ReSpect program

grid-1d

Specify the 1D uniform grid.

Input block

Extended variant

grid-1d:

input-units: [string]

output-units: [string]

number-of-points: [integer]

x-axis: [block]

Default

grid-1d:
  input-units      : Bohr
  output-units     : Angstrom
  number-of-points : not defined
  x-axis           : not defined

Example

grid-1d:
    input-units      : Bohr
    number-of-points : 100
    x-axis:
      atom: 8
      atom: 9

grid-1d:
    input-units      : Bohr
    output-units     : Bohr
    number-of-points : 200
    x-axis:
      point: 0.0e0 0.0e0 0.0e0
      point: 0.0e0 0.0e0 2.0e0

Note

All points are defined in the molecular coordinate system.

Information about the reference coordinate system of the output data can be found in .out_visual output file.

grid-2d

Specify the 2D uniform grid.

Input block

Extended variant

grid-2d:

input-units: [string]

output-units: [string]

output-format: [string]

frame-buffer: [real]

number-of-points: [formatted-string]

x-axis: [block]

plane-triangle: [block]

in-plane: [string]

in-plane: [block]

plain-format: [block]

Default

grid-2d:
  input-units     : Bohr
  output-units    : Angstrom
  output-format   : raw
  frame-buffer    : 4.0e0
  number-of-points: not defined
  x-axis          : not defined
  plane-triangle  : not defined
  in-plane        : not defined
  plain-format    : not defined

Example

grid-2d:
    input-units      : Bohr
    number-of-points : 100x100
    frame-buffer     : 2.0e0
    in-plane         : all-atoms
    output-format    : vti
    plane-triangle:
      atom:  10
      atom:  11
      point: 0.0e0 0.0e0 0.0e0
    x-axis:
      atom: 8
      atom: 9

grid-2d:
    input-units      : Bohr
    number-of-points : 100x100
    frame-buffer     : 2.0e0
    in-plane:
      point: 0.0e0 0.0e0 0.0e0
      atom:  1
      atom:  8
      atom:  5
    plane-triangle:
      atom:  10
      atom:  11
      atom:  1
    x-axis:
      point: 0.0e0 0.0e0 0.0e0
      point: 0.0e0 0.0e0 2.0e0

grid-2d:
    input-units      : Angstrom
    number-of-points : 50x100
    plain-format:
      origin: 0.0d0  0.0d0 -3.0d0
      x-edge: 3.0d0  0.0d0  0.0d0
      y-edge: 0.0d0  0.0d0  6.0d0

Note

Keyword plain-format is used as an alternative to the in-plane, plane-triangle, and frame-buffer keywords. It provides larger flexibility, but is more cumbersome to use.

All points/vectors in the input file are defined in the molecular coordinate system.

Data in the output files are referenced with respect to the relative coordinate system. More information can be found in .out_visual output file.

Warning

When specifying keyword plain-format, keywords in-plane, plane-triangle, and frame-buffer will be ignored.

grid-3d

Specify the 3D uniform grid.

Input block

Extended variant

grid-3d:

input-units: [string]

output-units: [string]

output-format: [string]

frame-buffer: [real]

number-of-points: [formatted-string]

in-cube: [string]

in-cube: [block]

plain-format: [block]

Default

grid-3d:
  input-units     : Bohr
  output-units    : Angstrom
  output-format   : raw
  frame-buffer    : 4.0e0
  number-of-points: not defined
  in-cube         : not defined
  plain-format    : not defined

Example

grid-3d:
    input-units      : Bohr
    output-units     : Angstrom
    number-of-points : 70x70x70
    in-cube          : all-atoms
    output-format    : cube
    frame-buffer     : 2.0e0

grid-3d:
    input-units:      Bohr
    frame-buffer:     3.0e0
    number-of-points: 100 x 100 x 60
    in-cube:
      atom: 3
      atom: 5
      point: 0.0e0  0.1e0  -3.0e0

grid-3d:
    input-units      : Angstrom
    number-of-points : 40x40x40
    plain-format:
      origin: -6.0e0  -6.0e0  -2.0e0
      x-edge: 12.0e0   0.0e0   0.0e0
      y-edge:  0.0e0  12.0e0   0.0e0
      z-edge:  4.0e0

Note

Keyword plain-format is used as an alternative to the in-cube and frame-buffer keywords. It provides larger flexibility, but is more cumbersome to use.

