Editing UPU (section)

== LIST OF COMMANDS ==

Listed alphabetically:

<p align="center" style="width:100%">
{| border="1"
 |- 
 |'''<TT>aassoct</TT>'''
 | attempt to specify atom types automatically by reading OUTCAR file in the current directory (no parameters needed)
 |- 
 |'''<TT>assoct ''element1 [element2] [...]''</TT>'''
 | associate the previously unspecified atom types with the user input (e.g. "<TT>assoct Pt N H</TT>")
 |- 
 |'''<TT>bye</TT>'''
 | exit
 |- 
 |'''<TT>cartesian</TT>'''
 | switch atom coordinates being shown in Cartesian format
 |- 
 |'''<TT>cell</TT>'''
 | print cell parameters
 |- 
 |'''<TT>cmd</TT>'''
 | 
 |- 
 |'''<TT>commandline</TT>'''
 | 
 |- 
 |'''<TT>curl</TT>'''
 | 
 |- 
 |'''<TT>direct</TT>'''
 | switch atom coordinates being shown in direct (=fractional) format
 |- 
 |'''<TT>deassoct</TT>'''
 | 
 |- 
 |'''<TT>exchange</TT>'''
 | 
 |- 
 |'''<TT>exit</TT>'''
 | exit
 |- 
 |'''<TT>export XSF&#124;AXSFF&#124;XYZ&#124;UNIXYZ&#124;XYZ_WTA&#124;UNIXYZ_WTA</TT>'''
 | convert and save the structure in a specified file format: XSF (XCrysDen file format), AXSFF (animation for XCrysDen - step-by-step creation), XYZ (Open Babel compatible), UNIXYZ (UniChem compat.)
 |- 
 |'''<TT>extract</TT>'''
 | 
 |- 
 |'''<TT>fractional</TT>'''
 | switch atom coordinates being shown in direct (=fractional) format
 |- 
 |'''<TT>identify</TT>'''
 | rotate the entire coordinate system by "identifying" any vector by other vector  (''e.g.'', <TT>identify x v 1 1 1</TT>)
 |- 
 |'''<TT>kpoints</TT>'''
 | 
 |- 
 |'''<TT>kpoints@ls</TT>'''
 | 
 |- 
 |'''<TT>kpoints@save</TT>'''
 | 
 |- 
 |'''<TT>kpoints@set</TT>'''
 | 
 |- 
 |'''<TT>la</TT>'''
 | list atoms
 |- 
 |'''<TT>label ''text''</TT>'''
 | change the label of the structure file (1<sup>st</sup> line in POSCAR) to a specified text
 |- 
 |'''<TT>layers@alook x&#124;y&#124;z</TT>'''
 | automatically search for atomic layers along the given axis
 |- 
 |'''<TT>layers@buckling ''nr''</TT>'''
 | perform comprehensive statistics on buckling of the given layer
 |- 
 |'''<TT>layers@create byatom&#124;bytype ''nr1 [nr2] [...]''</TT>'''
 | create an atomic layer defined by specific atom numbers (<TT>byatom</TT>) or atomic types (<TT>bytype</TT>)
 |- 
 |'''<TT>layers@delete [hard] ''nr1 [nr2] [...]''</TT>'''
 | delete a definition of an existing atomic layer(s); the "<TT>hard</TT>" switch causes removing the atoms from the unit cell
 |- 
 |'''<TT>layers@join</TT>'''
 | join (=concatenate) 2 or more atomic layers
 |- 
 |'''<TT>layers@look x&#124;y&#124;z ''nr''</TT>'''
 | find atomic layers along the given axis by splitting the corresponding lattice vector length into "</TT>nr</TT>" slides
 |- 
 |'''<TT>layers@ls</TT>'''
 | list atomic layers
 |- 
 |'''<TT>layers@measure spacing&#124;distance&#124;angle ''spec''</TT>'''
 | 
 |- 
 |'''<TT>layers@order x&#124;y&#124;z</TT>'''
 | order atom layers along the given axis; needed before starting measurements with layers
 |- 
 |'''<TT>layers@shift ''nr'' by ''x y z''</TT>'''
 | shift (translate) all atoms of a given layers in the direction specified by vector <TT>''x y z''</TT>
 |- 
 |'''<TT>list</TT>'''
 | list the POSCAR/CONTCAR file
 |- 
 |'''<TT>load ''file''</TT>'''
 | open (=load) the ''file'' (usually POSCAR/CONTCAR) to buffer
 |- 
 |'''<TT>loud</TT>'''
 | enter loud mode - UPU messages are not restricted
 |- 
 |'''<TT>ls</TT>'''
 | list the POSCAR/CONTCAR file 
 |- 
 |'''<TT>measure distance&#124;angle&#124;dihedral a ''nr1'' a ''nr2'' ''[a nr3] [a nr4] [short]''</TT>'''
 | measuring tool: explore distances (<TT>distance</TT>), angles (<TT>angle</TT>) or dihedral angles (<TT>dihedral</TT>) between specified atoms.
 |- 
 |'''<TT>open</TT>'''
 | open (=load) the ''file'' (usually POSCAR/CONTCAR) to buffer
 |- 
 |'''<TT>origin ''atomnr''</TT>'''
 | specify an atom to be a new origin of the coordinate system (i.e. shift all atoms' coordinates by the translation vector x,y,z of atom ''atomnr'')
 |- 
 |'''<TT>pbc</TT>'''
 | apply periodic boundary conditions (PBC) - all atoms sticking out of the unit cell will be moved inside; use with caution
 |- 
 |'''<TT>prefix ''number''</TT>'''
 | change the prefix factor (2<sup>nd</sup> line in POSCAR) to a specified number
 |- 
 |'''<TT>pretty</TT>'''
 | adjust vector coordinates to a "pretty" format with the accuracy of 1E-9
 |- 
 |'''<TT>quiet</TT>'''
 | enter quiet mode - reduce UPU messages to minimum
 |- 
 |'''<TT>quit</TT>'''
 | exit
 |- 
 |'''<TT>redo</TT>'''
 | redo the last reverted change by "<TT>undo</TT>"
 |- 
 |'''<TT>replicate ''x y z''</TT>'''
 | replicate the unit cell ''x-'', ''y-'' and ''z-''times in the corresponding directions
 |- 
 |'''<TT>rotate</TT>'''
 | 
 |- 
 |'''<TT>save ''[file]''</TT>'''
 | save the current state of the buffer (structure) to a ''file''
 |- 
 |'''<TT>scale A&#124;B&#124;C&#124;VOLUME&#124;LATTICE</TT> ''factor'''''
 | multiply lattice vector(s) or cell volume by a given <TT>factor</TT>&#62;
 |- 
 |'''<TT>script</TT>'''
 | 
 |- 
 |'''<TT>seldyn on&#124;off&#124;fix&#124;free</TT>'''
 | 
 |- 
 |'''<TT>select atom&#124;type ''nr1 [nr2] [...]''</TT>'''
 | activate selection on atom(s) of a specified <TT>atom</TT> number or <TT>type</TT>
 |- 
 |'''<TT>selection</TT>'''
 | 
 |- 
 |'''<TT>sense</TT>'''
 | check orthogonality of the unit cell basis vectors
 |- 
 |'''<TT>strain</TT>'''
 | 
 |- 
 |'''<TT>undo</TT>'''
 | undo the last change
 |- 
 |'''<TT>unselect atom&#124;type ''nr1 [nr2] [...]''</TT>'''
 | deactivate selection on atom(s) of a specified <TT>atom</TT> number or <TT>type</TT>
 |- 
 |'''<TT>update</TT>'''
 | perform UPU software update (eventualy downloads the latest version via internet with <TT>curl</TT> command); UPU possibly restarts
 |- 
 |}
</p>


