DGrid version 5 - Startseite | Max-Planck-Institut …kohout/Documents/2016_DGrid-5.0.pdfDGrid version 5.0 Miroslav Kohout Max-Planck-Institut für Chemische Physik fester Stoffe,

DGrid

version 5.0

Miroslav Kohout

Max-Planck-Institut für Chemische Physik fester Stoffe, Dresden


Program DGrid-5.0

http://www.cpfs.mpg.de/~kohout/dgrid.htmlWebsite

Download Source code: dgrid-5.0.tar.gz

Documentation: DGrid-5.0.pdf

Executable: dgrid-5.0-linux64.gz dgrid-5.0-win.exe.zip

Windows: dgrid-5.0.zip


gunzip dgrid-5.0.tar.gz

tar -xf dgrid-5.0.tar

Linux: directory src with source makefile

scripts: dgrid_para-5.0 dgrid_log dgrid_dglog

Window: directory src with source dgrid-5.0.vcproj

Program DGrid-5.0

directory DGrid-5.0

unzip dgrid-5.0.zip


Installation

1) enter directory DGrid-5.0

2) adapt the makefile

3) type make on command line

4) ln -s dgrid-5.0 path/dgrid

Program DGrid-5.0


Program DGrid-5.0

Utilities:

- File conversion- Slice completion- Grid refinement

Grid calculation

Grid evaluation

Visualization: Avizo ParaView

External programs

Single point calculation

Control file


Grid calculation

0.1 Bohr for visualizationGrid mesh For integration < 0.05 Bohr

Fields

ψ , ρ , ρs , τ , vP , t P , tW , ρex , ρ2, ρ2cond

ELI-D, ELI-q, ELIA, ELF, ELFKirzh

, LOL, OEP, PUC,

ALIE, LS, LNOs, Fermi orbitals, DAHD,

Space Momentum representation only for GTO and spherical STO

Correlation Gaussian: check proper data (HF?)

GAMESS: check orbital representation?


Equidistant grid

z

y

x

box around molecule

grid box


Interfaces

ADFGaussian MOLCASMolpro Turbomole

Wavefunction file in DGrid format

GAMESS

FHIaims

*.chk, *.wfn output File in molden format TAPE21

*.datSolid state

conversion: dgrid filename


wavefunction file in DGrid format

GAMESS HF-calculation for C3H6 with 6-31G basis

C3H6_HF_6-31G.outGAMESS output file

C3H6_HF_6-31G.gms

filename extender for GAMESS

conversion: dgrid C3H6_HF_6-31G.out


Control file for grid calculation

compute block

output writtento console

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|

wfn_1= C3H6_HF_6-31G.gms

compute:------------------------------------------ using wfn_1

ELI-D alpha-alpha rho

X: Y: Z: ----------------------------: origin= -10.7 -10.7 -13.8 intervals: ------------------------------------------: i-vector: 21.4 0.0 0.0 21 j-vector: 0.0 21.4 0.0 21 k-vector: 0.0 0.0 27.6 27 :------------------------------------------ compute_end

console

skipped

wavefunctiondescriptor

skipped



field choice

grid definition

title not parsed :-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|




X: Y: Z: ----------------------------: origin= -10.7 -10.7 -13.8 intervals: ------------------------------------------: i-vector: 21.4 0.0 0.0 21 j-vector: 0.0 21.4 0.0 21 k-vector: 0.0 0.0 27.6 27 :------------------------------------------ compute_end

console



field choice

grid definition

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|




mesh= 0.05 rho=0.001 :------------------------------------------ compute_end



grid regiony

x

initial box

y

x

ρ=0.001bohr−3

box not parallel with axes


Control file elid_rho.inp for grid calculation

field choice

grid definition

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|




mesh= 0.05 rho=0.001 parallel :------------------------------------------ compute_end