In contrast to the cumbersome use of plain-format keyword the use of in-cube and frame-buffer keywords is much more user friendly, where the only restriction is that the orientation of cube axes is parallel to the molecular axes.

All points/vectors in the input file are defined in the molecular coordinate system.

Data in the output files are referenced with respect to the relative coordinate system. More information can be found in .out_visual output file.

Warning

When specifying keyword plain-format, keywords in-cube and frame-buffer will be ignored.

Since some visualization programs recognize only cube form of the unit cell in the grid when reading .cube format, the edges of the 3D block are modified to fulfill this condition while keeping the number of points intact. The information describing the change can be found in the .out_visual file.

visualize

Define the quantity to visualize.

Input line

visualize:
                               
                                  
[string]

Default

visualize: not defined

Example

visualize: spin-density

perturbation

Define type of the perturbation.

Input line

perturbation:
                               
                                  
[string]

Default

perturbation: 0

Example

perturbation: Bx

transition

Define excited energy level(s) for visualization of the transition charge density.

Input line

transition:
                               
                                  
[formatted-string]

Default

transition: not defined

Example

transition: 1

transition: 1-3

Note

Specifying the range of excited states is useful when dealing with the degenerate energy levels.

motype

Define the type of the input molecular orbitals.

Input line

Default

motype: scf

Example

motype: lmo

select-mo

Select specific molecular orbital(s) to visualize.

Input line

select-mo:
                               
                                  
[formatted-string]

Default

select-mo: 1-[Nocc],[Nocc+1]-[Nmos]    # all occupied and all virtual MOs

Example

select-mo: 5

select-mo: 5-14

select-mo: 5-14,20

select-mo: 5-14,20-24

select-mo: 5,20

select-mo: 5,20-24

Note

Specifying the range of MOs is useful when dealing with the degenerate one-electron energy levels.

For visualization of perturbation-free densities any MO(s) (occupied or virtual) can be selected.

For visualization of response or transition densities only combination of occupied and virtual MO(s) can be selected.

active-atom

Specify the active atom to calculate property density in the case of visualization of the current density induced by the nuclear magnetic moment.

Input line

active-atom:
                               
                                  
[integer]

Default

none

Example

active-atom: 2

print-level

Set the amount of information printed in the output file.

Input line

print-level:
                               
                                  
[string]

Default

print-level: normal

Example

print-level: long

[string]	description
charge-density	Visualize the electron charge density or transition charge density when transition keyword is specified.
spin-density	The electron spin density
current-density	The electron current density.
current-flow	Flow of the current density through some 2D rectangle. Y dimension of the rectangle is integrated resulting in the 1D plot.

[string]	description
0	Without an external perturbation.
Bx	X component of the external magnetic field.
By	Y component of the external magnetic field.
Bz	Z component of the external magnetic field.
Ix	X component of the nuclear magnetic moment.
Iy	Y component of the nuclear magnetic moment.
Iz	Z component of the nuclear magnetic moment.

[formatted-string]	description
[integer]	Specify one excited energy level. The integer number corresponds to number of that level in the TDDFT output file (*out_tddft).
[N]-[M]	N < M; Specify the range of energy levels. The visualized function is then the sum of the defined transition densities.

[string]	description
scf	Canonical molecular orbitals.
lmo	Localized molecular orbitals.

[formatted-string]	description
[integer]	Specify one molecular orbital.
[N]-[M]	N < M; Specify the range of molecular orbitals. The visualized function is then the sum of the defined MO densities.
[occupied],[virtual]	Here [occupied] is one occupied MO [N] or range of occupied MOs [N]-[M] and [virtual] represents one virtual MO [K] or range of virtual MOs [K]-[L], where N < M < K < L. The resulting visualized density is the sum of the defined occupied and virtual MO indices. Index of the first virtual MO is Nocc+1 (number of occupied MOs plus one).

[string]	description
normal	Standard amount of information (recommended).
long	Additional information is printed in the .out file (may clog the output).
debug	New .dbg file will be created with even more information (mostly used for debugging purposes).
long-debug	New .dbg file will be created with potentially huge amount of information (it is feasible only for small systems).

[string]	description
Bohr	Atomic units: 0.52917721092e-10m.
Angstrom	1.0e-10m.

[string]	description
Bohr	Atomic units: 0.52917721092e-10m.
Angstrom	1.0e-10m.

[block]	description
atom: [integer]	Index of the atom in the input geometry.
point: [X] [Y] [Z]	Here X, Y and Z represent Cartesian components of the point. Unit of length is set by the keyword input-units.

