Re: [SIESTA-L] Nose MD
I am trying to run a constant temperature NOSE MD at 1500K. But each time, my job hangs at MD step 1. Can anyone help? Show your input and output files, otherwise it's hard to geuss where the error comes from. Also how is the atom projected DOS computed? The .EIG file contains the eigenvalues for total DOS but I don't seem to find any option to compute the projected DOS in the user manual Use the %block ProjectedDensityOfStates It will create DOS and PDOS files. PDOS is computed based on the population analysis of the atomic orbitals (more correctly, on each zeta) that you specify (i.e. DZ, DZP, etc.)
Re: [SIESTA-L] Large forces on Oxygens in SiO4H4
Thanks! Actually, that seems to have made the DFT calculations stable.
However, I must not be understanding what some features of the atom
program mean. When I had the core correction radius at the very small
value of 0.075, I got excellent agreement between the AE core charge
and PS core charge (as given by gnuplot charge.gplot) at all values of
r. When I increase the value to 0.66, I get good agreement beyond
0.66, but very poor before it (the PS charge curves are usually much
smaller than AE). In the atom manual, it says that the 4th column of
the PSCHARGE file contains the core charge density, multiplied by
4*pi*r**2 (so integrating this function up to some value r, gives the
total charge enclosed in r). With such large differences in the
charge density, the total charge contained within the cutoff is very
different between the PS and AE results. I read in Troullier and
Martins (1991) that a good pseudopotential encloses the same charge
density at the cutoff as the AE result. So as far as I'm
understanding it, by increasing the core correction radius to 0.66,
I'm getting stable DFT results, but no longer have "good"
pseudopotentials. What am I missing here?
I have attached a figure of gnuplot charge.gplot when the core
correction radius is set to 0.66.
Sincerely,
Sterling Paramore
On 7/3/07, Wolfgang Voegeli <[EMAIL PROTECTED]> wrote:
Dear Sterling,
Maybe your problem is caused by the very small radius for the core correction
in the pseudopotential input file. This leads to a very hard pseudopotential,
which is difficult to describe with the real-space grid. Increasing the
meshcutoff reduces the error, but the forces for a meshcutoff of 2000 Ry are
still 10 times higher than for the other atoms.
i think a rule of thumb for the radius for the partial core correction is the
radius where the valence and core charge are about equal. I recommend you to
try to increase the radius to something like that. The core radii in your
input file are also quite small, the O pseudopotential on the siesta webpage
uses 1.15 bohr.
For good results you will still have to increase the meshcutoff to 200-300 Ry.
Best regards,
Wolfgang
On Tuesday 03 July 2007 07:32, Sterling Paramore wrote:
> Dear SIESTA users,
>
> I'm very new to SIESTA, and I'm having a few problems generating
> pseudopotentials (PP) for Oxygen for use in simulations of
> orthosilicic acid (SiO4H4). I'm trying to follow the work of Ma,
> Foster, and Nieminen (2005,JCP 122, p144709) carefully, so I'm using
> GGA with the PBE functional (I've also been checking it with RPBE,
> which supposedly gives better agreement with experiment). I generated
> the PPs for O using the atom program with the following input file:
>
>pe Oxygen
> tm2 2.0 # PS flavor, logder R
> n=O c=rp # Symbol, XC flavor,{ |r|s}
>0.0
> 14 # norbs_core, norbs_valence
> 20 2.00 0.00 # 2s2
> 21 4.00 0.00 # 2p2
> 32 0.00 0.00 # 3d0
> 43 0.00 0.00 # 4f0
> 0.60 0.60 0.60 0.60 0.00 0.075
>
> With the above values, I get good agreement between the all-electron
> and pseudopotential orbital eigenvalues. I generated PP for Si and H
> using very similar input files as well. The problem I'm having is
> that when I go to run a SIESTA calculation (e.g, verlet MD or CG
> minimization), the forces on the oxygen atoms are 3-4 ORDERS of
> MAGNITUDE larger than the forces on the Si or H atoms. Obviously,
> this is not correct.
>
> The strangest issue I'm seeing is that if I generate the O PP with CA
> instead of RP (or PB), and then run SIESTA using GGA and PBE, the
> forces on the Os are comparable to those on Si and H (more like what I
> would expect). This suggests that there's some sort of instability
> that is being generated in the PP when using PB. However, I have
> tried varying just about everything I can in the PP generation with no
> luck. I have tried changing the cutoff from 0.40-2.00, using the full
> core charge by setting rcore_flag=-1, not using the new core
> correction at all (via pg), and even tried using the spin versions.
>
>
> The SIESTA input file I've been using is given below. If anyone has
> any ideas what I might be doing wrong, I'd really appreciate any help.