field choice

grid definition

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|





C3H6_HF_6-31G.gms.elid_r_a_aaC3H6_HF_6-31G.gms.rho_r

elid_rho.inp.DG_LOG


dgrid elid_rho.inp


field choice

grid definition

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|







elid_rho.inp.DG_LOG

dgrid elid_rho.inp


:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|







elid_rho.inp.DG_LOG

dgrid elid_rho.inp


:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|








elid_rho.inp.DG_LOG

dgrid elid_rho.inp


Parallel grid-calculation

Grid slices

Each slice computedon separate processor

using separate control file


:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|






dgrid_para-5.0 elid_rho.inp


:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|




mesh= 0.05 rho=0.001 parallel :------------------------------------------ slices=4 1 compute_end



elid_rho.inp-01elid_rho.inp-02elid_rho.inp-03elid_rho.inp-04

control files created by dgrid_para-5.0 script


:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|




mesh= 0.05 rho=0.001 parallel :------------------------------------------ slices=4 1 compute_end


C3H6_HF_6-31G.gms.elid_r_a_aa.slice-1C3H6_HF_6-31G.gms.rho_r.slice-1

elid_rho.inp-01.DG_LOG




C3H6_HF_6-31G.gms.elid_r_a_aa.slice-1C3H6_HF_6-31G.gms.rho_r.slice-1

elid_rho.inp-01.DG_LOG


dgrid C3H6_HF_6-31G.gms.elid_r_a_aa.slice-1 complete


unify slices


Electron density grid

ρ=0.31bohr−3


Basins

field grid_2field grid_1

search for basins evaluate basins

visualization

basin grid

integrate over basins


Basin search

First basinSecond basin

Third basin


Control file bsn_elid.inp for basin search

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|

field_1= C3H6_HF_6-31G.gms.elid_r_a_aa

basin:------------------------------------------ using field_1:------------------------------------------ basin_end

basin block

field descriptor



:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|

field_1= C3H6_HF_6-31G.gms.elid_r_a_aa

basin:------------------------------------------ using field_1:------------------------------------------ basin_end

field descriptor

C3H6_HF_6-31G.gms.elid_r_a_aa.bsn

C3H6_HF_6-31G.gms.elid_r_a_aa.bsn.LOGdgrid bsn_elid.inp

basin grid

basin info

basin block


ELI-D grid and basins

H

HH

H

H

ELI-D basincut by box



:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|

field_1= C3H6_HF_6-31G.gms.elid_r_a_aa field_2= C3H6_HF_6-31G.gms.rho_r

basin:------------------------------------------ using field_1

crop using field_2 0.001:------------------------------------------ basin_end

basin block

field descriptors



:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|


basin:------------------------------------------ using field_1

crop using field_2 0.001:------------------------------------------ basin_end

basin block

field descriptors

C3H6_HF_6-31G.gms.elid_r_a_aa.bsn_1

C3H6_HF_6-31G.gms.elid_r_a_aa.bsn_1.LOGdgrid bsn_elid.inp

H

H


QTAIM basins

QTAIM hydrogen basin

QTAIM carbon basin


Control file integrate.inp for integration over basins

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|

basin_1= C3H6_HF_6-31G.gms.elid_r_a_aa.bsn field_2= C3H6_HF_6-31G.gms.rho_r

integrate:------------------------------------------ using basin_1

over field_2:------------------------------------------ integrate_endintegrate block

