pyiron.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import matplotlib.pylab as plt\n",
    "import pandas as pd\n",
    "import ipywidgets as widgets\n",
    "from IPython.display import display\n",
    "\n",
    "from pyiron import Project"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "class GUIStructure:\n",
    "    def __init__(self, project, msg=None):\n",
    "        self.project = project\n",
    "        self.msg = msg\n",
    "        \n",
    "        self.count = 0\n",
    "        self.create_btn = widgets.Button(description='Refresh') \n",
    "        self.output_plot3d = widgets.Output(layout=widgets.Layout(width='50%', height='100%'))\n",
    "        self.cubic_ckb = widgets.Checkbox(value=True, description='Cubic')\n",
    "        self.ortho_ckb = widgets.Checkbox(value=False, description='Orthorombic')\n",
    "\n",
    "        self.element_drp = widgets.Dropdown(\n",
    "            options=['Al', 'Fe', 'Mg'],\n",
    "            value='Al',\n",
    "            description='Element:'\n",
    "        )\n",
    "        self.repeat_drp = widgets.Dropdown(\n",
    "            options=range(1, 6),\n",
    "            value=1,\n",
    "            description='Repeat:'\n",
    "        )\n",
    "\n",
    "        self.cubic_ckb.observe(self.refresh, names='value')\n",
    "        self.ortho_ckb.observe(self.refresh, names='value')\n",
    "        self.repeat_drp.observe(self.refresh, names='value')\n",
    "        self.element_drp.observe(self.refresh, names='value')\n",
    "        self.create_btn.on_click(self.refresh)\n",
    "        self.refresh()\n",
    "        \n",
    "    def gui(self):\n",
    "        return widgets.HBox([\n",
    "            widgets.VBox([self.element_drp, self.repeat_drp, self.cubic_ckb, self.ortho_ckb]), # , self.create_btn]), \n",
    "            self.output_plot3d])  \n",
    "        \n",
    "    def refresh(self, *args):\n",
    "        try:\n",
    "            struc = self.project.create_ase_bulk(self.element_drp.value, cubic=self.cubic_ckb.value, orthorhombic=self.ortho_ckb.value).repeat(self.repeat_drp.value)\n",
    "        except RuntimeError as e:\n",
    "            with self.output_plot3d:\n",
    "                self.output_plot3d.clear_output()\n",
    "                print ('Error: ', e)\n",
    "                return\n",
    "        self.structure = struc\n",
    "        self.view = struc.plot3d()\n",
    "\n",
    "        self.output_plot3d.clear_output()\n",
    "        with self.output_plot3d:\n",
    "            display(self.view) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "class PARAM_MD:\n",
    "    def __init__(self, gui_calc):\n",
    "        self.gui_calc = gui_calc\n",
    "        \n",
    "        self.temperature = widgets.IntSlider(description='Temperature: ', min=1, max=5000, steps=10, value=500)\n",
    "        self.n_ionic_steps = widgets.Dropdown(\n",
    "            options= [int(10**i) for i in range(8)],\n",
    "            value=10000,\n",
    "            description='n_ionic_steps:'\n",
    "        )\n",
    "        self.n_print = widgets.Dropdown(\n",
    "            options= [int(10**i) for i in range(6)],\n",
    "            value=100,\n",
    "            description='n_print:'\n",
    "        ) \n",
    "        \n",
    "    def gui(self):\n",
    "        self.temperature.observe(self.gui_calc.refresh, names='value')\n",
    "        self.n_ionic_steps.observe(self.gui_calc.refresh, names='value')\n",
    "        self.n_print.observe(self.gui_calc.refresh, names='value')\n",
    "        \n",
    "        return widgets.VBox([self.temperature, self.n_ionic_steps, self.n_print], layout={'border': '1px solid lightgray'})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "class PARAM_MIN:\n",
    "    def __init__(self, gui_calc):\n",
    "        self.gui_calc = gui_calc\n",
    "    \n",
    "        self.f_eps = widgets.Dropdown(\n",
    "            options= [10**(-i) for i in range(5)],\n",
    "            value=10**(-4),\n",
