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Merge pull request #1 from matlantis-pfcc/v1.1.0
Update to v1.1.0
2 parents 213e115 + 3b9bf2b commit 617a986

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‎docs/_static/1_1_welcome.ipynb

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‎docs/tutorials/ja/2_2_opt-algorithm.nblink ‎docs/tutorials/ja/1_4_ase_structure.nblink

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‎docs/tutorials/ja/1_4_ase_calculator.nblink ‎docs/tutorials/ja/1_5_ase_calculator.nblink

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‎docs/tutorials/ja/1_5_ase_playground.nblink ‎docs/tutorials/ja/1_6_ase_playground.nblink

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‎docs/tutorials/ja/1_6_diatomic_potential.nblink ‎docs/tutorials/ja/1_7_ase_playground2.nblink

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‎docs/tutorials/ja/1_8_diatomic_potential.nblink

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"path": "../../../tutorials/ja/1_8_diatomic_potential.ipynb",
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"../../../tutorials/assets",
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‎docs/tutorials/ja/2_2_opt_symmetry.nblink

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‎docs/tutorials/ja/2_3_opt-algorithm.nblink

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‎docs/tutorials/ja/7_1_conclusion.nblink

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‎docs/tutorials/ja/index.rst

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./6_*
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.. toctree::
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:caption: 7. おわりに
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:maxdepth: 1
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:glob:
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./7_*
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.. toctree::
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:caption: Appendix
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:maxdepth: 1

‎tutorials/en/4_2_phonon.ipynb

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"id": "a8f5b75e-4e4c-4068-a941-3a45e8b6180b",
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"metadata": {},
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"source": [
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"The calculation result is plotted in the above figure. We can see the result is agree with the [DFT](https://materialsproject.org/materials/mp-149/) and [experiment](https://webbook.nist.gov/cgi/cbook.cgi?ID=C7440213&Units=SI&Mask=2#Thermo-Condensed) results."
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"The calculation result is plotted in the above figure. We can see the result is agree with the [DFT](https://materialsproject.org/materials/mp-149/) and [experiment](https://webbook.nist.gov/cgi/cbook.cgi?ID=C7440213&Units=SI&Mask=2#Thermo-Condensed) results.\n",
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"\n",
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"DFT calculation results from\n",
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"\n",
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"A. Jain*, S.P. Ong*, G. Hautier, W. Chen, W.D. Richards, S. Dacek, S. Cholia, D. Gunter, D. Skinner, G. Ceder, K.A. Persson (*=equal contributions) \n",
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"The Materials Project: A materials genome approach to accelerating materials innovation\n",
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"APL Materials, 2013, 1(1), 011002. \n",
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"[doi:10.1063/1.4812323](http://dx.doi.org/10.1063/1.4812323) \n",
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"[[bibtex]](https://materialsproject.org/static/docs/jain_ong2013.349ca3156250.bib) \n",
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"Licensed under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) \n",
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"\n",
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"Experiment results from\n",
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"\n",
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"\"Condensed Phase Heat Capacity Data\" by Eugene S. Domalski and Elizabeth D. Hearing in NIST Chemistry WebBook, NIST Standard Reference Database Number 69, Eds. P.J. Linstrom and W.G. Mallard, National Institute of Standards and Technology, Gaithersburg MD, 20899, https://doi.org/10.18434/T4D303, (retrieved May, 2022)."
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]
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},
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{

