Re: [Pw_forum] kp

[ashkan shekaari]

Dear Giovanni,
Thank you so much for your explanatory response. So, as I understood, there
is no way to calculate band structure for a molecule and this is
nonsensical. Is it true?

On Nov 29, 2016 1:46 AM,  wrote:

> Just to add that plain wave is not a good approximation to reproduce
> molecular orbitals.
>
> Mortaza A
>
> PhD of Physics
> Ulm University, Germany
>
> On 28 Nov 2016, at 21:43, Giovanni Cantele 
> wrote:
>
> if you try to ask the question: "what the k-point mesh is for?" you can
> easily understand
> that a k-point mesh is for the Brillouin zone (BZ) sampling, that is,
> perform sums over k-points
> that approximate, with a required level of accuracy, the integral over the
> whole BZ. This is
> because in a crystal, the energy E(K) depends on the k vectors, and the
> same holds for the
> wave functions. However, when you build for example a cubic supercell
> including vacuum to
> simulate a molecule, you are actually dealing with a fictitious cubic
> crystal where the repeated
> units are sufficiently far apart from each other to not interact.
>
> Absence of interaction means flat (atomic-like) energy levels, that do not
> have dependence
> on the k vector. That is, the E(K) dispersion that you get in the case of
> a molecule, provided
> you include a sufficient vacuum space in your supercell, does not depend
> on k. If this is
> the case, you can use only the gamma point (a larger grid means large but
> useless
> computational time, because you are summing over eigenvalues at different
> k-points that
> are all the same!) for self consistency and BZ path is not needed, because
> if you select any
> path you should get flat, k-independent bands
>
> Giovanni
>
>
> On 28 Nov 2016, at 18:12, ashkan shekaari  wrote:
>
> Dear experts,
>
> Is it necessary using kpoint mesh when we are dealing with molecules?
>
> In the case of a molecule in cubic vacuum, what path in BZ should be
> selected?
> *--*
> *Regards,*
> *Ashkan Shekaari*
> *Plasma Physics Research Center*
> *Science and Research Branch*
> *I A U, 14778-93855 Tehran, Iran.*
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Re: [Pw_forum] kp

[meisam . a63]

Just to add that plain wave is not a good approximation to reproduce molecular 
orbitals.

Mortaza A

PhD of Physics 
Ulm University, Germany 

> On 28 Nov 2016, at 21:43, Giovanni Cantele  
> wrote:
> 
> if you try to ask the question: "what the k-point mesh is for?" you can 
> easily understand
> that a k-point mesh is for the Brillouin zone (BZ) sampling, that is, perform 
> sums over k-points
> that approximate, with a required level of accuracy, the integral over the 
> whole BZ. This is
> because in a crystal, the energy E(K) depends on the k vectors, and the same 
> holds for the
> wave functions. However, when you build for example a cubic supercell 
> including vacuum to
> simulate a molecule, you are actually dealing with a fictitious cubic crystal 
> where the repeated
> units are sufficiently far apart from each other to not interact.
> 
> Absence of interaction means flat (atomic-like) energy levels, that do not 
> have dependence
> on the k vector. That is, the E(K) dispersion that you get in the case of a 
> molecule, provided
> you include a sufficient vacuum space in your supercell, does not depend on 
> k. If this is
> the case, you can use only the gamma point (a larger grid means large but 
> useless
> computational time, because you are summing over eigenvalues at different 
> k-points that 
> are all the same!) for self consistency and BZ path is not needed, because if 
> you select any
> path you should get flat, k-independent bands
> 
> Giovanni
> 
> 
>> On 28 Nov 2016, at 18:12, ashkan shekaari  wrote:
>> 
>> Dear experts,
>> 
>> Is it necessary using kpoint mesh when we are dealing with molecules?
>> 
>> In the case of a molecule in cubic vacuum, what path in BZ should be 
>> selected?
>> --
>> Regards,
>> Ashkan Shekaari
>> Plasma Physics Research Center
>> Science and Research Branch
>> I A U, 14778-93855 Tehran, Iran.
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Re: [Pw_forum] spin-orbit interaction + pressure

[Maksim Markov]

Dear Maxim,

The results depend on pseudopotential you use. For example, you might have
different exchange-correlation parts or include (or not include) semi-core
states in valence. In this case it is not surprising that you have
different
results.