    "            description='Force conv.:'\n",
    "        )\n",
    "\n",
    "        self.max_iter = widgets.Dropdown(\n",
    "            options= [int(10**(i)) for i in range(5)],\n",
    "            value=100,\n",
    "            description='max iterations:'\n",
    "        )\n",
    "        self.n_print = widgets.Dropdown(\n",
    "            options= [int(10**i) for i in range(6)],\n",
    "            value=100,\n",
    "            description='n_print:'\n",
    "        ) \n",
    "        \n",
    "    def gui(self):\n",
    "        self.f_eps.observe(self.gui_calc.refresh, names='value')\n",
    "        self.max_iter.observe(self.gui_calc.refresh, names='value')\n",
    "        self.n_print.observe(self.gui_calc.refresh, names='value')\n",
    "        \n",
    "        return widgets.VBox([self.f_eps, self.max_iter, self.n_print], layout={'border': '1px solid lightgray'})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_generic_inp(job):\n",
    "    j_dic = job['input/generic/data_dict']\n",
    "    return {k:v for k,v in zip(j_dic['Parameter'], j_dic['Value'])}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [],
   "source": [
    "class GUI_CALC:\n",
    "    def __init__(self, gui_structure):\n",
    "        self.gui_structure = gui_structure\n",
    "        \n",
    "        self.project = self.gui_structure.project\n",
    "        self.msg = self.gui_structure.msg\n",
    "        \n",
    "        self.par_md = PARAM_MD(self)\n",
    "        self.par_min = PARAM_MIN(self)\n",
    "        \n",
    "        calc_opt = widgets.Tab()\n",
    "        calc_opt.set_title(0, 'MD')\n",
    "        calc_opt.set_title(1, 'Minimize')\n",
    "        calc_opt.set_title(2, 'Static')\n",
    "\n",
    "        calc_opt.children = [self.par_md.gui(), self.par_min.gui(), widgets.VBox()] \n",
    "        self.calc_opt = calc_opt\n",
    "        \n",
    "        self.output = widgets.Output(layout=widgets.Layout(width='50%', height='100%'))\n",
    "\n",
    "        self.job_name = widgets.Text(\n",
    "            value='',\n",
    "            placeholder='Type something',\n",
    "            description='Job Name:',\n",
    "            disabled=False\n",
    "        )\n",
    "\n",
    "        self.create_btn = widgets.Button(description='Refresh')\n",
    "        self.run_btn = widgets.Button(description='Run')\n",
    "        self.run_btn.style.button_color ='lightblue'\n",
    "\n",
    "        self.job_type = widgets.Dropdown(\n",
    "            options = ['Lammps', 'Vasp'],\n",
    "            value='Lammps',\n",
    "            description='Job Type:'\n",
    "        )\n",
    "\n",
    "        self.potential = widgets.Dropdown(\n",
    "            options = [''], #job.list_potentials(),\n",
    "    #         value='Lammps',\n",
    "            description='Potential:'\n",
    "        )\n",
    "        \n",
    "    def set_job_params(self, job):\n",
    "        self.struc = job.get_structure(-1)  # TODO: i_frame\n",
    "        self.potential.options = self.job.list_potentials()  \n",
    "        self.potential.value = job.potential['Name'].values[0]\n",
    "        generic_par = get_generic_inp(job)\n",
    "        if generic_par['calc_mode'] == 'md':\n",
    "            with self.msg:\n",
    "                print ('Temp: ', generic_par['temperature'])\n",
    "            self.par_md.temperature = generic_par['temperature']\n",
    "            self.par_md.n_ionic_steps = generic_par['n_ionic_steps'] \n",
    "    \n",
    "    def refresh_input(self, *args):\n",
    "        if self.struc is None:\n",
    "            with self.output:\n",
    "                print ('No structure')\n",
    "            return widgets.HBox([self.output])    \n",
    "\n",
    "        if self.job_name.value == \"\":\n",
    "            self.job_name.value = self.struc.get_chemical_formula()    \n",
    "\n",
    "        self.job = self.project.create_job(self.job_type.value, self.job_name.value)\n",