‎tutorials/input/BaTiO3_mp-5986_computed.cif

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# generated using pymatgen
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data_BaTiO3
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_symmetry_space_group_name_H-M 'P 1'
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_cell_length_a 4.00445700
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_cell_length_b 4.00445700
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_cell_length_c 4.20063600
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_cell_angle_alpha 90.00000000
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_cell_angle_beta 90.00000000
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_cell_angle_gamma 90.00000000
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_symmetry_Int_Tables_number 1
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_chemical_formula_structural BaTiO3
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_chemical_formula_sum 'Ba1 Ti1 O3'
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_cell_volume 67.36003732
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_cell_formula_units_Z 1
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loop_
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_symmetry_equiv_pos_site_id
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_symmetry_equiv_pos_as_xyz
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1 'x, y, z'
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loop_
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_atom_site_type_symbol
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_atom_site_label
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_atom_site_symmetry_multiplicity
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_atom_site_fract_x
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_atom_site_fract_y
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_atom_site_fract_z
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_atom_site_occupancy
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Ba Ba0 1 0.50000000 0.50000000 0.00413600 1
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Ti Ti1 1 0.00000000 0.00000000 0.52431300 1
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O O2 1 0.00000000 0.50000000 0.47934900 1
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O O3 1 0.50000000 0.00000000 0.47934900 1
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O O4 1 0.00000000 0.00000000 0.95885400 1

‎tutorials/ja/1_1_welcome.ipynb

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"\n",
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"計算を用いた材料開発といっても、多くの手法が存在しそれぞれが扱う空間・時間スケールは様々です。\n",
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"\n",
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"<figure style=\"width:640px\">\n",
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"<figure style=\"max-width:640px\">\n",
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"<img src=\"../assets/time-length-scale-small.png\"/>\n",
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"</figure>\n",
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"\n",

‎tutorials/ja/1_2_atomistic_simulation_intro.ipynb

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"\n",
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"本Tutorialの扱う、”原子シミュレーション”とはどんなことができるものなのでしょうか？その概要を説明します。\n",
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"\n",
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"材料のいろいろな性質は、原子レベルで説明することができます。例えば、機会的特性(弾性定数・ヤング率など)・熱物性(比熱など)・粘性・化学反応の起こりやすさ、、、などです。\n",
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"材料のいろいろな性質は、原子レベルで説明することができます。例えば、機械的特性(弾性定数・ヤング率など)・熱物性(比熱など)・粘性・化学反応の起こりやすさ、、、などです。\n",
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"原子シミュレーションを用いることで、原子を並べたときにどんな風に動くのかを再現したり、そもそも自然界ではどのように原子が並んでいるのかといったことを解析することができます。\n",
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"説明は追って行うことにして、まずは以下のコードをそのまま流してみましょう。"
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" - `matlantis-features`\n",
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" - `pfcc-extras`\n",
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"\n",
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"はMatlantis環境内で提供されているライブラリです。"
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"はMatlantis環境内で提供されているライブラリです。\n",
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"\n",
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"※`pfcc-extras`は、\"Package Launcher\"からフォルダをコピーし、内部のREADMEに従ってインストールを進めてください。<br/>\n",
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"※各ライブラリのインストール後、 インストールの反映にkernelの再起動が必要になる場合があります。インストールされたログが出たにもかかわらず、以降のimport が失敗する場合は、上部タブから\"Restart kernel...\"を選んでkernelの再起動をしてみてください。"
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"metadata": {},
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"outputs": [],
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"source": [
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"# !pip install pfp-api-client matlantis-features\n",
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"!pip install pfp-api-client matlantis-features\n",
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"# !pip install -e ../pfcc-extras # please specify the path"
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},

‎tutorials/ja/1_3_ase_basic.ipynb

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‎tutorials/ja/1_4_ase_structure.ipynb

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‎tutorials/ja/1_4_ase_calculator.ipynb ‎tutorials/ja/1_5_ase_calculator.ipynb

