NCI for solids: the critic2 program

NCIplot Urea Thymine Electride Conclusion

NCI for solids: the CRITIC2 program

Alberto Otero-de-la-Roza and Erin R. Johnson

School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced,California 95343, USA

A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 1 / 22


NCI basics

Reduced density gradient (RDG):

s =1

2(3π2)

|∇ρ|ρ4/3

Maps intermolecular contacts(i.e. Pauli repulsion zones).

Simpler to calculate thanBader’s topology.

Color-mapping and regionextent: strength of theinteraction.

Johnson et al., J. Am. Chem. Soc. 132 (2010) 6498–6506.

Contreras-García et al., J. Chem. Theory Comput. 7 (2011) 625–632.



NCI in solids

Molecular contacts in crystalpacking.

Related to low-frequencyintermolecular phonons.

Otero-de-la-Roza et al., Phys. Chem. Chem. Phys. 14 (2012) 12165–12172.



NCI in solids: how it’s done

1 Ingredients:I Crystal structureI ρ from a calculation...I ...or promolecular density

2 Calculate ρ and RDG on a grid3 Eliminate the uninteresting parts.

I Intramolecular (define fragments)I Crystal voids.

4 Generate the plots.

Example: urea



Critic2

CRITIC2 can do:

NCI plots

Bader integration (Q, V,...)

Critical points of ρ...and other fields (ELF, MEP,...)

Arithmetics with fields

Graphical representations:basins, planes, cubes,...

Otero-de-la-Roza et al., Comput. Phys. Commun. 180 (2009) 157–166.

Otero-de-la-Roza et al., Comput. Phys. Commun. (submitted)



Critic2: basin integration, YT algorithm

A P-doped Si surface176 atoms84 seconds (1 cpu).

crystal POSCAR Si H Pload CHGCARzpsp Si 4 H 1 P 5yt

An electride:71 atoms + 2 nnms14 seconds (1 cpu).

crystal TAGFEM.scf.outload TAGFEM.rho.cubezpsp cs 9 c 4 o 6 h 1yt

Yu, M. and Trinkle, D. R., J. Chem. Phys. 134 (2011) 064111



Critic2: critical points of the MEP



Critic2: other features

Crystal structure formats:CIF, QE (scf.out), VASP(POSCAR), WIEN2k (struct),elk (GEOMETRY.OUT), abinit(DEN), cube files. Also, inputby hand, maybe using a spacegroup.

Field formats: QE, VASP,abinit, WIEN2k, elk, PI,Gaussian,...

Format conversion (e.g. CIF toQE).

Crystal structurecrystal BZDMAZ01.cifcrystal BZDMAZ01.structcrystal POSCAR h c ncrystal BZDMAZ01.scf.outcrystal BZDMAZ01_o_DENcrystal GEOMETRY.OUTcrystal BZDMAZ01.cube

Fieldsload BZDMAZ01.cubeload CHGCARload BZDMAZ01_o_DENload BZDMAZ01.clmsumBZDMAZ01.structload STATE.OUT GEOMETRY.OUTload c.ion C h.ion H...



Copy the files

> scp [email protected]:transfer/NCI-solid/*/ .

Password: nciws2013


[email protected]:transfer/NCI-solid/*/

[email protected]:transfer/NCI-solid/*/


Urea: crystal structure and promolecular

Obtain the crystal structure

Download CIF file

From the literature

???

urea00.incritic

# Read structure: CIF filecrystal urea.cif# NCIplot (promolecular)nciplotendnciplot



Urea: format conversion

urea00.incritic

# Read structure: CIF filecrystal urea.cif# Convert CIF to other formatswrite urea_bleh.scf.inwrite urea_bleh.xyz molmotifwrite POSCARwrite urea.abinwrite urea.elk



Urea: the SCF calculation

Calculation (QE) of the density

pw.x < urea.scf.inpp.x < urea.pp.in

urea01.incritic

# Read structure and density# from the cube filecrystal urea.rho.cubeload urea.rho.cube# Pseudopotential Zzpsp C 4 H 1 N 5 O 6# Atomic charges and volumesyt



Urea: simple nciplot

urea02.incritic

# Read structure and densitycrystal urea.rho.cubeload urea.rho.cube

# Default nciplotnciplotendnciplot



Urea: simple nciplot

urea03.incritic

# Read structure and densitycrystal urea.rho.cubeload urea.rho.cube

# Default nciplotnciplot

# Complete the moleculesmolmotif

endnciplot



Urea: fragments

urea04.incritic

# Read structure and densitycrystal urea.rho.cubeload urea.rho.cube# Cut the fragments# write urea.xyz molmotifnciplot

molmotif# 2 fragmentsfragment frag1.xyzfragment frag2.xyz# smaller gridnstep 40 40 120

endnciplot



Thymine: simple nciplot

thymine01.incritic

# Read structure and densitycrystal rho.cubeload rho.cube# Default nciplotnciplot

molmotifendnciplot



Thymine: cut the fragments

thymine02.incritic

# Read crystal structurecrystal rho.cube# Write an xyz file# Complete the moleculeswrite crystal.xyz molmotif

fragment 1

fragment 2



Thymine: fragment NCIplotthymine03.incritic

# Read crystal structurecrystal rho.cubeload rho.cube# First plotnciplot

fragment fragment_1a.xyzfragment fragment_1b.xyzrhoparam2 0.95oname thymine_internstep 120 120 120

endnciplot# Second plotnciplot

fragment fragment_2a.xyzfragment fragment_2b.xyzfragment fragment_2c.xyzrhoparam2 0.95oname thymine_intranstep 120 120 120

endnciplot

fragment 1

fragment 2A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 18 / 22


Electride (bis(15-crown-5)-cesium): atomic charges

TAGFEM01.incritic

# Read structurecrystal TAGFEM.rho.cube# Then the densityload TAGFEM.rho.cube# Pseudopotential Zzpsp cs 9 c 4 o 6 h 1# Atomic chargesyt



Electride (bis(15-crown-5)-cesium): simple nciplot

TAGFEM02.incritic

# Read structurecrystal TAGFEM.rho.cube# Then the densityload TAGFEM.rho.cube# Simple nciplotnciplot

molmotifendnciplot



Electride (bis(15-crown-5)-cesium): crystal voids

TAGFEM03.incritic

# Read structurecrystal TAGFEM.rho.cube# Then the densityload TAGFEM.rho.cubenciplot

molmotif# Only the voidsvoid 0.0025

endnciplot



Closing remarks

Download CRITIC2 and the examples in this tutorial from:

http://azufre.quimica.uniovi.es/software.html

Fully documented, with examples.

Free licence (GNU/GPL v3).

Contact: [email protected]


http://azufre.quimica.uniovi.es/software.html

[email protected]

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NCI for solids: the critic2 program

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