basin descriptor

C3H6_HF_6-31G.gms.elid_r_a_aa.bsn.rho_r_ITGdgrid integrate.inp

field descriptor


/=========================\ | I N T E G R A T I O N | +-------------------------++---------------------------------------------------------------------------------------------------+| using field rho[r] spin = both pair = --- || || read from DGrid-5.0 grid file C3H6_HF_CCT.gms.rho_r || entitled: |+---------------------------------------------------------------------------------------------------+ BASIN VOLUME INTEGRAL MAXIMUM X Y Z ATOMS DIST ECCNT+--------------------------------------------------------------------------------------------------+| 1 48.858 1.0014 0.4356+ 2.690 -0.020 -1.650 H_3 0.07 - || 2 48.858 1.0014 0.4356+ 2.690 -0.020 1.650 H_6 0.07 - || 3 48.868 1.0011 0.4377+ -1.360 2.330 1.650 H_1 0.07 - || 4 48.868 1.0011 0.4377+ -1.360 2.330 -1.650 H_4 0.07 - || 5 48.875 1.0012 0.4379+ -1.360 -2.370 1.650 H_2 0.05 - || 6 48.875 1.0012 0.4379+ -1.360 -2.370 -1.650 H_5 0.05 - || 7 71.521 5.9324 102.0016+ -0.810 1.430 0.000 C_1 0.02 - || 8 71.637 5.9353 97.3094+ 1.640 -0.020 0.000 C_3 0.02 - || 9 71.777 5.9435 113.3074+ -0.810 -1.420 0.000 C_2 0.01 - |+--------------------------------------------------------------------------------------------------+| TOTAL | 508.137 23.8185 |+--------------------------------------------------------------------------------------------------+| DIFF | -606.587 |+--------------------------------------------------------------------------------------------------+

C3H6_HF_6-31G.gms.elid_r_a_aa.bsn.rho_r_ITG


Control file refine.inp for grid refinement

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|

field_1= C3H6_HF_6-31G.gms.rho_r

refine:------------------------------------------ using field_1

precision= 0.01:------------------------------------------ refine_endrefinement block

C3H6_HF_6-31G.gms.rho_r.rfndgrid refine.inp


Control file search.inp for critical points search

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|


search:------------------------------------------ using field_1 crop using field_1 0.001

attractors saddles:------------------------------------------ search_end

search block

C3H6_HF_6-31G.gms.rho_r.cps

C3H6_HF_6-31G.gms.rho_r.CPSdgrid search.inp

crit. points data

info


/===========================\ | attractors in region= 9 | +---------------------------+ # Bsn x y z value Laplacian curvature +--------------------------------------------------------------------------------------------------+ | 1 1 -1.3761 -2.3834 -1.6970 0.4325 - H5 | | 2 2 2.7521 0.0000 -1.6970 0.4325 - H3 | | 3 4 -1.3761 2.3834 -1.6970 0.4325 - H4 | | 4 5 -0.8212 -1.4224 0.0000 118.2036 - C2 | | 5 6 1.6425 0.0000 0.0000 118.2036 - C3 | | 6 8 -0.8212 1.4224 0.0000 118.2036 - C1 | | 7 9 -1.3761 -2.3834 1.6970 0.4325 - H2 | | 8 10 2.7521 0.0000 1.6970 0.4325 - H6 | | 9 12 -1.3761 2.3834 1.6970 0.4325 - H1 | +--------------------------------------------------------------------------------------------------+

/========================\ | saddles in region= 9 | +------------------------+ # x y z value Laplacian curvature ellip |V|/G H+------------------------------------------------------------------------------------------------------------------+| 1 -1.1607 -2.0104 -1.0545 0.2687 -0.8045 -0.6498 -0.6635 0.5088 0.02 5.900 -0.253 || 2 -1.1607 2.0104 1.0545 0.2687 -0.8045 -0.6498 -0.6635 0.5088 0.02 5.900 -0.253 || 3 -1.1607 -2.0104 1.0545 0.2687 -0.8045 -0.6498 -0.6635 0.5088 0.02 5.900 -0.253 || 4 -1.1607 2.0104 -1.0545 0.2687 -0.8045 -0.6498 -0.6635 0.5088 0.02 5.900 -0.253 || 5 2.3214 -0.0000 -1.0545 0.2687 -0.8045 -0.6635 -0.6498 0.5088 0.02 5.900 -0.253 || 6 2.3214 -0.0000 1.0545 0.2687 -0.8045 -0.6635 -0.6498 0.5088 0.02 5.900 -0.253 || 7 0.4718 0.8171 -0.0000 0.2207 -0.3142 0.3545 -0.2922 -0.3765 0.29 3.000 -0.157 || 8 0.4718 -0.8171 -0.0000 0.2207 -0.3142 0.3545 -0.2922 -0.3765 0.29 3.000 -0.157 || 9 -0.9436 -0.0000 -0.0000 0.2207 -0.3142 -0.2922 0.3545 -0.3765 0.29 3.000 -0.157 |+------------------------------------------------------------------------------------------------------------------+

