差分

このページの2つのバージョン間の差分を表示します。

--- ab_initio:original [2019/05/23 00:35] – [Jacapo - ASE python interface for Dacapo] kimi
+++ ab_initio:original [2019/05/23 01:06] – [Jacapo calculator] kimi
@@ 行 1: / 行 1: @@
-====== Jacapo - ASE python interface for Dacapo ======
+====== Jacapo  ======
+-- Dacapoに対するASEのpythonインターフェイス --
-https://wiki.fysik.dtu.dk/ase/ase/calculators/jacapo.html
+このページは[[https://wiki.fysik.dtu.dk/ase/ase/calculators/jacapo.html|本家サイト]]の日本語訳である。
 ===== Introduction =====
+JacapoはDacapoのためのASEのインターフェイスで、ASE((訳注：第３版))と完全な互換性がある。JacapoはNumeric pythonとASE第2版を用いていた古いDacapoインターフェイスを置き換えるものである。プログラムは元々John Kitchinによって開発され、詳細な説明書が多くの例題とともに[[http://gilgamesh.cheme.cmu.edu/doc/software/jacapo/index.html|ネットに公開]]((訳注：このURLは現在存在しない))されていた。
+JacapoはASEのオプション的な計算エンジンといった位置付けであり、前述の説明書とは若干の差異が生じているが、説明書自体もうメンテナンスをされていない。
-Jacapo is an ASE interface for Dacapo that is fully compatible with ASE. It replaces the old Dacapo interface using Numeric python and ASE2. The code was originally developed by John Kitchin and detailed documentation as well as many examples are available online:
-http://gilgamesh.cheme.cmu.edu/doc/software/jacapo/index.html
-Jacapo is included as an optional calculator in ASE and small differences to the above documentation may occur, and the documentation is no longer maintained.
 ===== Jacapo calculator =====
@@ 行 16: / 行 11: @@
 The Jacapo interface is automatically installed with ase and can be imported using:
-from ase.calculators.jacapo import Jacapo
+<code python>from ase.calculators.jacapo import Jacapo</code>
 (You will need to have a working installation of Dacapo, however.)
@@ 行 51: / 行 46: @@
 This is an example only - the parameters are not physically meaningful!
+<code python>
 from ase import Atoms, Atom
 from ase.io import write
@@ 行 72: / 行 68: @@
 print(atoms.get_potential_energy())
 write('Jacapo-test.traj', atoms)
+</code>
 Note that all calculator parameters should be set in the calculator definition itself. Do not attempt to use the calc.set_* commands as they are intended to be internal to the calculator. Note also that Dacapo can only operate with periodic boundary conditions, so be sure that pbc is set to True.
-Restarting from an old calculation
+===== Restarting from an old calculation =====
 If the file you specify to Jacapo with the nc keyword exists, Jacapo will assume you are attempting to restart an existing calculation. If you do not want this behavior, turn the flag deletenc to True in your calculator definition.
@@ 行 80: / 行 78: @@
 For example, it is possible to continue a geometry optimization with something like this:
+<code python>
 calc = Jacapo('old.nc', stay_alive=True)
 atoms = calc.get_atoms()
 dyn = QuasiNewton(atoms, logfile='qn.log')
 dyn.run(fmax=0.05)
+</code>
 Note, that the stay_alive flag is not stored in the .nc file and must be set when the calculator instance is created.
-Atom-projected density of states
+===== Atom-projected density of states =====
 To find the atom-projected density of states with Jacapo, first specify the ados dictionary in your calculator definition, as in:
+<code python>
 calc = Jacapo( ... ,
               ados={'energywindow': (-10., 5.),
@@ 行 95: / 行 97: @@
                     'npoints': 250,
                     'cutoff': 1.0})
+</code>
 After this is established, you can use the get_ados command to get the desired ADOS data. For example:
+<code python>
 energies, dos = calc.get_ados(atoms=[0],
                               orbitals=['d'],
                               cutoff='short',
                               spin=[0])
-Next  Previous
+</code>
+© Copyright 2017, ASE-developers. Last updated on Wed, 22 May 2019 07:03:39.