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tools:ase [2015/07/01 15:56] – [Remote Usage over SSH] oschuetttools:ase [2021/01/19 11:49] (current) oschuett
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 ====== Atomic Simulation Environment ====== ====== Atomic Simulation Environment ======
-The Atomistic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations. The code is freely available under the GNU LGPL license.+The Atomistic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizingand analyzing atomistic simulations. The code is freely available under the GNU LGPL license.
  
-The ASE comes with a plugin, a so-called calculator, for running simulations with CP2K. The source code of the calculator is in the file [[https://trac.fysik.dtu.dk/projects/ase/browser/trunk/ase/calculators/cp2k.py | ase/calculators/cp2k.py]]. It's documentation can be found [[https://wiki.fysik.dtu.dk/ase/ase/calculators/cp2k.html | here ]].+The ASE comes with a plugin, a so-called calculator, for running simulations with CP2K. The source code of the calculator is in the file [[https://gitlab.com/ase/ase/blob/master/ase/calculators/cp2k.py | ase/calculators/cp2k.py]]. It's documentation can be found [[https://wiki.fysik.dtu.dk/ase/ase/calculators/cp2k.html | here ]].
  
 For more information about ASE in general visit their [[https://wiki.fysik.dtu.dk/ase/ | project page]] For more information about ASE in general visit their [[https://wiki.fysik.dtu.dk/ase/ | project page]]
  
 =====Appetizing Example===== =====Appetizing Example=====
-The ASE provides a very convenient, high level interface to CP2K. It bring about the renown [[w>Python_(programming_language)|Pythonic]] productivity.Running a CP2K calculation can be as easy as this:+The ASE provides a very convenient, high level interface to CP2K. It bring about the renown [[w>Python_(programming_language)|Pythonic]] productivity. Running a CP2K calculation can be as easy as this:
 <code bash> <code bash>
 $ export ASE_CP2K_COMMAND="mpirun -n 2 cp2k_shell.popt" $ export ASE_CP2K_COMMAND="mpirun -n 2 cp2k_shell.popt"
 $ python $ python
 >>> from ase.calculators.cp2k import CP2K >>> from ase.calculators.cp2k import CP2K
->>> from ase.structure import molecule+>>> from ase.build import molecule
 >>> calc = CP2K() >>> calc = CP2K()
 >>> atoms = molecule('H2O', calculator=calc) >>> atoms = molecule('H2O', calculator=calc)
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 </code> </code>
  
-For more examples have a look at the test suite in [[ https://trac.fysik.dtu.dk/projects/ase/browser/trunk/ase/test/cp2k | ase/test/cp2k]].+For more examples have a look at the test suite in [[ https://gitlab.com/ase/ase/tree/master/ase/test/calculator/cp2k | ase/test/calculator/cp2k]].
  
 <note warning> <note warning>
-The environment variable ''$ASE_CP2K_COMMAND'' has point to the **CP2K-shell** binary.+The environment variable ''$ASE_CP2K_COMMAND'' must point to the **CP2K-shell** binary.
 </note> </note>
  
 =====Remote Usage over SSH===== =====Remote Usage over SSH=====
-The ASE calculator communicate with the CP2K-shell solely over stdin/stdout pipes. Therefore, one can launch the CP2K-shell on a remote host via ssh. For this environment variable ''$ASE_CP2K_COMMAND'' just has to be setup accordingly:+The ASE calculator communicate with the CP2K-shell solely over stdin/stdout pipes. Therefore, one can launch the CP2K-shell on a remote host via ssh. For this the environment variable ''$ASE_CP2K_COMMAND'' has to be setup accordingly:
 <code bash> <code bash>
-export ASE_CP2K_COMMAND="ssh your_compute_hosts \"/path/to/cp2k_shell.sdbg\""+export ASE_CP2K_COMMAND="ssh your-compute-host.com \"mpirun -np 2 /path/to/cp2k_shell.popt\""
 </code> </code>
tools/ase.1435766218.txt.gz · Last modified: 2020/08/21 10:15 (external edit)