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 originucv
= unit cell vectorsucu
= unit cell unitssco
= supercell originscv
= supercell vectorsscu
= supercell unitssct
= supercell translational symmetry
Rules:
- if
uc = T
thenuco
/ucv
are read from parameter file elseuco
/ucv
are set tosfo
/sfv
- if
sc = T
thensco
/scv
are read from parameter file elsesco
/scv
are set touco
/ucv
- if
uc = T
anducu = latvec
thenuco
/ucv
are scaled bysfv
- if
sc = T
andscu = latvec
thensco
/scv
are scaled byucv
- if
sct = T
thenscv
is used for translational symmetry elseucv
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.