Changes between Version 4 and Version 5 of StartersTutorial


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Timestamp:
Jul 7, 2010, 1:26:23 PM (14 years ago)
Author:
FrederikHeber
Comment:

second section adapted

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  • StartersTutorial

    v4 v5  
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    42 Note that we will always add the ''-o xyz'' switch such that ''test.xyz'' is updated, too.
     42Note that we will always add the ''-o xyz'' switch such that ''test.xyz'' is updated, too. Now, we have created a ''pcp'' config file called ''test.conf'' (''.conf'' is the suffix of the pcp format), containing all information of ''test.xyz'' along with information specific to this type of quantum mechanical solver (plane wave).
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    4444Let's continue and define the simulation box:
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    49 Note that the '''!BoxLength''' entry in ''test.conf'' has changed, while the file ''test.conf.xyz'' has not changed at all.
     49Note that the '''!BoxLength''' entry in ''test.conf'' has changed. Note also that the sequence of the atoms has changed. In ''pcp'' they are always written sorted by element. This sorting has then also been used in the ''xyz'' file. So, our oxygen atom that had an index of 0 above, has now an index of 2.
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    5151Regarding the positions and our domain box, we have set the water molecule a bit right on the corner. Let's shift the molecule a bit
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    57 Note that we explicitely stated here to have periodic boundary conditions active. Hence, the coordinates get wrapped around. If we parse in a config file, all atoms are automatically put into a single moleculde, here referenced by its index 0.
     57Note that we explicitely stated here to have periodic boundary conditions active. Hence, the coordinates get wrapped around, which is exactly what happened to the z component of one of the hydrogens. Note that if we parse in a config file, all atoms are automatically put into a single molecule, here referenced by its index 0.
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    59 Tedious of entering ''-i test.conf -o xyz'' all the time? If you don't want to check the xyz file, you may also just say ''test.conf'' in its place, which will store information to this pcp config file only.
    60 
    61 A better approach for making sure all atoms are inside the domain is to use the bound-in-box action:
     59A better approach for making sure all atoms are inside the domain is to use the center on edge and add empty boundary action:
    6260{{{
    63 ./src/molecuilder -i test.conf -o xyz --bound-in-box
     61./src/molecuilder -i test.conf -o xyz -O -c "5, 5, 5"
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    6563
    66 Note that this action has no parameter. It has used the box size specified above. As we have already translated the water molecule, nothing should have happened.
     64This action will always produce a rectangular domain, i.e. the extension of the water molecule with an additional boundary of 5 angstroem in every direction.
    6765
    6866== Parsing in another water molecule ==