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DOC.md
@ -4,19 +4,19 @@ There is no obligation to put any order in the keywords
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## MANDATORY KEYWORDS
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1.BATH bath_radius
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1. BATH bath_radius
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1.PSEUDO first_shell_radius
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1. PSEUDO first_shell_radius
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1.OUTPUT output_file_name
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1. OUTPUT output_file_name
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1.PATTERN nAtom1 labelAtom1 nAtom2 labelAtom2 ...
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1. PATTERN nAtom1 labelAtom1 nAtom2 labelAtom2 ...
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Not that, if you have more than once the Atom1, you will have to place it again at the end (for example, 5 Ir 8 Sr 6 O 5 Ir)
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1.NPATTERN nPattern
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1. NPATTERN nPattern
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1.LATTICE
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1. LATTICE
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a cell_parameter_a
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b cell_parameter_b
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c cell_parameter_c
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@ -26,59 +26,59 @@ Not that, if you have more than once the Atom1, you will have to place it again
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1. ATOMS label charge neighbours radius_of_the_coordination_sphere ...
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1.SYMOP
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1. SYMOP
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x,y,z
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...
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POMYS
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1.GENERATOR
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1. GENERATOR
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atom1 x_frac y_frac z_frac
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...
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ROTARENEG
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1.END_OF_INPUT
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1. END_OF_INPUT
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## OPTIONNAL KEYWORDS
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1.TRANSLATE x y z
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1. TRANSLATE x y z
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Crystal MET has some trouble finding specific pattern, sometimes forcing a translation can help finding it
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1.CENTER atom1 atom2 ...
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1. CENTER atom1 atom2 ...
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Will chose the atom (or the center of the atoms) as the center of the sphere
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1.X_AXIS atom1 atom2 ...
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1. X_AXIS atom1 atom2 ...
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Will chose the atom (or the center of the atoms) as the x axis
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1.Y_AXIS atom1 atom2 ...
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1. Y_AXIS atom1 atom2 ...
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Will chose the atom (or the center of the atoms) as the y axis
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1.Z_AXIS atom1 atom2 ...
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1. Z_AXIS atom1 atom2 ...
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Will chose the atom (or the center of the atoms) as the z axis
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1.NOTINPP atoms not in the first shell
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1. NOTINPP atoms not in the first shell
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1.COLOR
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1. COLOR
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Shows the bath sorted with colors
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1.NOCOLOR
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1. NOCOLOR
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Shows the bath sorted by atoms
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1.SEEFRAG
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1. SEEFRAG
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Shows the fragment once found (recommended)
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1.OPTIMIZATION
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1. OPTIMIZATION
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Will use an optimization method to set the total charge to 0 by slightly changing the charges of the outer shell atoms
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1.EVJEN
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1. EVJEN
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Simili Evjen method to calculate the charge of the atom on the outer shell, note that OPTIMIZATION and EVJEN keywords can not be used together
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