Update DOC.md

DOC.md

@@ -1,60 +1,84 @@
-## Writing an INPUT file
+# Writing an INPUT file
+
+There is no obligation to put any order in the keywords
+
+## MANDATORY KEYWORDS
+
+1.BATH bath_radius
+
+1.PSEUDO first_shell_radius
+
+1.OUTPUT output_file_name
+
+1.PATTERN nAtom1 labelAtom1 nAtom2 labelAtom2 ...  
+
+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)
+
+1.NPATTERN nPattern
+
+1.LATTICE
+  a cell_parameter_a
+  b cell_parameter_b
+  c cell_parameter_c
+  alpha cell_angle_alpha
+  beta cell_angle_beta
+  gamma cell_angle_gamma
+
+1. ATOMS label charge neighbours radius_of_the_coordination_sphere ...
+
+1.SYMOP
+   x,y,z
+   ...
+   POMYS
+   
+1.GENERATOR
+  atom1 x_frac y_frac z_frac
+  ...
+  ROTARENEG
+  
+1.END_OF_INPUT
 
 
-# MANDATORY KEYWORDS
+## OPTIONNAL KEYWORDS
 
-CIF system.cif
+1.TRANSLATE x y z
 
-BATH bath_radius
+Crystal MET has some trouble finding specific pattern, sometimes forcing a translation can help finding it
 
-PSEUDO first_shell_radius
+1.CENTER  atom1 atom2 ...
 
-OUTPUT output_file_name
+Will chose the atom (or the center of the atoms) as the center of the sphere
 
-PATTERN nAtom1 labelAtom1 nAtom2 labelAtom2 ...  (little tricky there, if there is more than 1 atom1, you have to put it another time)
+1.X_AXIS atom1 atom2 ...
 
-NPATTERN nPattern
+Will chose the atom (or the center of the atoms) as the x axis
 
-LATTICE
-a .
-b .
-c .
-alpha .
-beta .
-gamma .
+1.Y_AXIS  atom1  atom2 ...
 
-ATOMS label charge neighbours radius_of_the_neighbouring_sphere ...
+Will chose the atom (or the center of the atoms) as the y axis
 
-DIST 
-atom1 atom2 distance 
-...
-TSID
+1.Z_AXIS atom1  atom2 ...
 
-END_OF_INPUT
+Will chose the atom (or the center of the atoms) as the z axis
 
+1.NOTINPP atoms not in the first shell
 
+1.COLOR  
 
-OPTIONNAL KEYWORDS
+Shows the bath sorted with colors
 
-TRANSLATE x y z
+1.NOCOLOR 
 
-CENTER  atom1 atom2 ...
+Shows the bath sorted by atoms
 
-X_AXIS atom1 atom2 ...
+1.SEEFRAG  
 
-Y_AXIS  atom1  atom2 ...
+Shows the fragment once found (recommended)
 
-Z_AXIS atom1  atom2 ...
+1.OPTIMIZATION  
 
-NOTINPP atoms not in the first shell
+Will use an optimization method to set the total charge to 0 by slightly changing the charges of the outer shell atoms
 
-COLOR  see the bath sorted with colors
-
-NOCOLOR see the bath sorted by atoms
-
-SEEFRAG  see the fragment once found (recommended)
-
-OPTIMIZATION  to optimize the total charge of the bath to be 0 by slightly changing the charges of the outer shell atoms
-
-EVJEN  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
+1.EVJEN 
+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