Best regards,

Maksim Markov, Doctorant
Laboratoire des Solides Irradies
Ecole Polytechnique

Route de Saclay
91128 Palaiseau

tel: +33 1 69 33 44 97


> Dear Lorenzo,
>
> I have a question too.
> How to get accurate total energy calculations for phase diagrams?
> I have read 2 papers from respective journals dealing with the same object
> but having (!) different results.
> In my calls I have result which is medium between these two papers.
>
> Thank you, Maxim.
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Re: [Pw_forum] Question regarding QE-GPU 6 availability

[Filippo Spiga]

On Nov 28, 2016, at 4:16 PM, Josue Itsman Clavijo Penagos 
 wrote:
> I'd like to openly answer if the GPU feature is already available for QE v. 6 
> , since I'm testing that QE version and it seems to me the GPU tarball its 
> located nowhere among the installation packages.

No, it is not. Too early for any release.

--
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Re: [Pw_forum] kp

[Giovanni Cantele]

if you try to ask the question: "what the k-point mesh is for?" you can easily 
understand
that a k-point mesh is for the Brillouin zone (BZ) sampling, that is, perform 
sums over k-points
that approximate, with a required level of accuracy, the integral over the 
whole BZ. This is
because in a crystal, the energy E(K) depends on the k vectors, and the same 
holds for the
wave functions. However, when you build for example a cubic supercell including 
vacuum to
simulate a molecule, you are actually dealing with a fictitious cubic crystal 
where the repeated
units are sufficiently far apart from each other to not interact.

Absence of interaction means flat (atomic-like) energy levels, that do not have 
dependence
on the k vector. That is, the E(K) dispersion that you get in the case of a 
molecule, provided
you include a sufficient vacuum space in your supercell, does not depend on k. 
If this is
the case, you can use only the gamma point (a larger grid means large but 
useless
computational time, because you are summing over eigenvalues at different 
k-points that 
are all the same!) for self consistency and BZ path is not needed, because if 
you select any
path you should get flat, k-independent bands

Giovanni


> On 28 Nov 2016, at 18:12, ashkan shekaari  wrote:
> 
> Dear experts,
> 
> Is it necessary using kpoint mesh when we are dealing with molecules?
> 
> In the case of a molecule in cubic vacuum, what path in BZ should be selected?
> --
> Regards,
> Ashkan Shekaari
> Plasma Physics Research Center
> Science and Research Branch
> I A U, 14778-93855 Tehran, Iran.
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[Pw_forum] B_field per Rydberg

[Mems Aghaee]

Hiplz look at the end of my scf.out:why magnetic field is per Rydberg?and how 
can i convert that to Tesla?.total energy = -253.04759495 Ry
 Harris-Foulkes estimate = -253.04758781 Ry
 estimated scf accuracy < 0.0452 RyThe total energy is the sum of the 
following terms:one-electron contribution = -127.46773250 Ry
 hartree contribution = 72.38794581 Ry
 xc contribution = -27.02379306 Ry
 ewald contribution = -170.94380974 Ry
 smearing contrib. (-TS) = -0.00020546 Rytotal magnetization = 5.00 Bohr 
mag/cell
 absolute magnetization = 5.00 Bohr mag/cell
 Magnetic field = 0.3285968 
Ryconvergence has been achieved in 6 
iterations.

and my scf.in:

 calculation = "scf",
 prefix = "Fe",
 pseudo_dir = "./",
 outdir = "./TMP",
/

 ibrav = 3,
 celldm(1) = 5.45,
constrained_magnetization = "total",
nspin=2,
fixed_magnetization (3) = 5,
 nat = 1,
 ntyp = 1,
 ecutwfc = 28,
 ecutrho = 300,
 starting_magnetization(1)=0.5
 occupations='smearing'
 smearing='mp'
 degauss=0.015
lambda=1
/

 conv_thr = 1.D-5,
 mixing_beta = 0.3D0,
/

/
ATOMIC_SPECIES
Fe 55.845 Fe.pbe-sp-van_ak.UPF
ATOMIC_POSITIONS (angstrom)
Fe 0.0 0.0 0.0
K_POINTS automatic
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Re: [Pw_forum] Running in Parallel

[Mofrad, Amir Mehdi (MU-Student)]

I used to run the older version of QE in parallel on a cluster using SLURM with 
the following command in job script and it worked fine.

  mpirun pw.x -inp $INPUTFILE


However, after I compiled it to the newer version 6, apparently the simulation 
gets frozen (it dumps some information on the output file though). It 
recognizes the parallel version also (writes down the number of processors at 
the beginning of the output file). So I can't diagnose what the problem is. Any 
help would be thoroughly appreciated.


