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surface code

Input file structure (surface.inp)

header text                   
inputfilename file            
inputfileformat cube|xsf      
outputfilename file           
outputfileformat povray       
isovalue (0.0,1.0)            
sign positive|negative|both   
power 0|1|2                   
algorithm cube|tetrahedron    
smooth T|F                    
box T|F                       
basis T|F                     
uc T|F                        
uco                           
ucox ucoy ucoz                
ucv                           
ucv1x ucv1y ucv1z             
ucv2x ucv2y ucv2z             
ucv3x ucv3y ucv3z             
ucu bohr|angstrom|latvec      
sc T|F                        
sco                           
scox scoy scoz                
scv                           
scv1x scv1y scv1z             
scv2x scv2y scv2z             
scv3x scv3y scv3z             
scu bohr|angstrom|latvec      
sct T|F

Example (HOMO of benzene)

header C6H6_band_15
inputfilename C6H6.b_15.cube
inputfileformat cube
outputfilename C6H6.b_15.pov
outputfileformat povray
isovalue 0.9
sign both
power 1
algorithm cube
smooth T
box F
basis F
uc F
uco
0.0 0.0 0.0
ucv
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
ucu latvec
sc T
sco
-0.5 -0.5 -0.5
scv
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
scu latvec
sct T

Documentation

The isosurface is defined by isovalue * max |psi| for power = 0 and by integral_v |psi|^power = isovalue * integral |psi|^power for power > 0 where psi is the scalar field and v is the volume inside the isosurface.

Note that espresso already outputs |psi|^2, setting power = 2 yields |psi|^4 in this case, to produce |psi|^2 isosurface set power = 1.

algorithm stands for marching cubes and marching tetrahedra smooth defines whether to average normals for smooth rendering

box specifies whether to generate supercell box in povray script

basis specifies whether to generate coordinate axes in povray script

Acronyms:

  • sfo = scalar field origin (read from volumetric file)
  • sfv = scalar field vectors (read from volumetric file)
  • uco = unit cell origin
  • ucv = unit cell vectors
  • ucu = unit cell units
  • sco = supercell origin
  • scv = supercell vectors
  • scu = supercell units
  • sct = supercell translational symmetry

Rules:

  • if uc = T then uco/ucv are read from parameter file else uco/ucv are set to sfo/sfv
  • if sc = T then sco/scv are read from parameter file else sco/scv are set touco/ucv
  • if uc = T and ucu = latvec then uco/ucv are scaled by sfv
  • if sc = T and scu = latvec then sco/scv are scaled by ucv
  • if sct = T then scv is used for translational symmetry else ucv is used for translational symmetry

Hints:

  • In most cases, set uc = F, uc = T is only needed if volumetric data do not span the whole unit cell and the supercell is being used, so the correct unit cell must be defined.

  • Use sc = T to construct the supercell spanning several unit cells or to assemble the unit cell around the origin of the coordinate system as in benzene example above (sco = (-0.5 -0.5 -0.5) in latvec units).

  • The supercell may span a fractional number of unit cells, in this case set sct = F to produce the correct bonds at the faces of the supercell.