fix integration test (#833)

Author: jan-janssen

notebooks/5-1-gpaw.ipynb

@@ -18,9 +18,9 @@
    "source": [
     "import subprocess\n",
     "from ase.build import bulk\n",
-    "from atomistics.workflows.evcurve.helper import (\n",
-    "    analyse_structures_helper as evcurve_analyse_structures,\n",
-    "    generate_structures_helper as evcurve_generate_structures,\n",
+    "from atomistics.workflows import (\n",
+    "    analyse_results_for_energy_volume_curve,\n",
+    "    get_tasks_for_energy_volume_curve,\n",
     ")\n",
     "import matplotlib.pyplot as plt\n",
     "import pprint\n",
@@ -66,7 +66,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "structure_dict = evcurve_generate_structures(\n",
+    "task_dict = get_tasks_for_energy_volume_curve(\n",
     "    structure=bulk(\"Al\", a=4.05, cubic=True),\n",
     "    num_points=7,\n",
     "    vol_range=0.05,\n",
@@ -77,7 +77,7 @@
   {
    "metadata": {},
    "cell_type": "markdown",
-   "source": "The resulting dictionary of structures `structure_dict` is transformed to simplify the parallel execution:",
+   "source": "The resulting dictionary of structures `task_dict` is transformed to simplify the parallel execution:",
    "id": "8bf60b7b0f5af31a"
   },
   {
@@ -87,7 +87,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "task_loop_dict = {k: {\"calc_energy\": v} for k, v in structure_dict.items()}"
+    "task_loop_dict = {k: {\"calc_energy\": v} for k, v in task_dict[\"calc_energy\"].items()}"
    ]
   },
   {
@@ -219,12 +219,12 @@
     "            task_dict=v, \n",
     "            kpts=(3, 3, 3), \n",
     "            encut=300,\n",
-    "            resource_dict={\"cores\": 2},\n",
+    "            resource_dict={\"cores\": 1},\n",
     "        )\n",
     "    sleep(1)\n",
     "    pprint.pp(subprocess.check_output([\"flux\", \"jobs\", \"-a\"], universal_newlines=True).split(\"\\n\"))\n",
     "    result_dict = {\n",
-    "        k: f.result()[-1] \n",
+    "        k: f.result()\n",
     "        for k, f in tqdm(future_dict.items())\n",
     "    }\n",
     "    sleep(1)\n",
@@ -244,9 +244,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fit_dict = evcurve_analyse_structures(\n",
+    "fit_dict = analyse_results_for_energy_volume_curve(\n",
     "    output_dict={\"energy\": result_dict},\n",
-    "    structure_dict=structure_dict,\n",
+    "    task_dict=task_dict,\n",
     "    fit_type=\"polynomial\",\n",
     "    fit_order=3,\n",
     ")"
@@ -416,12 +416,12 @@
     "            task_dict=v, \n",
     "            kpts=(3, 3, 3), \n",
     "            encut=300,\n",
-    "            resource_dict={\"cores\": 2},\n",
+    "            resource_dict={\"cores\": 1},\n",
     "        )\n",
     "    sleep(1)\n",
     "    pprint.pp(subprocess.check_output([\"flux\", \"jobs\", \"-a\"], universal_newlines=True).split(\"\\n\"))\n",
     "    result_dict = {\n",
-    "        k: f.result()[-1] \n",
+    "        k: f.result()\n",
     "        for k, f in tqdm(future_dict.items())\n",
     "    }\n",
     "    sleep(1)\n",
@@ -441,9 +441,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fit_dict = evcurve_analyse_structures(\n",
+    "fit_dict = analyse_results_for_energy_volume_curve(\n",
     "    output_dict={\"energy\": result_dict},\n",
-    "    structure_dict=structure_dict,\n",
+    "    task_dict=task_dict,\n",
     "    fit_type=\"polynomial\",\n",
     "    fit_order=3,\n",
     ")"

notebooks/5-2-quantum-espresso.ipynb

@@ -19,9 +19,9 @@
     "import os\n",
     "import subprocess\n",
     "from ase.build import bulk\n",
-    "from atomistics.workflows.evcurve.helper import (\n",
-    "    analyse_structures_helper as evcurve_analyse_structures,\n",
-    "    generate_structures_helper as evcurve_generate_structures,\n",
+    "from atomistics.workflows import (\n",
+    "    analyse_results_for_energy_volume_curve,\n",
+    "    get_tasks_for_energy_volume_curve,\n",
     ")\n",
     "import matplotlib.pyplot as plt\n",
     "import pprint\n",
@@ -90,7 +90,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "structure_dict = evcurve_generate_structures(\n",
+    "task_dict = get_tasks_for_energy_volume_curve(\n",
     "    structure=bulk(\"Al\", a=4.15, cubic=True),\n",
     "    num_points=7,\n",
     "    vol_range=0.05,\n",
@@ -101,7 +101,7 @@
   {
    "metadata": {},
    "cell_type": "markdown",
-   "source": "The resulting dictionary of structures `structure_dict` is transformed to simplify the parallel execution:",
+   "source": "The resulting dictionary of structures `task_dict` is transformed to simplify the parallel execution:",
    "id": "91dc9dc13d40835e"
   },
   {
@@ -111,7 +111,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "task_loop_dict = {k: {\"calc_energy\": v} for k, v in structure_dict.items()}"
+    "task_loop_dict = {k: {\"calc_energy\": v} for k, v in task_dict[\"calc_energy\"].items()}"
    ]
   },
   {
@@ -273,9 +273,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fit_dict = evcurve_analyse_structures(\n",
+    "fit_dict = analyse_results_for_energy_volume_curve(\n",
     "    output_dict={\"energy\": result_dict},\n",
-    "    structure_dict=structure_dict,\n",
+    "    task_dict=task_dict,\n",
     "    fit_type=\"polynomial\",\n",
     "    fit_order=3,\n",
     ")"
@@ -475,9 +475,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fit_dict = evcurve_analyse_structures(\n",
+    "fit_dict = analyse_results_for_energy_volume_curve(\n",
     "    output_dict={\"energy\": result_dict},\n",
-    "    structure_dict=structure_dict,\n",
+    "    task_dict=task_dict,\n",
     "    fit_type=\"polynomial\",\n",
     "    fit_order=3,\n",
     ")"