'''Note:''' 

All UPU commands are non-destructive to the original structure file unless you use the "<TT>save</TT>" (overwrites the open file or creates a new one) or "<TT>export</TT>" (always creates a new file) command.

'''Remarks on the <TT>measure</TT> command:'''

1. Specially, "<TT>measure distance</TT>" without parameters prints the full distance matrix.

2. Use the optional "<TT>short</TT>" keyword if a you measure malformed quatities caused by atoms' shift due to PBC conditions (when atoms "run out of the cell and appear on the other side").  
Example: "<TT>measure angle a 0 a 1 a 7 short</TT>" is the smallest possible angle between atoms # 1-2-8.

3. Alternatively, instead of "<TT>a ''nr''</TT>" arguments ("a" stands for "atom"), you may specify measurements using atom's image defined as "<TT>i ''nr x y z''</TT>"  ("<TT>i</TT>" stands for "image of atom", "<TT>nr</TT>" is the node atom, "<TT>x y z</TT>" is the imaging (translation) direction along the lattice vectors, ).  
Example: "<TT>measure angle a 3 i 3 0 0 -1 a 4</TT>" uses atom #4, an image of an atom # 4 (in a the first neighbouring cell lying below in ''z''-direction) and atom # 5 - useful for measuring tilting angles on surfaces ''etc.''.