    "#         if self.job.status == 'finished':\n",
    "#             self.set_job_params(self.job)\n",
    "#         else:    \n",
    "        self.job.structure = self.struc\n",
    "        self.potential.options = self.job.list_potentials()     \n",
    "        \n",
    "    def refresh(self, job=None, *args):\n",
    "#         if job is None:\n",
    "        self.struc = self.gui_structure.structure\n",
    "        self.view = self.gui_structure.view\n",
    "        self.job_name.value = self.struc.get_chemical_formula() \n",
    "\n",
    "        self.refresh_input()\n",
    "        self.refresh_job_name()\n",
    "        \n",
    "    def refresh_job_name(self, *args):     \n",
    "        pr = self.project\n",
    "            \n",
    "        self.output.clear_output()    \n",
    "        if self.job_name.value in pr.list_nodes():\n",
    "            self.run_btn.style.button_color ='red'\n",
    "            self.run_btn.description = 'Delete'\n",
    "            with self.output:\n",
    "#                     print (\"test: \", job_name.value, pr.list_nodes(), job_name.value in pr.list_nodes(), run_btn.style.button_color)                      \n",
    "                self.job = pr.load(self.job_name.value)\n",
    "                display(self.job.animate_structure())  \n",
    "        else:\n",
    "            self.run_btn.style.button_color ='lightgreen'\n",
    "            self.run_btn.description = 'Run'\n",
    "            with self.output:\n",
    "                display(self.view)  \n",
    "#                 print (\"test: \", self.job_name.value, pr.list_nodes(), self.job_name.value in pr.list_nodes(), self.run_btn.style.button_color)    \n",
    "            \n",
    "    def on_run_btn_clicked(self, b):\n",
    "        if b.description == 'Run':\n",
    "            self.job.potential = self.potential.value\n",
    "            if self.job_type.value == 'MD':\n",
    "                self.job.calc_md(temperature=self.par_md.temperature.value, n_ionic_steps=self.par_md.n_ionic_steps.value, n_print=self.par_md.n_print.value)\n",
    "            elif self.job_type.value == 'Minimize': \n",
    "                self.job.calc_minimize(f_eps=self.par_min.f_eps.value, max_iter=self.par_min.max_iter.value, n_print=self.par_min.n_print.value)\n",
    "            else:\n",
    "                self.job.calc_static()\n",
    "            self.job.run()\n",
    "            self.refresh()\n",
    "        elif b.description == 'Delete':\n",
    "            self.job.remove()\n",
    "            self.refresh()\n",
    "            \n",
    "    def gui(self):\n",
    "        self.job_type.observe(self.refresh, names='value')\n",
    "        self.job_name.on_submit(self.refresh_job_name)\n",
    "        self.potential.observe(self.refresh, names='value')\n",
    "\n",
    "        self.create_btn.on_click(self.refresh)   \n",
    "        self.run_btn.on_click(self.on_run_btn_clicked)\n",
    "        job_box = widgets.VBox([self.job_type, self.job_name, self.potential], layout={'border': '1px solid lightgray'})\n",
    "\n",
    "        return widgets.HBox([widgets.VBox([self.calc_opt, job_box, self.create_btn, self.run_btn]), self.output])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [],
   "source": [
    "class GUI_EXPLORER:\n",
    "    def __init__(self, project, msg=None):\n",
    "        self.project = project\n",
    "        self.msg = msg\n",
    "        \n",
    "        self.output = widgets.Output(layout=widgets.Layout(width='50%', height='100%'))        \n",
    "        self.groups = widgets.Select(options=[], description='Group:')\n",
    "        self.nodes = widgets.Select(options=[], description='Nodes:')\n",
    "        self._update()\n",
    "\n",
    "        self.groups.observe(self.refresh_group, names='value')\n",
    "        self.nodes.observe(self.refresh_node, names='value')\n",
    "        \n",
    "    def refresh(self, *args):\n",
    "        pass\n",
    "    \n",
    "    @property\n",
    "    def structure(self):\n",