>
> Sincerely,
> Sterling Paramore
>
> #
> ---
>-- # FDF for orthosilicic acid
> #
> #
> ---
>--
>
> SystemName Orthosilicic Acid
> SystemLabelSiO4H4
>
> #
> ### Species identification
> #
>
> NumberOfSpecies3
> NumberOfAtoms 9
>
> %block ChemicalSpeciesLabel
> 1 14 Si
> 2 8 O
> 3 1 H
> %endblock ChemicalSpeciesLabel
>
> #
> ### DFT Definitions
>
> XC.functional GGA
> XC.authors RPBE
>
> #
> ### Basis Definiti
Re: [SIESTA-L] Pseud for Gd and Er
Hi Kitaura, Looks like materials with f electrons are tricky beasts to describe with DFT. I have seen recently a PRL from 2000 (Chris J. Pickard et al) where the authors use ultrasoft pseudos to describe these materials. However, one of their conclusions is that they need to use GGA and they get lattice constants which are in the usual 1% agreement of the method, while they claim that LDA gives pretty bad results. Are you using GGA or LDA? Maybe nonlinear core corrections, if you haven't included them, could be of help to improve your results. Marcos > Dear Siesta users, > > Could somebody provide me a pseudopotential and basis-set files of Gd and > Er. > I can not obtain accurate results such as lattice constant, bulk modulus > when using > pseudopotential I created by myself. I need these files! > I would appreciate your any hints or help. > Thanks in advance. > > Best regards, > R. Kitaura > -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Condensed Matter and Statistical Physics Sector International Centre for Theoretical Physics Trieste, Italy I have become so addicted to vi that I try to exit OpenOffice by typing :wq!
Re: [SIESTA-L] Large forces on Oxygens in SiO4H4
Dear Sterling,
Maybe your problem is caused by the very small radius for the core correction
in the pseudopotential input file. This leads to a very hard pseudopotential,
which is difficult to describe with the real-space grid. Increasing the
meshcutoff reduces the error, but the forces for a meshcutoff of 2000 Ry are
still 10 times higher than for the other atoms.
i think a rule of thumb for the radius for the partial core correction is the
radius where the valence and core charge are about equal. I recommend you to
try to increase the radius to something like that. The core radii in your
input file are also quite small, the O pseudopotential on the siesta webpage
uses 1.15 bohr.
For good results you will still have to increase the meshcutoff to 200-300 Ry.
Best regards,
Wolfgang
On Tuesday 03 July 2007 07:32, Sterling Paramore wrote:
> Dear SIESTA users,
>
> I'm very new to SIESTA, and I'm having a few problems generating
> pseudopotentials (PP) for Oxygen for use in simulations of
> orthosilicic acid (SiO4H4). I'm trying to follow the work of Ma,
> Foster, and Nieminen (2005,JCP 122, p144709) carefully, so I'm using
> GGA with the PBE functional (I've also been checking it with RPBE,
> which supposedly gives better agreement with experiment). I generated
> the PPs for O using the atom program with the following input file:
>
>pe Oxygen
> tm2 2.0 # PS flavor, logder R
> n=O c=rp # Symbol, XC flavor,{ |r|s}
>0.0
> 14 # norbs_core, norbs_valence
> 20 2.00 0.00 # 2s2
> 21 4.00 0.00 # 2p2
> 32 0.00 0.00 # 3d0
> 43 0.00 0.00 # 4f0
> 0.60 0.60 0.60 0.60 0.00 0.075
>
> With the above values, I get good agreement between the all-electron
> and pseudopotential orbital eigenvalues. I generated PP for Si and H
> using very similar input files as well. The problem I'm having is
> that when I go to run a SIESTA calculation (e.g, verlet MD or CG
> minimization), the forces on the oxygen atoms are 3-4 ORDERS of
> MAGNITUDE larger than the forces on the Si or H atoms. Obviously,
> this is not correct.
>
> The strangest issue I'm seeing is that if I generate the O PP with CA
> instead of RP (or PB), and then run SIESTA using GGA and PBE, the
> forces on the Os are comparable to those on Si and H (more like what I
> would expect). This suggests that there's some sort of instability
> that is being generated in the PP when using PB. However, I have
> tried varying just about everything I can in the PP generation with no
> luck. I have tried changing the cutoff from 0.40-2.00, using the full
> core charge by setting rcore_flag=-1, not using the new core
> correction at all (via pg), and even tried using the spin versions.
>
>
> The SIESTA input file I've been using is given below. If anyone has
> any ideas what I might be doing wrong, I'd really appreciate any help.
