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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
NCIplot Urea Thymine Electride Conclusion
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.
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 2 / 22
NCIplot Urea Thymine Electride Conclusion
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.
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 3 / 22
NCIplot Urea Thymine Electride Conclusion
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
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 4 / 22
NCIplot Urea Thymine Electride Conclusion
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)
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 5 / 22
NCIplot Urea Thymine Electride Conclusion
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
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 6 / 22
NCIplot Urea Thymine Electride Conclusion
Critic2: critical points of the MEP
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 7 / 22
NCIplot Urea Thymine Electride Conclusion
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...
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 8 / 22
NCIplot Urea Thymine Electride Conclusion
Copy the files
> scp [email protected]:transfer/NCI-solid/*/ .
Password: nciws2013
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 9 / 22
NCIplot Urea Thymine Electride Conclusion
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
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 10 / 22
NCIplot Urea Thymine Electride Conclusion
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
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 11 / 22
NCIplot Urea Thymine Electride Conclusion
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
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 12 / 22
NCIplot Urea Thymine Electride Conclusion
Urea: simple nciplot
urea02.incritic
# Read structure and densitycrystal urea.rho.cubeload urea.rho.cube
# Default nciplotnciplotendnciplot
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 13 / 22
NCIplot Urea Thymine Electride Conclusion
Urea: simple nciplot
urea03.incritic
# Read structure and densitycrystal urea.rho.cubeload urea.rho.cube
# Default nciplotnciplot
# Complete the moleculesmolmotif
endnciplot
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 14 / 22
NCIplot Urea Thymine Electride Conclusion
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
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 15 / 22
NCIplot Urea Thymine Electride Conclusion
Thymine: simple nciplot
thymine01.incritic
# Read structure and densitycrystal rho.cubeload rho.cube# Default nciplotnciplot
molmotifendnciplot
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 16 / 22
NCIplot Urea Thymine Electride Conclusion
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
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 17 / 22
NCIplot Urea Thymine Electride Conclusion
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
NCIplot Urea Thymine Electride Conclusion
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
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 19 / 22
NCIplot Urea Thymine Electride Conclusion
Electride (bis(15-crown-5)-cesium): simple nciplot
TAGFEM02.incritic
# Read structurecrystal TAGFEM.rho.cube# Then the densityload TAGFEM.rho.cube# Simple nciplotnciplot
molmotifendnciplot
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 20 / 22
NCIplot Urea Thymine Electride Conclusion
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
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 21 / 22
NCIplot Urea Thymine Electride Conclusion
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]
A. Otero & E. Johnson (UC Merced) critic2 NCI Workshop (June 2013) 22 / 22