{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Type 1 transition "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import json\n",
    "import matplotlib.pylab as plt\n",
    "%matplotlib inline\n",
    "\n",
    "from tyssue import Sheet, config\n",
    "from tyssue import SheetGeometry as geom\n",
    "\n",
    "# What we're here for\n",
    "from tyssue.topology.sheet_topology import type1_transition\n",
    "\n",
    "## model and solver\n",
    "from tyssue.dynamics.sheet_vertex_model import SheetModel as model\n",
    "from tyssue.solvers.quasistatic import QSSolver\n",
    "\n",
    "# 2D plotting\n",
    "from tyssue.draw import sheet_view\n",
    "\n",
    "#I/O\n",
    "from tyssue.io import hdf5\n",
    "plt.style.use('bmh')\n",
    "\n",
    "import logging\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![Type 1 transition](../../doc/illus/t1_transition.png)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "solver = QSSolver()\n",
    "\n",
    "h5store = 'data/small_hexagonal.hf5'\n",
    "datasets = hdf5.load_datasets(h5store,\n",
    "                              data_names=['face', 'vert', 'edge'])\n",
    "specs = config.geometry.cylindrical_sheet()\n",
    "sheet = Sheet('emin', datasets, specs)\n",
    "\n",
    "\n",
    "geom.update_all(sheet)\n",
    "\n",
    "nondim_specs = config.dynamics.quasistatic_sheet_spec()\n",
    "dim_model_specs = model.dimensionalize(nondim_specs)\n",
    "sheet.update_specs(dim_model_specs, reset=True)\n",
    "\n",
    "solver_settings = {'options': {'gtol':1e-4}}\n",
    "\n",
    "sheet.get_opposite()\n",
    "sheet.vert_df.is_active = 0\n",
    "\n",
    "active_edges = (sheet.edge_df['opposite'] > -1)\n",
    "active_verts = set(sheet.edge_df[active_edges]['srce'])\n",
    "\n",
    "sheet.vert_df.loc[active_verts, 'is_active'] = 1\n",
    "\n",
    "fig, ax = sheet_view(sheet, ['z', 'x'],\n",
    "                     edge={'head_width': 0.5},\n",
    "                     vert={'visible': False})\n",
    "fig.set_size_inches(10, 6)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "res = solver.find_energy_min(sheet, geom, model, **solver_settings)\n",
    "fig, ax = sheet_view(sheet, mode=\"quick\", coords=['z', 'x'])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from tyssue.topology.sheet_topology import type1_transition"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "type1_transition(sheet, 84)\n",
    "geom.update_all(sheet)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "fig, ax = sheet_view(sheet, ['z', 'x'], mode=\"quick\")\n",
    "\n",
    "ax.set_xlim(3, 10)\n",
    "ax.set_ylim(0, 5)\n",
    "\n",
    "ax.set_aspect('equal')\n",
    "fig.set_size_inches(8, 5)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "res = solver.find_energy_min(sheet, geom, model)\n",
    "print(res['success'])\n",
    "fig, ax = sheet_view(sheet, ['z', 'x'], mode=\"quick\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sheet.validate()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Type 1 transitions can also be performed on edge faces"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from tyssue.generation import three_faces_sheet\n",
    "\n",
    "sheet = Sheet('3f', *three_faces_sheet())\n",
    "geom.update_all(sheet)\n",
    "fig, ax = sheet_view(sheet, edge={'head_width': 0.05})\n",
    "fig.set_size_inches(8, 8)\n",
    "\n",
    "for face, data in sheet.face_df.iterrows():\n",
    "    ax.text(data.x, data.y, face)\n",
    "for vert, data in sheet.vert_df.iterrows():\n",
    "    ax.text(data.x, data.y+0.1, vert)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "type1_transition(sheet, 0, epsilon=0.4)\n",
    "sheet.reset_index()\n",
    "\n",
    "geom.update_all(sheet)\n",
    "\n",
    "fig, ax = sheet_view(sheet, edge={'head_width': 0.05})\n",
    "fig.set_size_inches(8, 8)\n",
    "for face, data in sheet.face_df.iterrows():\n",
    "    ax.text(data.x, data.y, face)\n",
    "\n",
    "for vert, data in sheet.vert_df.iterrows():\n",
    "    ax.text(data.x, data.y+0.1, vert)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "type1_transition(sheet, 16, epsilon=0.5)\n",
    "\n",
    "geom.update_all(sheet)\n",
    "\n",
    "fig, ax = sheet_view(sheet, edge={'head_width': 0.05})\n",
    "fig.set_size_inches(8, 8)\n",
    "for face, data in sheet.face_df.iterrows():\n",
    "    ax.text(data.x, data.y, face)\n",
    "\n",
    "for vert, data in sheet.vert_df.iterrows():\n",
    "    ax.text(data.x, data.y+0.1, vert)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sheet.validate()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "type1_transition(sheet, 17, epsilon=0.5)\n",
    "\n",
    "geom.update_all(sheet)\n",
    "print(sheet.validate())\n",
    "\n",
    "fig, ax = sheet_view(sheet, edge={'head_width': 0.05})\n",
    "fig.set_size_inches(8, 8)\n",
    "for face, data in sheet.face_df.iterrows():\n",
    "    ax.text(data.x, data.y, face)\n",
    "\n",
    "for vert, data in sheet.vert_df.iterrows():\n",
    "    ax.text(data.x, data.y+0.1, vert)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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