[DFTB-Plus-User] DFTB-Plus-User Digest, Vol 36, Issue 1
Ashwin Ramasubramaniam
ashwin.ramasubramaniam at gmail.com
Thu Dec 9 22:54:08 CET 2010
Reinaldo, Balint,
Thanks for your e-mails. I was hoping that the Ni parameters were fit
to bulk phases before fitting to biological systems was done. But I
guess this is not so.
thanks again,
-Ashwin.
On Wed, Dec 8, 2010 at 6:00 AM, <dftb-plus-user-request at dftb-plus.info> wrote:
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> Today's Topics:
>
> 1. Problems with Ni-Ni parameter set (Ashwin Ramasubramaniam)
> 2. Re: Problems with Ni-Ni parameter set (Reinaldo Pis Diez)
> 3. Re: Problems with Ni-Ni parameter set (B?lint Aradi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 7 Dec 2010 13:09:19 -0500
> From: Ashwin Ramasubramaniam <ashwin.ramasubramaniam at gmail.com>
> Subject: [DFTB-Plus-User] Problems with Ni-Ni parameter set
> To: dftb-plus-user at dftb-plus.info
> Message-ID:
> <AANLkTinqpH1OJKbo-xc=g_e6jivcHMmukJwtzHM1j50v at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello,
>
> I seem to be having trouble getting the Ni-Ni parameter set to
> correctly reproduce the bulk Ni fcc structure with the trans3d
> parameter set. I try to generate an energy vs. lattice parameter curve
> using the script below:
>
> =========
> #! /bin/bash
>
> for a in 3.49 3.50 3.51 3.52 3.53 3.54 3.55 3.56 3.57 3.58 3.59 3.60
> do
>
> b=$(echo "$a/2"|bc -l)
>
> cat >dftb_in.hsd <<!
> Geometry = {
> Periodic = Yes
> LatticeVectors [Angstrom] = {
> $b $b 0.0
> $b 0.0 $b
> 0.0 $b $b
> }
> TypeNames = { "Ni" }
> TypesAndCoordinates [relative] = {
> 1 0.00 0.00 0.00
> }
> }
>
> Hamiltonian = DFTB {
> SCC = Yes
> SCCTolerance = 1e-5
> MaxAngularMomentum = {
> Ni = "d"
> }
> SlaterKosterFiles = Type2FileNames {
> Prefix = ""
> Separator = "-"
> Suffix = ".skf"
> }
> KPointsAndWeights = SupercellFolding {
> 21 0 0
> 0 21 0
> 0 0 21
> 0.0 0.0 0.0
> }
>
> SpinPolarisation = NonColinear {
> InitialSpins = {
> AtomSpin = {
> Atoms = 1:-1
> SpinPerAtom = 0.0 0.0 1.0
> }
> }
> }
> SpinConstants = {
> Ni = {
> # Wss Wsp Wsd Wps Wpp Wpd Wds Wdp Wdd
> -0.016 -0.012 -0.003 -0.012 -0.022 -0.001 -0.003 -0.001 -0.018
> }
> }
> Filling = MethfesselPaxton {
> Temperature [K] = 0.0
> Order = 2
> }
> }
> !
>
> dftb+
>
> echo $a >> SUMMARY
> grep Mermin detailed.out >> SUMMARY
>
> done
> ============
>
> The resulting output looks like this:
>
> 3.49
> Total Mermin free energy: -1.9957949329 H -54.3083 eV
> 3.50
> Total Mermin free energy: -1.9991749718 H -54.4003 eV
> 3.51
> Total Mermin free energy: -2.0024539886 H -54.4895 eV
> 3.52
> Total Mermin free energy: -2.0055871453 H -54.5748 eV
> 3.53
> Total Mermin free energy: -2.0085331500 H -54.6550 eV
> 3.54
> Total Mermin free energy: -2.0112561646 H -54.7291 eV
> 3.55
> Total Mermin free energy: -2.0137270004 H -54.7963 eV
> 3.56
> Total Mermin free energy: -2.0159245062 H -54.8561 eV
> 3.57
> Total Mermin free energy: -2.0178337657 H -54.9081 eV
> 3.58
> Total Mermin free energy: -2.0194447286 H -54.9519 eV
> 3.59
> Total Mermin free energy: -2.0207743557 H -54.9881 eV
> 3.60
> Total Mermin free energy: -2.0218200760 H -55.0165 eV
>
>
> The bulk lattice parameter for fcc-Ni is about 3.52 A... clearly, the
> energy is still decreasing monotonically at 3.60 A. Am I doing
> something trivially wrong here or were the Slater-Koster parameters
> not fit to the bulk fcc phase?
>
> thanks,
> -Ashwin.
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 07 Dec 2010 15:42:57 -0300
> From: Reinaldo Pis Diez <reinaldo.pisdiez at gmail.com>
> Subject: Re: [DFTB-Plus-User] Problems with Ni-Ni parameter set
> To: User list for DFTB+ related questions
> <dftb-plus-user at dftb-plus.info>
> Message-ID: <4CFE8031.2010109 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear Ashwin,
>
> The only parameters for nickel I could found are those from the
> trans3d set. The short description accompanying that set states that
> it was developed to simulate biological systems. Thus, I guess that
> parameters for nickel should reproduce well some results for Ni(II)
> within bio-inorganic systems.
