[Pw_forum] How to show more digits in the results?

[Mike Marchywka]

> Date: Sun, 31 Aug 2014 21:41:11 -0400 
> From: akohlmey at gmail.com 
> To: pw_forum at pwscf.org 
> Subject: Re: [Pw_forum] How to show more digits in the results? 
> 
> 
> On Sep 1, 2014 1:16 AM, "Haibei Huang" 
> mailto:haibeih at student.unimelb.edu.au>> 
> wrote: 
>> 
>> Dear Axel, 
>> 
>> Thanks for your reply. 
>> 
>> The truth is that I was trying to diagonalize a matrix made of a 
> serials of Energies obtained by pw.x, while some of elements in the 
> matrix is quite small (e.g. 10^-7 or 10-^8). Thus, I would like to know 
> how many digits I could trust in Energies. Or at least I should keep 
> the Energies and these small elements in the same scale, say 10^-8. 
> 
> For that, you do _not_ need more digits for exactly the reason I gave 
> you. If you output more digits, you are just adding random numbers. 
> Literally. 

I suppose in general there could be offset problems with energies and you are 
adding
some large fixed amount to a small change of interest. Or, you could want to 
examine
the numerical issues.?

> 
>> 
>> Please let me know if you or anyone know how to change the code 
> showing more digits in pw.x. 
> 
> Many people know (including me). But why should anybody tell you, if 
> what you want is a stupid thing? Have you talked about this with your 
> adviser? 
> 
> In general, please spent a little time learning about the systematic 
> errors of DFT, the numerical precision of floating point numbers, the 
> accuracy of a self-consistent calculation and error propagation. 
> 
> You should quickly see the folly of your request. 
> 
>> Best regards 
>> Haibei 
>> 
>> 
>> On Sun, Aug 31, 2014 at 1:51 PM, Axel Kohlmeyer 
> mailto:akohlmey at gmail.com>> wrote: 
>>> 
>>> 
>>> On Aug 30, 2014 10:57 PM, "Haibei Huang" 
> mailto:haibeih at student.unimelb.edu.au>> 
> wrote: 
 
 Dear All, 
 
 I am aware of that the QE will only show at most 8 digits after 
> the decimal point in the output file, while more digits are needed in 
> my calculation. 
 
 Could any of you provide a way to increase the number digits after 
> the decimal point? 
>>> 
>>> What is the point of using more digits, when the error is larger? 
> You could just add random digits and have the same effect. 
>>> 
 
 Thanks for your time! 
 Looking forward to your reply! 
 Regards 
 Haibei 
 
 
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[Pw_forum] Conergence Delay

[Mike Marchywka]

> From: paolo.giannozzi at uniud.it
> To: pw_forum at pwscf.org
> Date: Sun, 18 May 2014 22:25:05 +0200
> Subject: Re: [Pw_forum] Conergence Delay
>
> On Sat, 2014-05-17 at 15:35 +, Elliot Menkah wrote:
>
>> I have this relax calculation running on 16 cores.
>> Its been running for the past 73 days.
>
> ... and you don't find anything strange in it?!?
>
>> Can anyone please help me understand the interpretation
>> as to when it would converge
>
> nobody can help you. Convergence depends upon many different factors.
> Ill-chosen input data or even well-chosen input data for nasty systems
> may never converge. Each self-consistency step should converge in no
> more than a few tens of iterations. If it doesn't, it is pointless
> to insist.

As I understand the situation currently, convergence is pretty much empirical?
there is not a lot of theory on what will and will not converge if you play with
the mixing parameter. Is this more or less accurate or are there specific
references that you could suggest for more details? this question is not so
much directed at the immediate point of this thread but more general curiosity.

Thanks.



>
> P.
>> . Especially the non-human-readable iteration number.
>>
>> iteration #*** ecut= 60.00 Ry beta=0.20
>> Davidson diagonalization with overlap
>> ethr = 4.68E-11, avg # of iterations = 3.4
>>
>> negative rho (up, down): 0.229E-04 0.227E-04
>>
>> total cpu time spent up to now is 5498418.9 secs
>>
>> total energy = -3906.86845896 Ry
>> Harris-Foulkes estimate = -3906.86845896 Ry
>> estimated scf accuracy < 0.0077 Ry
>>
>>
>> Kind Regards,
>>
>> Elliot
>>
>
> --
> Paolo Giannozzi, Dept. Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
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[Pw_forum] tpss: too many bands are not converged

[Mike Marchywka]

> From: paolo.giannozzi at uniud.it
> To: pw_forum at pwscf.org
> Date: Fri, 25 Apr 2014 03:42:06 +0200
> Subject: Re: [Pw_forum] tpss: too many bands are not converged
>
> On Thu, 2014-04-24 at 09:03 -0400, Mike Marchywka wrote:
>
>> By free volume, you mean places where n and likely grad everything are 
>> numerical noise?
>
> exactly: the regions of space where the charge has decayed to noise.
> Apparently (the current implementation of) meta-GGA doesn't like the
> presence of such large regions (and it doesn't seem to like H atoms
> as well). Even plain GGA diverges in those regions: it is less of a
> problem, but still, the exact energy values depend upon how the

Does it actually diverge or just reach some kind of limit cycle with
amplitude in energy greater than convergence criteria? ?

