DGrid

A manual is available for version 4.6 and for version 4.5. Source code for 4.6. DGrid is used for preparing cube files containing ELF (η(r) ) or RHO (ρ(r) ) values. The primary input looks like this.

./dgrid-4.6 filename.fchk (creates a .g09 file)
./dgrid-4.6 -n 8 filename.inp (shown below, including a selection of MOs at the bottom to eg compute only π contributions etc. The flag -n 8 invokes 8 processors, but the parallel streams have to be set up in the input (not shown below, see manual).

:TITLE
:------------------------------------------------------------------|
::[1.1.1] propellane
:------------------------------------------------------------------|

:KEYWORDS
:-------------------------------------------------------------------
 basis=propellane.g09

:result=aa
 output=.

:format=cube  (remove comment to actually compute a cube)

:CHOOSE THE DESIRED PROPERTIES
:-----------------------------------------
 compute=rho         
 compute=ELF-cs
 compute=rho laplacian
 compute=energy-dens      
:compute=ELI-D    triplet
:-----------------------------------------


 GRID_DEFINITION:   vectors
:----------------------------
:             X     Y     Z
:----------------------------
 origin:    -10.0  -10.0  -10.0
                               INTERVALS:
:---------------------------------------
 i-vector:  20.0   0.0   0.0     150
 j-vector:   0.0  20.0   0.0     150
 k-vector:   0.0   0.0  20.0     150

USERS_OCCUPATION_INPUT: occupation

:---------------------------------------------------------
:SYM 		# 	ALPHA 	BETA
:---------------------------------------------------------
NONE           49     1.00000000000    1.00000000000
NONE           48     1.00000000000    1.00000000000
NONE           47     1.00000000000    1.00000000000
NONE           43     1.00000000000    1.00000000000

occupation_end
end

./dgrid-4.5 propellane.g03.rho_r refine 0.05 (or 0.025 for better precision). Note that the format has to be native (i.e. NOT a cube).

The cube dimensions and origin may need experimentation (one can obtain good estimates by running the grid09 program, which prints them out). Note also that more than around 150 points per edge of cube is too time consuming for other than small molecules.

./dgrid-4.5 bas.inp where the input file looks like

::
:-------------------
 property =propellane.g09.elf_cs_r
 crop     =propellane.g09.rho_r         0.0001
 integrate=propellane.g09.rho_r.rfn

 output=.

 eli_core
:top=1.45

END

The commands:

property=SiCl5.g03.elf_cs_r 
crop=SiCl5.g03.rho_r  0.0001

means that the ELF basins are searched within regions where the density is higher then 0.0001 (i.e., cropped by 0.0001 envelope).

The refined density will be integrated (you can use also the unrefined density file, but then the charges will be less precise). The eli_core command gathers all the core basins of ELF into single core basin. You can set the command top= to such value, that the lone-pair basins will form a single basin (otherwise you will see two basins - look at the ELF isosurface) An alternative bas file might be

::
:-------------------
 property =propellane.g09.rho_r
 crop     =propellane.g09.rho_r         0.0001
 integrate=propellane.g09.rho_r.rfn

 output=.

 eli_core
:top=1.45

END

This locates basins in the rho function rather than the ELF function, and would then be used with the following top.inp file:

:TITLE
:-----------------------------------------------------------|
:: density basins
:-----------------------------------------------------------|
:KEYWORDS
:---------------------------------------------------------
property =N2-nbo.g09.rho_r.bsn
output=.
topology
icl_graph=full
end

which gives a full QTAIM analysis of the critical points. This latter technique is particularly useful when you might want to calculate QTAIM on a subset of orbitals (specified as above).

The rho or ELF cubes can be reduced (compressed by a factor of around 150) to a .jvxl by inspecting the page here.

Using CC Wavefunctions

Dgrid can accept coupled cluster wavefunctions from an .fchk file. To prepare the file appropriately, add the following to the CCSD calculation

# CCSD/basis density=cc  ...
...
--Link1--
%Chk=name
# Guess=(save,only,naturalorbitals) geom=allcheck chkbasis

Update: Version 4.5

This new version has the following new features

The search for critical points is done with new approach, which allows to identify the attractors, minima (cages), as wel as the saddle (BCPs) and ring critical points.
The molecular graph can be computed separately by a utility. Additionally, besides the interconnection lines from saddle points to attractors (i.e., molecular graph) also the interconnection lines from ring points to minima are determined.
For Gauss-type basis the overlap integrals over basins can be computed. From this the evaluation of fluctuation and delocalization indices (cf. work of X. Fradera) are performed.
Source code for interfaces to 2 visualization tools are included (Avizo and OpenDX).