From: pw_forum-boun...@pwscf.org  on behalf of 
Filippo SPIGA 
Sent: Wednesday, November 23, 2016 4:57:06 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] Running in Parallel

On Nov 22, 2016, at 11:48 PM, Mofrad, Amir Mehdi (MU-Student) 
 wrote:
> After I compiled version 6 I can't run it in parallel.

A bit more information about how you compiled and how your run will be useful 
to understand your problem

--
Filippo SPIGA ~ Quantum ESPRESSO Foundation ~ http://www.quantum-espresso.org


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Re: [Pw_forum] spin-orbit interaction + pressure

[Максим Арсентьев]

Dear Lorenzo,

I have a question too.
How to get accurate total energy calculations for phase diagrams?
I have read 2 papers from respective journals dealing with the same object
but having (!) different results.
In my calls I have result which is medium between these two papers.

Thank you, Maxim.
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[Pw_forum] kp

[ashkan shekaari]

Dear experts,

Is it necessary using kpoint mesh when we are dealing with molecules?

In the case of a molecule in cubic vacuum, what path in BZ should be
selected?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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Re: [Pw_forum] Question regarding QE-GPU 6 availability

[Josue Itsman Clavijo Penagos]

Thank you very much, Prof. Giannozzi. I'll look that link you kindly
provide.

-- 
*Prof. Josué Clavijo, PhD*
*Cristiano, nacido de nuevo*

Profesor Asistente
Universidad Nacional de Colombia
Sede Bogotá
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Re: [Pw_forum] Question regarding QE-GPU 6 availability

[Paolo Giannozzi]

On Mon, Nov 28, 2016 at 5:16 PM, Josue Itsman Clavijo Penagos <
jiclavi...@unal.edu.co> wrote:

>
> Also, just to clarify: Is the Adaptively Compressed Operator for EXX
>  activated just by compiling with the -D__EXX_ACE flag added inside
> make.sys after the ./configure step?
>

inside "make.inc" (new name, to prevent trouble with mailers not liking
*.sys files).


> it is almost absolutely clear to me that the public QE packages are
> already corrected
>

not sure what you mean, anyway: a few more fixes can be found in the
snapshots in http://qe-forge.org/snapshots/

Paolo
-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] spin-orbit interaction + pressure

[Andrey Chibisov]

Dear Dr. Lorenzo,
Thanks a lot for your comments.

29.11.2016, 00:22, "Lorenzo Paulatto" :
> On Monday, November 28, 2016 11:45:01 PM CET Andrey Chibisov wrote:
>>  Can I use the spin-orbit interaction with pressure?
>
> You can, because the pressur estill exists, but it cannot be computed, hence
> the following limitations apply:
> 1. you won't be able to know how much pressure you are actually applying
> without doing finite difference derivation
> 2. you won't be able to use automatic optimisation of the cell volume (i.e.
> vc-relax)
>
> hth
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Université Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www: http://www-int.impmc.upmc.fr/~paulatto/
> mail: 23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05
>
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-- 
Best regards,
Andrey Chibisov. Ph.D.
Numerical method of mathematical physics Laboratory,
Computational Center, Russian Academy of Sciences.
Khabarovsk, Russia
Web page: https://www.researchgate.net/profile/A_Chibisov
http://ru.linkedin.com/pub/andrey-chibisov/55/253/986/en
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[Pw_forum] Question regarding QE-GPU 6 availability

[Josue Itsman Clavijo Penagos]

Dear all,

I'd like to openly answer if the GPU feature is already available for QE v.
6 , since I'm testing that QE version and it seems to me the GPU tarball
its located nowhere among the installation packages.

Also, just to clarify: Is the Adaptively Compressed Operator for EXX
 activated just by compiling with the -D__EXX_ACE flag added inside
make.sys after the ./configure step? I'm asking that just in case, since it
is almost absolutely clear to me that the public QE packages are already
corrected as colleagues/fellows such as simone and others suggested
somewhere in the forum.

