Current Directory Is: \", os.getcwd())"
    ]
@@ -103,7 +109,7 @@
    "outputs": [],
    "source": [
     "! mkdir -p ./00-aimd\n",
-    "ui_helper.gen_aimd_config(cp2k_search_path=CP2K_DATA, out_dir='./00-aimd')"
+    "ui_helper.gen_aimd_config(out_dir='./00-aimd', **CP2K_DEFAULTS)"
    ]
   },
   {
@@ -221,7 +227,7 @@
    "source": [
     "train_dir = os.path.abspath('./01-train/work_dir')\n",
     "! mkdir -p  {train_dir}\n",
-    "ui_helper.gen_training_config(cp2k_search_path=CP2K_DATA, out_dir='./01-train')\n",
+    "ui_helper.gen_training_config(out_dir='./01-train', **CP2K_DEFAULTS)\n",
     "! ai2-kit tool yaml load {AI2KIT_EXECUTOR_CONFIG} - set_value \"executors.ikkem.work_dir\" {train_dir} - dump > ./01-train/executor.yml"
    ]
   },
@@ -337,7 +343,6 @@
     "生成模拟所需lammps以及plumed配置文件，依据反应坐标配置plumed输入文件\n",
     "* `plumed.dat`, plumed 的配置, 需要由用户定义增强采样的反应坐标, 以及其它所需的命令\n",
     "  * 例如增加 `CV1: DISTANCE ATOMS=14,15`，根据具体的研究目标进行配置\n",
-    "* 命令中的 `--dp_models` 需指向模型对应的地址\n",
     " \n",
     "以下命令可以在 生成基本的作业模板，模板生成后可进入 `./02-simluation` 目录对其进行检查和编辑"
    ]
@@ -349,7 +354,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ui_helper.gen_lammps_config('./01-train/work_dir/', './02-simulation')"
+    "ui_helper.gen_lammps_config('./01-train/work_dir/', out_dir='./02-simulation')"
    ]
   },
   {
@@ -379,7 +384,7 @@
    "outputs": [],
    "source": [
     "# 提交作业\n",
-    "! (cd ./00-aimd && sbatch lammps.sbatch)"
+    "! (cd ./02-simulation/ && sbatch lammps.sbatch)"
    ]
   },
   {
@@ -423,14 +428,6 @@
     "ax.set_title(r'$Free \\ energy \\ curve$');"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "9e92ff49-b4c8-40d2-98f0-00bd3dd94ea0",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": null,