C3H6_HF_6-31G.gms.rho_r.CPS


Control file icl.inp for interconnection (molecular) graph

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|

cps_1= C3H6_HF_6-31G.gms.rho_r.cps

ICL_graph:------------------------------------------ using cps_1

saddles:------------------------------------------ ICL_graph_end

ICL block

C3H6_HF_6-31G.gms.rho_r.cps.graph.str

C3H6_HF_6-31G.gms.rho_r.cps.graph.LOGdgrid icl.inp

data for visualization

H

H


QTAIM basins

QTAIM hydrogen basin

QTAIM carbon basin

Bond path

Saddle point


Control file search2.inp for critical points search and graph

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|


search:------------------------------------------ using field_1 crop using field_1 0.001

attractors saddles

save cps_1:------------------------------------------ search_end

ICL_graph:------------------------------------------ using cps_1

saddles:------------------------------------------ ICL_graph_end

search block

ICL block


Control file search2.inp for critical points search and graph

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|


basin:------------------------------------------ using field_1 crop using field_1 0.001

save basin_1:------------------------------------------ basin_end

basin_2= C3H6_HF_6-31G.gms.elid_r_a_aa.bsn

intersections:------------------------------------------ using basin_2

with basin_1:------------------------------------------ intersections_end

basin block

intersect. block

C3H6_HF_6-31G.gms.elid_r_a_aa.bsn.isect-rho_r.bsn


Basin intersection

ELI-D hydrogen basin

Intersection with QTAIM carbon basin


Control file analyse.inp for the intersection analysis

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|

basin_1= C3H6_HF_6-31G.gms.elid_r_a_aa.isect-rho_r.bsn rfn_1 = C3H6_HF_6-31G.gms.rho_r.rfn

isect_analyze:------------------------------------------ using basin_1 integrate rfn_1

basin_set=1:------------------------------------------ isect_analyze_end

analyze block

C3H6_HF_6-31G.gms.elid_r_a_aa.bsn.isect-rho_r.bsn.ISECT


/======================================================\ | Intersections of ELI-D[r] basins by rho[r] basins | +------------------------------------------------------+

basin descriptor volume % integ % +----------------------------------------------------------------------------+| 1-8 C_3xC_3 0.820 100.00 2.0924 100.00 |+----------------------------------------------------------------------------+| total | 0.820 100.00 2.0924 100.00 |+----------------------------------------------------------------------------+

basin descriptor volume % integ % +----------------------------------------------------------------------------+| 4-7 C_2-C_1xC_1 13.398 49.61 0.8842 49.73 || 4-9 C_2-C_1xC_2 13.611 50.39 0.8940 50.27 |+----------------------------------------------------------------------------+| total | 27.009 100.00 1.7782 100.00 |+----------------------------------------------------------------------------+

basin descriptor volume % integ % +----------------------------------------------------------------------------+| 7-7 H_1xC_1 21.882 30.93 1.0323 50.77 || 7-3 H_1xH_1 48.868 69.07 1.0011 49.23 |+----------------------------------------------------------------------------+| total | 70.750 100.00 2.0334 100.00 |+----------------------------------------------------------------------------+




basin descriptor volume % integ % +----------------------------------------------------------------------------+| 1-8 C_3xC_3 0.820 100.00 2.0924 100.00 |+----------------------------------------------------------------------------+| total | 0.820 100.00 2.0924 100.00 |+----------------------------------------------------------------------------+