Best regards,


*Josué Clavijo, PhD*
*Christian, born again*

Assistant Professor
Universidad Nacional de Colombia
Sede Bogotá
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Re: [Pw_forum] BLYP

[Paolo Giannozzi]

Sorry, I meant: input_dft='b3lyp', not input_dft=b3lyp

On Mon, Nov 28, 2016 at 5:01 PM, Paolo Giannozzi 
wrote:

> input_dft='blyp', not input_dft=blyp. The best choice would be to use
> pseudopotentials caomputed for B3LYP, but since there aren't any (not that
> I know), BLYP pseudopotentials is the second best choice.
>
> Paolo
>
> On Mon, Nov 28, 2016 at 3:21 PM, ashkan shekaari 
> wrote:
>
>> Dear experts,
>>
>> Is it sensible to use input_dft=b3lyp with blyp pseudopotentials?
>> *--*
>> *Regards,*
>> *Ashkan Shekaari*
>> *Plasma Physics Research Center*
>> *Science and Research Branch*
>> *I A U, 14778-93855 Tehran, Iran.*
>>
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>>
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>


-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] Parallelization of version of QE (v. 6. 0) on cluster

[Paolo Giannozzi]

On Mon, Nov 28, 2016 at 4:48 PM, Ullah, Habib  wrote:

We recently installed QE (v.6.0) on our cluster, but it is in serial not
> parallel. Our previous version (QE 5.1.1) was successfully installed in
> parallel, but don’t know why this one is not parallelizing.
>

because "configure" does not recognize your parallel environment (compiler
and libraries). Look into file "config.log": the answer is hidden there

Paolo
-- 
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Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] BLYP

[Paolo Giannozzi]

input_dft='blyp', not input_dft=blyp. The best choice would be to use
pseudopotentials caomputed for B3LYP, but since there aren't any (not that
I know), BLYP pseudopotentials is the second best choice.

Paolo

On Mon, Nov 28, 2016 at 3:21 PM, ashkan shekaari  wrote:

> Dear experts,
>
> Is it sensible to use input_dft=b3lyp with blyp pseudopotentials?
> *--*
> *Regards,*
> *Ashkan Shekaari*
> *Plasma Physics Research Center*
> *Science and Research Branch*
> *I A U, 14778-93855 Tehran, Iran.*
>
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-- 
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Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [Pw_forum] spin-orbit interaction + pressure

[Lorenzo Paulatto]

On Monday, November 28, 2016 11:45:01 PM CET Andrey Chibisov wrote:
> Can I use the spin-orbit interaction with pressure?

You can, because the pressur estill exists, but it cannot be computed, hence 
the following limitations apply:
1. you won't be able to know how much pressure you are actually applying 
without doing finite difference derivation
2. you won't be able to use automatic optimisation of the cell volume (i.e. 
vc-relax)


hth

-- 
Dr. Lorenzo Paulatto 
IdR @ IMPMC -- CNRS & Université Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05

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[Pw_forum] BLYP

[ashkan shekaari]

Dear experts,

Is it sensible to use input_dft=b3lyp with blyp pseudopotentials?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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Re: [Pw_forum] error *** No rule to make target `../flib/ptools.a',

[Bramha Pandey]

Thank You Prof. Paolo.
Now it is working by generating make.inc file using ./configuration.

-- 
Regards
Dr. Bramha P Pandey
Asstt. Prof. ECE Deptt.
GLA University, Mathura (U.P)
India-281406.

On Sun, Nov 27, 2016 at 7:43 PM, Paolo Giannozzi 
wrote:

> On Sun, Nov 27, 2016 at 6:38 AM, Bramha Pandey 
> wrote:
>
> I have also observed that 'flib' folder is not there in qe-6.0 folder from
>> official site.
>>
>
> nor is there any need for it any longer
>
>
>> I will appreciate for your suggestions regarding this issue.
>>
>
> rebuild a new make.inc file instead of copying an old one
>
> Paolo
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
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Re: [Pw_forum] spin-orbit interaction + pressure

[Максим Арсентьев]

of course, this is like usual geom. opt. but with pressure


2016-11-28 17:45 GMT+04:00 Andrey Chibisov :

> Dear Colleagues,
> I want to apply a pressure to the silicene. The system relaxes, but the
> pressure tensor is not printed.
> There is a message:
>  Message from routine stres:
>  noncollinear stress + GGA not implemented
> Can I use the spin-orbit interaction with pressure?
>
> --
> Best regards,
> Andrey Chibisov. Ph.D.
> Numerical method of mathematical physics Laboratory,
> Computational Center, Russian Academy of Sciences.
> Khabarovsk, Russia
> Web page: https://www.researchgate.net/profile/A_Chibisov
> http://ru.linkedin.com/pub/andrey-chibisov/55/253/986/en
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-- 
Best wishes,
Maxim Arsent'ev, Ph.D. (Chemistry)
Laboratory of research of nanostructures
Institute of Silicate Chemistry of RAS
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[Pw_forum] spin-orbit interaction + pressure

[Andrey Chibisov]

Dear Colleagues,
I want to apply a pressure to the silicene. The system relaxes, but the 
pressure tensor is not printed.
There is a message:
 Message from routine stres:
 noncollinear stress + GGA not implemented
Can I use the spin-orbit interaction with pressure?