    "        if self.view is not None:\n",
    "            return self.node.get_structure(self.view.frame)\n",
    "        \n",
    "    def gui(self):\n",
    "        return widgets.HBox([\n",
    "            widgets.VBox([self.groups, self.nodes]), \n",
    "            self.output])  \n",
    "    \n",
    "    def _update(self):\n",
    "        groups = [\".\", \"..\"] + self.project.list_groups()\n",
    "        nodes = [\".\"] + self.project.list_nodes()\n",
    "        self.groups.options = groups\n",
    "        self.nodes.options = nodes        \n",
    "        \n",
    "    def refresh_group(self, *args):\n",
    "        if self.groups.value != '.':\n",
    "            self.project = self.project[self.groups.value]\n",
    "            self._update() \n",
    "\n",
    "    def refresh_node(self, *args):\n",
    "        self.view = None\n",
    "        if self.nodes.value is not None:\n",
    "            node = self.project[self.nodes.value] \n",
    "            if hasattr(node, 'animate_structure'):\n",
    "                self.output.clear_output()\n",
    "                with self.output:\n",
    "                    print ('animate')\n",
    "                    self.view = node.animate_structure()\n",
    "                    display(self.view)\n",
    "                    self.node = node\n",
    "            elif hasattr(node, 'list_groups'):\n",
    "                self.project = node \n",
    "                self._update()                     "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [],
   "source": [
    "class GUI_PYIRON:    \n",
    "    def __init__(self, project):\n",
    "        self.msg = widgets.Output(layout={'border': '1px solid black'})\n",
    "        self.msg.append_stdout('')\n",
    "        self.msg.append_stderr('')\n",
    "        self.clear_msg = widgets.Button(description='Clear')\n",
    "        \n",
    "        self.gui_structure = GUIStructure(project=project, msg=self.msg)\n",
    "        self.gui_calc = GUI_CALC(self.gui_structure)\n",
    "        self.gui_explorer = GUI_EXPLORER(project)\n",
    "        \n",
    "    def on_clear_msg_clicked(self, b):\n",
    "        self.msg.clear_output()\n",
    "        \n",
    "    def gui(self):\n",
    "\n",
    "        tab = widgets.Tab()\n",
    "        tab.set_title(0, 'Structure')\n",
    "        tab.set_title(1, 'Calculate')\n",
    "        tab.set_title(2, 'Explorer')\n",
    "        tab.children = [self.gui_structure.gui(), self.gui_calc.gui(), self.gui_explorer.gui()]\n",
    "        \n",
    "        self.tab_children = [self.gui_structure, self.gui_calc, self.gui_explorer]\n",
    "        \n",
    "        def on_value_change(change):\n",
    "            sel_ind = change['new']\n",
    "            self.msg.clear_output()\n",
    "            with self.msg:\n",
    "                print (sel_ind, type(tab.children[sel_ind]), hasattr(self.tab_children[sel_ind], 'refresh'))\n",
    "            self.tab_children[sel_ind].refresh()\n",
    "            \n",
    "            \n",
    "        self.clear_msg.on_click(self.on_clear_msg_clicked)\n",
    "        tab.observe(on_value_change, names='selected_index')\n",
    "        return widgets.VBox([tab, widgets.HBox([self.msg, self.clear_msg])], layout={'border': '4px solid lightgray'})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "44eab1410a154187b7bc15c2f86cf2b9",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(Tab(children=(HBox(children=(VBox(children=(Dropdown(description='Element:', options=('Al', 'Fe…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "pr1 = Project('test')\n",
    "\n",
    "gp = GUI_PYIRON(pr1)\n",
    "gp.gui()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "TODO: \n",
    "- output messages (i.e. when starting job; redirect output)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [],
   "source": [
    "# job = pr1['Al32']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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