basin descriptor volume % integ % +----------------------------------------------------------------------------+| 4-7 C_2-C_1xC_1 13.398 49.61 0.8842 49.73 || 4-9 C_2-C_1xC_2 13.611 50.39 0.8940 50.27 |+----------------------------------------------------------------------------+| total | 27.009 100.00 1.7782 100.00 |+----------------------------------------------------------------------------+

basin descriptor volume % integ % +----------------------------------------------------------------------------+| 7-7 H_1xC_1 21.882 30.93 1.0323 50.77 || 7-3 H_1xH_1 48.868 69.07 1.0011 49.23 |+----------------------------------------------------------------------------+| total | 70.750 100.00 2.0334 100.00 |+----------------------------------------------------------------------------+


H

H

C-C


Basin intersection

QTAIM carbon basin

Intersection withELI-D C-C basin


Control file analyse.inp for the intersection analysis

:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|

basin_1= C3H6_HF_6-31G.gms.elid_r_a_aa.isect-rho_r.bsn rfn_1 = C3H6_HF_6-31G.gms.rho_r.rfn

isect_analyze:------------------------------------------ using basin_1 integrate rfn_1

basin_set=2:------------------------------------------ isect_analyze_end

analyze block

C3H6_HF_6-31G.gms.elid_r_a_aa.bsn.isect-rho_r.bsn.ISECT_1



basin descriptor volume % integ % +----------------------------------------------------------------------------+| 9-1 H_3xH_3 48.858 100.00 1.0014 100.00 |+----------------------------------------------------------------------------+| total | 48.858 100.00 1.0014 100.00 |+----------------------------------------------------------------------------+

basin descriptor volume % integ % +----------------------------------------------------------------------------+| 8-7 H_6xC_1 0.003 0.00 0.0000 0.00 || 3-7 C_1xC_1 0.823 1.15 2.0939 35.30 || 4-7 C_2-C_1xC_1 13.398 18.73 0.8842 14.91 || 5-7 C_3-C_1xC_1 13.521 18.90 0.8898 15.00 || 7-7 H_1xC_1 21.882 30.60 1.0323 17.40 || 10-7 H_4xC_1 21.894 30.61 1.0319 17.40 |+----------------------------------------------------------------------------+| total | 71.521 100.00 5.9321 100.00 |+----------------------------------------------------------------------------+




basin descriptor volume % integ % +----------------------------------------------------------------------------+| 9-1 H_3xH_3 48.858 100.00 1.0014 100.00 |+----------------------------------------------------------------------------+| total | 48.858 100.00 1.0014 100.00 |+----------------------------------------------------------------------------+

basin descriptor volume % integ % +----------------------------------------------------------------------------+| 8-7 H_6xC_1 0.003 0.00 0.0000 0.00 || 3-7 C_1xC_1 0.823 1.15 2.0939 35.30 || 4-7 C_2-C_1xC_1 13.398 18.73 0.8842 14.91 || 5-7 C_3-C_1xC_1 13.521 18.90 0.8898 15.00 || 7-7 H_1xC_1 21.882 30.60 1.0323 17.40 || 10-7 H_4xC_1 21.894 30.61 1.0319 17.40 |+----------------------------------------------------------------------------+| total | 71.521 100.00 5.9321 100.00 |+----------------------------------------------------------------------------+




:-------------------------------------------|::C3H6 HF / 6-31G :-------------------------------------------|


basin:------------------------------------------ using field_1 crop using field_2 0.001

ELID_core:------------------------------------------ basin_end

basin block

field descriptors


Re atom

D

4f14

6s2

5d5

5p6

5s2

D = ∑ iV D

M. Kohout, Faraday Discuss. 135 (2007) 43F.R. Wagner, V.Bezugly, M. Kohout, Yu. Grin,Chem. Eur. J. 13 (2007) 5724

6th shell

Large 5d contributionIn the valence shell

‘Properly’ resolved atomic shell structure is importantto get ‘appealing’ descriptors of the ‘chemical’ situation