-- 
Best regards,
Andrey Chibisov. Ph.D.
Numerical method of mathematical physics Laboratory,
Computational Center, Russian Academy of Sciences.
Khabarovsk, Russia
Web page: https://www.researchgate.net/profile/A_Chibisov
http://ru.linkedin.com/pub/andrey-chibisov/55/253/986/en
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[Pw_forum] problem using "ibrav" in cp.x

[周凯旋]

Dear all!
 Before I run Cp.X, I have set the symmetry of crystal structure. So when I 
run Cp.X ,is it necessary  to set the "ibrav"? If I set the "ibrav", I always 
get an error.  %%%
 Error in routine  ortho (1):
  ortho went bananas
  

School of Renewable Energy, North China Electric Power University, 
Beijing, 102206, China




 






 






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Re: [Pw_forum] binding energy

[Giovanni Cantele]

1) maybe providing at least the inputs of the total, species1 and species2 runs 
would help

2) is E_{species1} the energy of the whole  cluster without the ligand?

3) what are the cell sizes and k-point grids used in the three calculations?

4) please kindly provide also your affiliation in posting to this forum, as 
usually requested

Giovanni

> On 28 Nov 2016, at 12:03, Moosavi Seyed Mohamad 
>  wrote:
> 
> Hi 
> 
> I calculated the binding energy of a cluster (species1) with a ligand(species 
> 2) with this formula:
> E_{total} - E_{species1} - E_{species2}
> 
> I run PAW in a cubic cell large enough to avoid periodicity effects in the 
> calculations (10 angstrom each side).
> The geometry converges very well to a 2.1 angstrom distance between species, 
> as we expected.
> 
> However, the results are surprising from two respects.
> First, the binding energy is too high. ~500 kcal/mol
> 
> Second, when I add new monomer to species2 (make a dimer), in principle, the 
> binding energy should remain constant (The bond length remains the same).
> However, I get extra ~200kcal/mol in the energy.
> 
> The number of electrons:
> cluster (species1): 499
> monomer (species2): 60
> dimer (species2): 102
> 
> So, something should be wrong with the formula or a scaling factor is  needed 
> here.
> I am wondering if you can guide me through this.
> 
> Best regards
> Mohamad
> 
> 
> ​
> 
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-- 

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele

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[Pw_forum] binding energy

[Moosavi Seyed Mohamad]

Hi

I calculated the binding energy of a cluster (species1) with a ligand(species 
2) with this formula:
E_{total} - E_{species1} - E_{species2}

I run PAW in a cubic cell large enough to avoid periodicity effects in the 
calculations (10 angstrom each side).
The geometry converges very well to a 2.1 angstrom distance between species, as 
we expected.

However, the results are surprising from two respects.
First, the binding energy is too high. ~500 kcal/mol

Second, when I add new monomer to species2 (make a dimer), in principle, the 
binding energy should remain constant (The bond length remains the same).
However, I get extra ~200kcal/mol in the energy.

The number of electrons:
cluster (species1): 499
monomer (species2): 60
dimer (species2): 102

So, something should be wrong with the formula or a scaling factor is  needed 
here.
I am wondering if you can guide me through this.

Best regards
Mohamad


?

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[Pw_forum] problem using 'vc-relax'

[Ankush Bharti]

hi



while running a calculation with 'vc-relax' following error appears
%%
 task # 0
 from scale_h : error # 1
 Not enough space allocated for radial FFT: try restarting with a larger 
cell_factor.
 %%

what is this al about?what is required to get the job done???

regards
ankush bharti

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[Pw_forum] binding energy

[Moosavi Seyed Mohamad]

?Hi


I calculated the binding energy of a cluster (species1) with a ligand(species 
2) with this formula:

E_{total} - E_{species1} - E_{species2}


I run PAW in a cubic cell large enough to avoid periodicity effects in the 
calculations (10 angstrom each side).

The geometry converges very well to a 2.1 angstrom distance between species, as 
we expected.


However, the results are surprising from two respects.

First, the binding energy is too high. ~500 kcal/mol


Second, when I add new monomer to species2 (make a dimer), in principle, the 
binding energy should remain constant (The bond length remains the same).

However, I get extra ~200kcal/mol in the energy.


The number of electrons:

cluster (species1): 499

monomer (species2): 60

dimer (species2): 102


So, something should be wrong with the formula or a scaling factor is  needed 
here.

I am wondering if you can guide me through this.


Best regards

Mohamad



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