> potential is cut off. The divergence comes from gradient corrections
> to exchange: there is no divergence in atoms with the correct large-r

so this is related to PP and lack of exponential decay giving more weight
to "free volume" than it should physically have? I had been doing some
tests with analytical hydrogen since it was easy to check :) That is not noise
alone then but a modelling issue.?

> limit of the charge density, but this is not of much help in plane-wave
> calculations of condensed-matter systems.

Molecular crystals better or worse than say metals??

>From what I can tell of the TPSS "z" anyway, trying to calculate it
as a ratio of intermediate real quantities seems to allow for many errors
such as aliasing that may occur by taking magnitudes. ?I did some
algebra it looks like the magnitude of the grad of the wf angle is more direct 
but I have
not checked the math or tested it much although IIRC some related results
vs analytical hydrogen did not appear obviously wrong but this was hardly a 
complete test.



>
> (disclaimer: this is what I remember. I looked at this problem several
> years ago for meta-GGA, many years ago for GGA)


Thanks, I'm just trying to understand a few things and see if I can play with
the problematic terms and evaluate some alternatives.

>
> Paolo
>> AFAICT, the converge of SCF is largely empirical
>> as there does not seem to be much theory here. In any case, you would like 
>> to think that the areas lacking "physics" should not be that
>> big a factor in the overall calculation and if that is not the case there 
>> may be something interesting here to explore :)
>>
>>> You can try to decrease the size of the unit-cell in order to minimize the 
>>> free space it contains. Of course, this will be at the expense of the 
>>> inter-polyemer interaction you probably want to avoid.
>>>
>>> Nevertheless, this will probably not cure your problem, which to my 
>>> knowledge has no other solution than changing the meta-GGA functional to a 
>>> GGA one.
>>
>> I took a look at the "z" parameter which being a ratio could have some issue 
>> with small denominators. With some initial work,
>> it looks like there are better ways to calculate it than directly from real 
>> quantities such as n and grad mags,
>> but I am still trying to test what may be trivially wrong math :)
>> I think my latest result was something to the effect that you could reduce z 
>> to A/(A+B)( both non-negative)
>> if you calculate everything from psi and the grad of psi expressed in polar 
>> form, not much different from some formula
>> for current densities, and maybe find a limit when A and B are both zero.
>>
>> I had originally hoped to try to test it for trivial issues in JDFTX and c++ 
>> or c with libxc using an expanded interface scheme
>> to let me pass z or grad psi in polar form but it will require a bit of 
>> effort. Curious if anyone else here has examined
>> this or has literature references they care to share. Seems disconcerting 
>> that something with physical meaning would have these
>> kinds of implementation issues - perhaps something else can be learned from 
>> investigating.
>>
>> Thanks.
>>
>>> Best regards,
>>>
>>> Yves
>>>
>>>
>>>
>>> Le 24 avr. 2014 ? 13:36, Davide Tiana a ?crit :
>>>
>>>>
>>>> Dear all,
>>>> I've been trying to calculate a polymer using tpss. I already fully
>>>> optimised it with different functional (pbesol, pw91, hse) and
>>>> pseudopotential (nc, paw). For some reason (apologise my ignorance if
>>>> it should be well known) when I try to calculate using tpss nc the
>>>> system simply does not converge cra

[Pw_forum] tpss: too many bands are not converged

[Mike Marchywka]

> From: yves.ferro at univ-amu.fr
> Date: Thu, 24 Apr 2014 14:18:10 +0200
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] tpss: too many bands are not converged
>
> Dear Davide,
>
> Mete-GGA functional such as TPSS are known to have convergency problems and 
> numerical instabilities during scf cycles, specifically when the unit-cell 
> contains a lot of free volume, such as in your case probably.

By free volume, you mean places where n and likely grad everything are 
numerical noise? ?AFAICT, the converge of SCF is largely empirical
as there does not seem to be much theory here. ?In any case, you would like to 
think that the areas lacking "physics" should not be that
big a factor in the overall calculation and if that is not the case there may 
be something interesting here to explore :)

> You can try to decrease the size of the unit-cell in order to minimize the 
> free space it contains. Of course, this will be at the expense of the 
> inter-polyemer interaction you probably want to avoid.
>
> Nevertheless, this will probably not cure your problem, which to my knowledge 
> has no other solution than changing the meta-GGA functional to a GGA one.