>
> Sincerely,
> Sterling Paramore
>
> #
> ---
>-- # FDF for orthosilicic acid
> #
> #
> ---
>--
>
> SystemName Orthosilicic Acid
> SystemLabelSiO4H4
>
> #
> ### Species identification
> #
>
> NumberOfSpecies3
> NumberOfAtoms 9
>
> %block ChemicalSpeciesLabel
> 1 14 Si
> 2 8 O
> 3 1 H
> %endblock ChemicalSpeciesLabel
>
> #
> ### DFT Definitions
>
> XC.functional GGA
> XC.authors RPBE
>
> #
> ### Basis Definitions
> #
>
> User-Basis .false.
> #PAO.BasisSize SZ
> PAO.BasisSize DZP
> PAO.BasisType split
>
> PAO.EnergyShift 272 meV
>
>
> #
> #Boundary Conditions
> #
>
> LatticeConstant 0. Ang
>
> %block LatticeVectors
> 1.000 0.000 0.000
> 0.000 1.000 0.000
> 0.000 0.000 1.000
> %endblock LatticeVectors
>
>
> AtomicCoordinatesFormat Ang
> %block AtomicCoordinatesAndAtomicSpecies
> -0.968900.876400.04850 1
> -1.834701.939201.08230 2
> 0.225001.75900 -0.81420 2
> -0.21160 -0.346300.98630 2
> -2.058700.15050 -1.06140 2
> -1.49050 -0.43130 -1.62660 3
> -0.284602.43880 -1.32300 3
> -1.140202.360201.64900 3
> 0.429900.140101.56310 3
> %endblock AtomicCoordinatesAndAtomicSpecies
>
> #
> # MD Definitions
> #
>
> WriteForces .true.
>
> MD.TypeOfRun CG
> MD.NumCGsteps 10
[SIESTA-L] Large forces on Oxygens in SiO4H4
Dear SIESTA users,
I'm very new to SIESTA, and I'm having a few problems generating
pseudopotentials (PP) for Oxygen for use in simulations of
orthosilicic acid (SiO4H4). I'm trying to follow the work of Ma,
Foster, and Nieminen (2005,JCP 122, p144709) carefully, so I'm using
GGA with the PBE functional (I've also been checking it with RPBE,
which supposedly gives better agreement with experiment). I generated
the PPs for O using the atom program with the following input file:
pe Oxygen
tm2 2.0 # PS flavor, logder R
n=O c=rp # Symbol, XC flavor,{ |r|s}
0.0
14 # norbs_core, norbs_valence
20 2.00 0.00 # 2s2
21 4.00 0.00 # 2p2
32 0.00 0.00 # 3d0
43 0.00 0.00 # 4f0
0.60 0.60 0.60 0.60 0.00 0.075
With the above values, I get good agreement between the all-electron
and pseudopotential orbital eigenvalues. I generated PP for Si and H
using very similar input files as well. The problem I'm having is
that when I go to run a SIESTA calculation (e.g, verlet MD or CG
minimization), the forces on the oxygen atoms are 3-4 ORDERS of
MAGNITUDE larger than the forces on the Si or H atoms. Obviously,
this is not correct.
The strangest issue I'm seeing is that if I generate the O PP with CA
instead of RP (or PB), and then run SIESTA using GGA and PBE, the
forces on the Os are comparable to those on Si and H (more like what I
would expect). This suggests that there's some sort of instability
that is being generated in the PP when using PB. However, I have
tried varying just about everything I can in the PP generation with no
luck. I have tried changing the cutoff from 0.40-2.00, using the full
core charge by setting rcore_flag=-1, not using the new core
correction at all (via pg), and even tried using the spin versions.
The SIESTA input file I've been using is given below. If anyone has
any ideas what I might be doing wrong, I'd really appreciate any help.
Sincerely,
Sterling Paramore
# -
# FDF for orthosilicic acid
#
# -
SystemName Orthosilicic Acid
SystemLabelSiO4H4
#
### Species identification
#
NumberOfSpecies3
NumberOfAtoms 9
%block ChemicalSpeciesLabel
1 14 Si
2 8 O
3 1 H
%endblock ChemicalSpeciesLabel
#
### DFT Definitions
XC.functional GGA
XC.authors RPBE
#
### Basis Definitions
#
User-Basis .false.
#PAO.BasisSize SZ
PAO.BasisSize DZP
PAO.BasisType split
PAO.EnergyShift 272 meV
#
#Boundary Conditions
#
LatticeConstant 0. Ang
%block LatticeVectors
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
-0.968900.876400.04850 1
-1.834701.939201.08230 2
0.225001.75900 -0.81420 2
-0.21160 -0.346300.98630 2
-2.058700.15050 -1.06140 2
-1.49050 -0.43130 -1.62660 3
-0.284602.43880 -1.32300 3
-1.140202.360201.64900 3
0.429900.140101.56310 3
%endblock AtomicCoordinatesAndAtomicSpecies
#
# MD Definitions
#
WriteForces .true.
MD.TypeOfRun CG
MD.NumCGsteps 10