> In other words, it is not strange that you are unable to find the
> expected lattice constant for bulk nickel.
> Regards,
>
> Reinaldo
>
> On 12/07/2010 03:09 PM, Ashwin Ramasubramaniam wrote:
>> Hello,
>>
>> I seem to be having trouble getting the Ni-Ni parameter set to
>> correctly reproduce the bulk Ni fcc structure with the trans3d
>> parameter set. I try to generate an energy vs. lattice parameter curve
>> using the script below:
>>
>> =========
>> #! /bin/bash
>>
>> for a in 3.49 3.50 3.51 3.52 3.53 3.54 3.55 3.56 3.57 3.58 3.59 3.60
>> do
>>
>> b=$(echo "$a/2"|bc -l)
>>
>> cat>dftb_in.hsd<<!
>> Geometry = {
>> Periodic = Yes
>> LatticeVectors [Angstrom] = {
>> $b $b 0.0
>> $b 0.0 $b
>> 0.0 $b $b
>> }
>> TypeNames = { "Ni" }
>> TypesAndCoordinates [relative] = {
>> 1 0.00 0.00 0.00
>> }
>> }
>>
>> Hamiltonian = DFTB {
>> SCC = Yes
>> SCCTolerance = 1e-5
>> MaxAngularMomentum = {
>> Ni = "d"
>> }
>> SlaterKosterFiles = Type2FileNames {
>> Prefix = ""
>> Separator = "-"
>> Suffix = ".skf"
>> }
>> KPointsAndWeights = SupercellFolding {
>> 21 0 0
>> 0 21 0
>> 0 0 21
>> 0.0 0.0 0.0
>> }
>>
>> SpinPolarisation = NonColinear {
>> InitialSpins = {
>> AtomSpin = {
>> Atoms = 1:-1
>> SpinPerAtom = 0.0 0.0 1.0
>> }
>> }
>> }
>> SpinConstants = {
>> Ni = {
>> # Wss Wsp Wsd Wps Wpp Wpd Wds Wdp Wdd
>> -0.016 -0.012 -0.003 -0.012 -0.022 -0.001 -0.003 -0.001 -0.018
>> }
>> }
>> Filling = MethfesselPaxton {
>> Temperature [K] = 0.0
>> Order = 2
>> }
>> }
>> !
>>
>> dftb+
>>
>> echo $a>> SUMMARY
>> grep Mermin detailed.out>> SUMMARY
>>
>> done
>> ============
>>
>> The resulting output looks like this:
>>
>> 3.49
>> Total Mermin free energy: -1.9957949329 H -54.3083 eV
>> 3.50
>> Total Mermin free energy: -1.9991749718 H -54.4003 eV
>> 3.51
>> Total Mermin free energy: -2.0024539886 H -54.4895 eV
>> 3.52
>> Total Mermin free energy: -2.0055871453 H -54.5748 eV
>> 3.53
>> Total Mermin free energy: -2.0085331500 H -54.6550 eV
>> 3.54
>> Total Mermin free energy: -2.0112561646 H -54.7291 eV
>> 3.55
>> Total Mermin free energy: -2.0137270004 H -54.7963 eV
>> 3.56
>> Total Mermin free energy: -2.0159245062 H -54.8561 eV
>> 3.57
>> Total Mermin free energy: -2.0178337657 H -54.9081 eV
>> 3.58
>> Total Mermin free energy: -2.0194447286 H -54.9519 eV
>> 3.59
>> Total Mermin free energy: -2.0207743557 H -54.9881 eV
>> 3.60
>> Total Mermin free energy: -2.0218200760 H -55.0165 eV
>>
>>
>> The bulk lattice parameter for fcc-Ni is about 3.52 A... clearly, the
>> energy is still decreasing monotonically at 3.60 A. Am I doing
>> something trivially wrong here or were the Slater-Koster parameters
>> not fit to the bulk fcc phase?
>>
>> thanks,
>> -Ashwin.
>> _______________________________________________
>> DFTB-Plus-User mailing list
>> DFTB-Plus-User at dftb-plus.info
>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 08 Dec 2010 06:41:46 +0100
> From: B?lint Aradi <balint.aradi at bccms.uni-bremen.de>
> Subject: Re: [DFTB-Plus-User] Problems with Ni-Ni parameter set
> To: User list for DFTB+ related questions
> <dftb-plus-user at dftb-plus.info>
> Message-ID: <4CFF1A9A.6080207 at bccms.uni-bremen.de>
> Content-Type: text/plain; charset="utf-8"
>
>> The only parameters for nickel I could found are those from the
>> trans3d set. The short description accompanying that set states that
>> it was developed to simulate biological systems. Thus, I guess that
>> parameters for nickel should reproduce well some results for Ni(II)
>> within bio-inorganic systems.
>> In other words, it is not strange that you are unable to find the
>> expected lattice constant for bulk nickel.
>> Regards,
>>
>
> Yes, it is as Reinaldo says. This set was never tested for bulk
> systems. So, there is a good chance, the the repulsive potential is too
> long ranged, giving strange effects in bulk.
>
> Best regards,
>
> B?lint
>
> --
> Dr. B?lint Aradi
> Bremen Center for Computational Materials Science, University of Bremen
> http://www.bccms.uni-bremen.de/en/~b_aradi
>
>
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