{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2d0d7690-c44d-43ed-9dd2-54044ddfa12a",
   "metadata": {},
   "outputs": [],
   "source": [
    "from matlanticgrrm.visualize import view, view_images, view_with_index\n",
    "from matlanticgrrm.atomslist import pfp_calculator,set_calculator\n",
    "from matlanticgrrm.vibrations import ListVibrations, vib_graphs\n",
    "from matlanticgrrm.io import lread, lwrite\n",
    "from ase.io import read,iread,write\n",
    "from pathlib import Path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "847e4e4d-47cf-42a5-b5e8-82f0428825df",
   "metadata": {},
   "outputs": [],
   "source": [
    "neb_ts = lread(Path(\"*.traj\").expanduser()) # TS構造のインポート"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2e31d3a5-6d55-416b-a245-ed4520817c86",
   "metadata": {},
   "outputs": [],
   "source": [
    "set_calculator(neb_ts,pfp_calculator)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6d9e20ce-5d3a-4742-8407-8028f19750e5",
   "metadata": {},
   "outputs": [],
   "source": [
    "view_with_index(neb_ts[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f7620590-6b08-45e6-811b-1a9789a065b7",
   "metadata": {},
   "outputs": [],
   "source": [
    "indices = [_, _, _,] # 動かす原子のindex番号を控える\n",
    "vib = ListVibrations(neb_ts,errorlog=\"VIB.log\",indices=indices)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3afb41c2-e025-4d60-8816-dfb199098435",
   "metadata": {},
   "source": [
    "ListVibrationについては[Document](https://kt19906.github.io/MatlanticGrrm/src/modules/vibrations.html#matlanticgrrm.vibrations.ListVibrations)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "047b7f99-4d03-49d3-8710-e02003fc8357",
   "metadata": {},
   "outputs": [],
   "source": [
    "vib.summary(html=\"vib_table.html\");"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6a306250-695f-4ee1-a921-da0843350667",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "vib.write_mode()"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3.7",
   "language": "python",
   "name": "python37"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
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   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
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