[string]	description
Bohr	Atomic units: 0.52917721092e-10m.
Angstrom	1.0e-10m.

[string]	description
Bohr	Atomic units: 0.52917721092e-10m.
Angstrom	1.0e-10m.

[string]	description
raw	Files with .raw suffix are produced. Each line corresponds to one grid point. Data in the columns are described in the .out_visual file.
vti	Files with .vti suffix are produced. VTI belongs to the VTK format family. It can be read for example by ParaView visualization application.

[formatted-string]	description
[N1] x [N2]	N1 and N2 represent number of points for x and y axis, respectively.

[block]	description
atom: [integer]	Index of the atom in the input geometry.
point: [X] [Y] [Z]	Here X, Y and Z represent Cartesian components of the point. Unit of length is set by the keyword input-units.

[block]	description
atom: [integer]	Index of the atom in the input geometry.
point: [X] [Y] [Z]	Here X, Y and Z represent Cartesian components of the point. Unit of length is set by the keyword input-units.

[string]	description
all-atoms	2D rectangle will contain projections of all atoms of the molecule.

[block]	description
atom: [integer]	Index of the atom in the input geometry.
point: [X] [Y] [Z]	Here X, Y and Z represent Cartesian components of the point. Unit of length is set by the keyword input-units.

[block]	description
origin: [X] [Y] [Z]	X, Y and Z represent Cartesian components of the origin of the rectangle in the molecular coordinate system.
x-edge: [X] [Y] [Z]	Here X, Y and Z represent vector components of the x edge of the rectangle. The vector is defined with respect to the new origin defined by the origin keyword.
y-edge: [X] [Y] [Z]	Here X, Y and Z represent vector components of the y edge of the rectangle. The vector is defined with respect to the new origin defined by the origin keyword.

[string]	description
Bohr	Atomic units: 0.52917721092e-10m.
Angstrom	1.0e-10m.

[string]	description
Bohr	Atomic units: 0.52917721092e-10m.
Angstrom	1.0e-10m.

[string]	description
raw	Files with .raw suffix are produced. Each line corresponds to one grid point. Data in the columns are described in the .out_visual file.
vti	Files with .vti suffix are produced. VTI belongs to the VTK format family. It can be read for example by ParaView visualization application.
cube	Standardized Gaussian cube files .cube are produced. Content of the cube files is described in the .out_visual file. Cube file contains only scalar data, therefore multiple cube files are produced if visualization of the vector field was requested.

[formatted-string]	description
[N1] x [N2] x [N3]	N1, N2 and N3 represent number of points for x, y and z axis, respectively.

[string]	description
all-atoms	3D block/cube will contain all atoms of the molecule.

[block]	description
atom: [integer]	Index of the atom in the input geometry.
point: [X] [Y] [Z]	Here X, Y and Z represent Cartesian components of the point. Unit of length is set by the keyword input-units.

[block]	description
origin: [X] [Y] [Z]	X, Y and Z represent Cartesian components of the origin of the cube.
x-edge: [X] [Y] [Z]	Here X, Y and Z represent vector components of the x edge of the rectangle. The vector is defined with respect to the new origin defined by the origin keyword.
y-edge: [X] [Y] [Z]	Here X, Y and Z represent vector components of the y edge of the rectangle. The vector is defined with respect to the new origin defined by the origin keyword.
z-edge: [real]	[real] is the length of the z edge of the cube. Orientation of the z edge is set to be orthogonal to the x and y edge following the right hand rule.

Latest Posts

Webpage update

July 17, 2024

Program update: ReSpect 5.3.0

July, 2024

Latest Publications

Book chapter on relativistic real-time electron dynamics

May, 2024

Book chapter on relativistic theory of EPR and (p)NMR

May, 2024

Useful Links

Our Contacts

Hylleraas Centre
Department of Chemistry
UiT The Arctic University of Norway
Tromsø, NO-9037 Norway
Email: info@respectprogram.eu

grid-1d

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Note

grid-2d

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Note

Warning

grid-3d

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Note

Warning

visualize

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perturbation

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transition

Read more

Note

motype

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select-mo

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Note

active-atom

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print-level

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Latest Posts

Webpage update

Program update: ReSpect 5.3.0

Latest Publications

Book chapter on relativistic real-time electron dynamics

Book chapter on relativistic theory of EPR and (p)NMR

Useful Links

Our Contacts