Changes between Version 2 and Version 3 of StartersTutorial


Ignore:
Timestamp:
Jul 7, 2010, 8:24:18 AM (14 years ago)
Author:
FrederikHeber
Comment:

changed vectors and box matrices to a single string (change in code for negative integers being faultily recognized as arguments)

Legend:

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  • StartersTutorial

    v2 v3  
    1111Execute:
    1212{{{
    13 ./src/molecuilder -i test.conf -o pcp xyz -a 6 --position 0 0 0
     13./src/molecuilder -i test.conf -o pcp xyz -a 6 --position "0, 0, 0"
    1414}}}
    1515
    … …  
    2222Let's continue and define the simulation box:
    2323{{{
    24 ./src/molecuilder -i test.conf -o xyz -B 10 0 10 0 0 10
     24./src/molecuilder -i test.conf -o xyz -B "10, 0, 10, 0, 0, 10"
    2525}}}
    2626
    … …  
    2929We add the two remaining hydrogen atoms:
    3030{{{
    31 ./src/molecuilder -i test.conf -o xyz -a 1 --position 0.758602 0. 0.504284
    32 ./src/molecuilder -i test.conf -o xyz -a 1 --position 0.758602 0. -0.504284
     31./src/molecuilder -i test.conf -o xyz -a 1 --position "0.758602, 0., 0.504284"
     32./src/molecuilder -i test.conf -o xyz -a 1 --position "0.758602, 0., -0.504284"
    3333}}}
    3434
    … …  
    4545
    4646{{{
    47 ./src/molecuilder -i test.conf -o xyz -t -5 0 0 --molecule-by-id 0 --periodic 1
     47./src/molecuilder -i test.conf -o xyz -t "-5, 0, 0" --molecule-by-id 0 --periodic 1
    4848}}}
    4949
    … …  
    6868If we would like to place it right-away somewhere else, we would use this call:
    6969{{{
    70 ./src/molecuilder -i test.conf -o xyz -p water.xyz -t 5 0 0 --molecule-by-id 1 --periodic 1
     70./src/molecuilder -i test.conf -o xyz -p water.xyz -t "5, 0, 0" --molecule-by-id 1 --periodic 1
    7171}}}
    7272which would translate the newly parsed-in molecule, getting index 1, bey (5,0,0), adhering to periodic boundary conditions.