ターミナルを起動し、計算用サーバにリモートログインする。

$ ssh sstg1
sstg1:~$

sshの終了の仕方

sstg1:~$ exit
$ 

sstg1:~$ python
Python 2.7.3 (default, Sep 26 2013, 20:03:06) 
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from ase import Atoms
>>> box1 = Atoms(cell = (4.0, 4.0, 4.0), pbc = True)
>>> from ase import Atom
>>> box1.append(Atom('C', (2.0, 2.0, 2.0)))
>>> box1.append(Atom('O', (3.1, 2.0, 2.0)))
>>> from ase.calculators.jacapo import Jacapo
>>> solver1 = Jacapo(nbands = 6)
>>> box1.set_calculator(solver1)
>>> solver1.calculate()
>>> print box1.get_total_energy()
-591.604035353
>>> exit()
sstg1:~$ 

sstg1:~$ python
Python 2.7.3 (default, Sep 26 2013, 20:03:06) 
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> a1 = (4.0, 0.0, 0.0)
>>> a2 = (0.0, 4.0, 0.0)
>>> a3 = (0.0, 0.0, 4.0)
>>> from ase import Atoms
>>> box1 = Atoms(cell = [a1, a2, a3], pbc = True)
>>> v1 = (2.0, 2.0, 2.0)
>>> v2 = (3.1, 2.0, 2.0)
>>> from ase import Atom
>>> atom1 = Atom('C', v1)
>>> atom2 = Atom('O', v2)
>>> box1.append(atom1)
>>> box1.append(atom2)
>>> from ase.calculators.jacapo import Jacapo
>>> solver1 = Jacapo(nbands = 6)
>>> box1.set_calculator(solver1)
>>> solver1.calculate()
>>> print box1.get_total_energy()
-591.604035353
>>> exit()
sstg1:~$ 

from ase import Atoms
a1 = (4.0, 0.0, 0.0)
a2 = (0.0, 4.0, 0.0)
a3 = (0.0, 0.0, 4.0)
box1 = Atoms(cell = [a1, a2, a3], pbc = True)
 
from ase import Atom
v1 = (2.0, 2.0, 2.0)
atom1 = Atom('C', v1)
v2 = (3.1, 2.0, 2.0)
atom2 = Atom('O', v2)
 
box1.append(atom1)
box1.append(atom2)
 
from ase.calculators.jacapo import Jacapo
solver1 = Jacapo(nbands = 6)
 
box1.set_calculator(solver1)
solver1.calculate()
 
print box1.get_total_energy()

1. co.pyをsstg1にCyberDuckを使って転送
   
2. co.pyをsstg1で実行

   sstg1:~$ ls
   Examples  co.py
   sstg1:~$ python co.py
   -591.604035353
   sstg1:~$ ls
   Examples  co.data  co.py  out.nc  out.txt

   実行する前に既にout.ncが存在するとうまく実行できないことがあるので、既にout.ncが存在しているときは、先にout.ncを削除する。

   sstg1:~$ ls
   Examples  co.data  co.py  out.nc  out.txt
   sstg1:~$ rm out.nc
   sstg1:~$ ls
   Examples  co.data  co.py  out.txt

C (6) — 4

O (8) — 6

Si (14) — 4

H (1) — 1

CO → 4+6 = 10 → 10/2 = 5 → 5+x = 8

実習の詳細はcoの全エネルギー計算を参照のこと。