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"$$\\mathbf{F} = -\\frac{\\partial V}{\\partial \\mathbf{r}} $$\n",
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"\n",
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"\n",
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"まとめると、<b>系の時間発展$\\mathbf{r}(t)$を知るために必要な力$\\mathbf{F}$の情報は、ポテンシャルエネルギー$V\\mathbf(r) $がわかれば計算できる。</b>ということになります。\n",
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"まとめると、<b>系の時間発展$\\mathbf{r}(t)$を知るために必要な力$\\mathbf{F}$の情報は、ポテンシャルエネルギー$V\\mathbf(r)$がわかれば計算できる。</b>ということになります。\n",
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"[Note] 本チュートリアルでは、簡単のため、[古典力学](https://en.wikipedia.org/wiki/Classical_mechanics)の知識のみで説明を行いました。<br/>\n",
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"[解析力学](https://en.wikipedia.org/wiki/Analytical_mechanics#Hamiltonian_mechanics)を習ったことのある方向けの言葉で説明をすると、ハミルトニアンにより支配方程式が規定されるため、\n",
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"\n",
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"$$ \\mathcal{H} | \\Phi \\rangle = E | \\Phi \\rangle $$\n",
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"\n",
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"非相対論に基づき、原子核がM個と電子がN個からなる系を考えた場合のハミルトニアン $ \\mathcal{H} $は、[原子単位系](https://ja.wikipedia.org/wiki/%E5%8E%9F%E5%AD%90%E5%8D%98%E4%BD%8D%E7%B3%BB)で以下のようにかけます。\n",
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"非相対論に基づき、原子核がM個と電子がN個からなる系を考えた場合のハミルトニアン $\\mathcal{H}$は、[原子単位系](https://ja.wikipedia.org/wiki/%E5%8E%9F%E5%AD%90%E5%8D%98%E4%BD%8D%E7%B3%BB)で以下のようにかけます。\n",
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"\n",
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"$$ \\mathcal{H} = - \\sum_{i=1}^N \\frac{1}{2} \\nabla^2_i - \\sum_{A=1}^M \\frac{1}{2 M_A} \\nabla^2_A - \\sum_{i=1}^N \\sum_{A=1}^M \\frac{Z_A}{r_{iA}} + \\sum_{i=1}^N \\sum_{j>i}^N \\frac{1}{r_{ij}} + \\sum_{A=1}^M \\sum_{B>A}^M \\frac{Z_A Z_B}{R_{AB}} $$\n",
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"\n",
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"そうするとN個の電子に対するSchrödinger方程式は\n",
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"\n",
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"$$ \\mathcal{H}_{elec} = - \\sum_{i=1}^N \\frac{1}{2} \\nabla^2_i - \\sum_{i=1}^N \\sum_{A=1}^M \\frac{Z_A}{r_{iA}} + \\sum_{i=1}^N \\sum_{j>i}^N \\frac{1}{r_{ij}} $$\n",
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"$$ \\mathcal{H}_{\\rm{elec}} = - \\sum_{i=1}^N \\frac{1}{2} \\nabla^2_i - \\sum_{i=1}^N \\sum_{A=1}^M \\frac{Z_A}{r_{iA}} + \\sum_{i=1}^N \\sum_{j>i}^N \\frac{1}{r_{ij}} $$\n",
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"\n",
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"として、以下のようにかけます。\n",
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"\n",
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"$$ \\mathcal{H}_{elec} | \\Phi_{elec} \\rangle = E_{elec} | \\Phi_{elec} \\rangle \\tag{1} $$\n",
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"$$ \\mathcal{H}_{\\rm{elec}} | \\Phi_{\\rm{elec}} \\rangle = E_{\\rm{elec}} | \\Phi_{\\rm{elec}} \\rangle \\tag{1} $$\n",
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"原子核が静止しているときの全エネルギーは、\n",
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"$$ V = E_{elec} + \\sum_{A=1}^M \\sum_{B>A}^M \\frac{Z_A Z_B}{R_{AB}} $$\n",
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"$$ V = E_{\\rm{elec}} + \\sum_{A=1}^M \\sum_{B>A}^M \\frac{Z_A Z_B}{R_{AB}} $$\n",
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"\n",
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"とかけます。これが、ポテンシャルエネルギーと対応付けられます。\n",
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"\n",

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