Changes between Version 10 and Version 11 of StartersTutorial


Ignore:
Timestamp:
Jul 29, 2010, 10:22:23 AM (15 years ago)
Author:
FrederikHeber
Comment:

selectors now have to be in front of the action

Legend:

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  • StartersTutorial

    v10 v11  
    2828Let's briefly fix atom 0's element, i.e. convert it from carbon to oxygen.
    2929{{{
    30 ./src/molecuilder -i test.xyz -E 8 --atom-by-id 0
     30./src/molecuilder -i test.xyz  --select-atom-by-id 0 -E 8
    3131}}}
    3232
    33 This will change the element of atom with index 0 to 8, i.e. make it an oxygen.
     33Note that we first have to select the desired atom, then specify the action on it. This will change the element of atom with index 0 to 8, i.e. make it an oxygen.
    3434
    3535== Changing the simulation domain ==
    … …  
    5252
    5353{{{
    54 ./src/molecuilder -i test.conf -o xyz -t "-5, 5, 5" --molecule-by-id 0 --periodic 1
     54./src/molecuilder -i test.conf -o xyz --select-molecule-by-id 0 -t "-5, 5, 5" --periodic 1
    5555}}}
    5656
    … …  
    7373If we would like to place it right-away somewhere else, we would use this call:
    7474{{{
    75 ./src/molecuilder -i test.conf -o xyz -p water.xyz -t "15, 15, 15" --molecule-by-id 1 --periodic 1
     75./src/molecuilder -i test.conf -o xyz -p water.xyz --select-molecule-by-id 1 -t "15, 15, 15" --periodic 1
    7676}}}
    7777which would translate the newly parsed-in molecule, getting index 1, by (15,15,15), adhering to periodic boundary conditions.
    … …  
    9898The last step is especially needed for the following tesselation of the second molecule only:
    9999{{{
    100 ./src/molecuilder -i test.conf -I -N 3. --nonconvex-file NonConvexEnvelope --molecule-by-id 2
     100./src/molecuilder -i test.conf -I --select-molecule-by-id 2 -N 3. --nonconvex-file NonConvexEnvelope
    101101}}}
    102102
    … …  
    107107We will end this tutorial by doing some analysis on these two water molecules, namely a pair correlation
    108108{{{
    109 ./src/molecuilder -i test.conf -v 3 -C E --elements 1 8 --output-file output-point.csv --bin-output-file bin_output-point.csv --bin-start 0 --bin-end 20
     109./src/molecuilder -i test.conf -v 3 --select-all-molecules -C E --elements 1 8 --output-file output-point.csv --bin-output-file bin_output-point.csv --bin-start 0 --bin-end 20
    110110}}}
    111111
    112112and a surface correlation analysis.
    113113{{{
    114 ./src/molecuilder -i test.conf -v 3 -I -C S --elements 1 --output-file output-surface.csv --bin-output-file bin_output-surface.csv --bin-start 0 --bin-width 1. --bin-end 20 --molecule-by-id 2
     114./src/molecuilder -i test.conf -v 3 -I --select-all-molecules -C S --elements 1 --output-file output-surface.csv --bin-output-file bin_output-surface.csv --bin-start 0 --bin-width 1. --bin-end 20 --molecule-by-id 2
    115115}}}
    116116