How to generate a mixed pseudopotential Objectives Generate a mixed pseudopotential to be used in the Virtual Crystal Approximation or in simulations at constant electric displacement Most important reference IOP PUBLISHING JOURNAL OF PHYSICS: CONDENSED MATTER J. Phys.: Condens. Matter 22 (2010) 415401 (16pp) doi:10.1088/0953-8984/22/41/415401 An efficient computational method for use in structural studies of crystals with substitutional disorder ˜ Roberta Poloni, Jorge I´niguez, Alberto Garc´ıa and Enric Canadell Institut de Ci`encia de Materials de Barcelona (CSIC), Campus UAB, 08193 Bellaterra, Spain E-mail: albertog@icmab.es Received 11 June 2010 Published 23 September 2010 Online at stacks.iop.org/JPhysCM/22/415401 Abstract We present a computationally efficient semi-empirical method, based on standard first-principles techniques and the so-called virtual crystal approximation, for determining the average atomic structure of crystals with substitutional disorder. We show that, making use of a minimal amount of experimental information, it is possible to define convenient figures of merit that allow us to recast the determination of the average atomic ordering within the unit cell as a minimization problem. We have tested our approach by applying it to a wide variety of How to compile the code to run the pseudopotential mixer The code is included in the Siesta distribution, within the Util/VCA directory Assuming we are in the directory where the sources are stored, simply I. Siesta ENERGY FUNCTIONAL FOR A DIEL $ cd Util/VCA $ make It will use the same arch.make file as for the compilation of SIESTA (no need to copy it again to the Util/VCA directory) mixps fractional This will generate two executable files: (program to mix pseudopotentials) (program that multiplies the strength of a pseudopotential by a given fraction) How to mix two pseudopotentials Create a new directory in the directory where you generate your pseudopotentials ENERGY FOR A DIELECTRIC INSIDE AN Copy there the two pseudosI.you want toFUNCTIONAL mix (in this example, O and F) Cite1,2 . I. ENERGY FUNCTIONAL FOR A DIELECTRI $ cd ../atom/Tutorial/PS_Generation $ mkdir VCA-O-F Cite$ 1,2 cd. VCA-O-F $ cp ../O/O.tm2.psf ./O.psf cd ../F/F.tm2.psf ./F.psf cd $../atom/Tutorial/PS_Generation $ $ mkdir VCA-O-F XC.functional GGA $ cd XC.authors VCA-O-F PBE .true. $ cp ../O/O.tm2.psf ./O.psf Copy there the twoSpinPolarized pseudos you want to mix (in this example, O and F) $ cd nsppol ../F/F.tm2.psf ./F.psf 2 # Number of spin polarizations $ spinat 0.0 0.0 1.0 ixc 11 ~/siesta/Util/VCA/mixps occopt 3 O F # Spin for atoms # Integer for exchange-correlatio 0.9 # Occupation Option Mixing parameter: InNumber this example of spinmetal) pola Fermi-Dirac smearing #(finite-temperature 90% of the #first atomfor atoms Spin Temperature of smearing (in Ha) nsppol 2 # spinat 0.0 0.0 1.0# Labels of the two atoms involved tsmear 0.01 ixc 11 10% of the second atom # Integer for exchang Output of $ mkdir VCA-O-F $ cd VCA-O-F $ cp ../O/O.tm2.psf ./O.psf the mixing of the pseudopotential $ cd ../F/F.tm2.psf ./F.psf $ ~/siesta/Util/VCA/mixps O F 0.9 nsppol 2 spinat 0.0 1.0 Labels of the two atoms 0.0 involved ixc 11 occopt OF-0.90000.psf Mixing parameter:# InNumber this example of spin pola 90% of the #first atomfor atoms Spin 10% of the second atom # Integer for exchang New files: # Occupation Option 3 # Fermi-Dirac smearing (finite-tempera # Temperature of smearing (in Ha) Pseudopotential file with the mixture of the two pseudos tsmear 0.01 Name of the mixed file: Symbols of the two original pseudopotentials, followed by the mixing parameter (up to five decimal places) OF-0.90000.synth Bloch “SyntheticAtoms” to be used in SIESTA %block SyntheticAtoms 1 2 2 3 4 2.000000 4.100000 0.000000 %endblock SyntheticAtoms MIXLABEL 0.000000 Final label used In this particular example a virtual with a charge of 6.1 electrons is generated 0.9 * 6 (electrons in O) + 0.1*7 (electrons in F) = 6,1 electrons in the Virtual Atom 2.0 electrons in the s chanel and 4.1 electrons in the p channel Some notes on the mixed pseudopotentials Once SIESTA reads the new mixed pseudopotential, it proceeds as usual, and generates: - the local part of the pseudopotential - the Kleinman-Bylander projectors - the basis set Those quantities are not a true mix of the corresponding quantities of the individual atoms. The basis set is generated by SIESTA using the mixed pseudopotential (no mixing of the basis set has been implemented). To see how to generate a basis set for a mixed atom, see the Tutorial “How to run with a finite constraint electric displacement” Uses of the Virtual Crystal Approximation To study substitutional disorder IOP PUBLISHING JOURNAL OF PHYSICS: CONDENSED MATTER J. Phys.: Condens. Matter 22 (2010) 415401 (16pp) doi:10.1088/0953-8984/22/41/415401 An efficient computational method for use in structural studies of crystals with substitutional disorder ˜ Roberta Poloni, Jorge I´niguez, Alberto Garc´ıa and Enric Canadell Institut de Ci`encia de Materials de Barcelona (CSIC), Campus UAB, 08193 Bellaterra, Spain E-mail: albertog@icmab.es 11 June 2010 ToReceived perform calculations at constrained electric displacement Published 23 September 2010 see the Tutorial “How to run with a finite constraint electric displacement” Online at stacks.iop.org/JPhysCM/22/415401 Abstract We present a computationally efficient semi-empirical method, based on standard first-principles techniques and the so-called virtual crystal approximation, for determining the average atomic structure of crystals with substitutional disorder. We show that, making use of a minimal amount of experimental information, it is possible to define convenient figures of merit that allow us to recast the determination of the average atomic ordering within the unit cell as a minimization problem. We have tested our approach by applying it to a wide variety of