I took a look at the "z" parameter which being a ratio could have some issue 
with small denominators. With some initial work,
it looks like there are better ways to calculate it than directly from real 
quantities such as n and grad mags,?
but I am still trying to test what may be trivially wrong math :)
I think my latest result was something to the effect that you could reduce z to 
A/(A+B)( both non-negative)
?if you calculate everything from?psi and the grad of psi expressed in polar 
form, not much different from some formula
for current densities, ?and maybe find a limit when A and B are both zero.?

I had originally hoped to try to test it for trivial issues in JDFTX and c++ or 
c with libxc using an expanded interface scheme
to let me pass z or grad psi in polar form but it will require a bit of effort. 
?Curious if anyone else here has examined
this or has literature references they care to share. Seems disconcerting that 
something with physical meaning would have these
kinds of implementation issues - perhaps something else can be learned from 
investigating.?

Thanks.

> Best regards,
>
> Yves
>
>
>
> Le 24 avr. 2014 ? 13:36, Davide Tiana a ?crit :
>
>>
>> Dear all,
>> I've been trying to calculate a polymer using tpss. I already fully
>> optimised it with different functional (pbesol, pw91, hse) and
>> pseudopotential (nc, paw). For some reason (apologise my ignorance if
>> it should be well known) when I try to calculate using tpss nc the
>> system simply does not converge crashing with this error:
>>
>> Error in routine c_bands (1):
>> too many bands are not converged
>>
>> After some reaserch in old pw-forum mails, I tried decreasing
>> mixing_beta=0.2, increasing mixing_ndim=12, as well as mixing mode TF
>> and local-TF.
>> everythings failed.
>>
>> Does anyone have any tips or idea of why the system can't converge?
>>
>> Thanks a lot,
>> Davide
>>
>>
>>
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[Pw_forum] Hubbard U on surface

[Mike Marchywka]

> Date: Tue, 22 Apr 2014 17:26:23 +0200
> From: Thomas.Brumme at impmc.upmc.fr
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Hubbard U on surface
>
> Hi,
>
> I think that this is not universal since
>
> - U in general depends on the structure of your system. The structure is
> changed due to the interaction with the surface.
> Thus, I think that there should be a difference between, e.g.,
> adsorption on Au(111) and Cu(111) since in the former case
> you might have physisorption while in the latter it is probably
> chemisorption
>
> - also an extension to other metal center is not straightforward. This
> increase in U might be happening for Fe but what
> is with Cu, or Co?

well, if you define a metal as having infinite bulk conductivity and
then consider things like image charge does that explain anything??
You could try replacing the metal with an idealized model for what you
think is causing the behavior I suppose.?


>
>
> On the other hand, if you're using the method of Cococcioni et al., U is
> calculated by changing the occupation of the iron
> d-orbitals. This occupation however depends on the system and it is
> definitely different for the molecule on the surface.
> And it crucially depends on the molecule, the metal center, the surface,
> and so on...
>
> For example, some kind of backbonding can occur. The iron donates
> electrons to the ligand. However, if you adsorb
> the molecule the ligand forms a bond with the metal surfaces (even if it
> might be weak in case of Au(111) ), and the metal
> surfaces in turn donates some charge to the iron, effectively increasing
> the occupation compare to the vacuum case.
> This might change U...
>
> Thus, I think it is not universal, but I'm not entirely sure, so please
> correct me if I'm wrong.
>
> Thomas
>
> On 04/22/2014 04:21 PM, ?? wrote:
>> Dear all:
>> I have calculated Hubbard U of transition metal coordinations like
>> Fe(porphyrin) with linear response method.I find the Hubbard U usually is
>> larger when the molecule adsorped on metal surface than it is in vaccum. Is
>> this universal? Is there any explain available?
>> Thanks.
>>
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>
> --
> Dr. rer. nat. Thomas Brumme
> Institut de Min?ralogie, de Physique des Mat?riaux, et de Cosmochimie
> Sorbonne Universit?s - UPMC Univ Paris 06
> 4 Place Jussieu
> 75005 Paris
>
> Tel: +33 (0) 1 442 77204
>
> email: Thomas.Brumme at impmc.upmc.fr
>
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[Pw_forum] QE interface with LIBXC

[Mike Marchywka]

> Date: Mon, 21 Apr 2014 14:48:03 -0400 
> From: ananyamondol3 at gmail.com 
> To: pw_forum at pwscf.org 
> Subject: [Pw_forum] QE interface with LIBXC 
> 
> Hi QE users, 
> Dose anyone have the LIBXC version of Quantum espresso? 
> I don't get any response from the authors of the QE interface with libxc. 
> Thanking You 

I have no idea about this specific issue but I was trying to put together an 
interface
for lbxc that was more or less portable to other libraries and programs. That 
is, it
is a name-value interface which would seem to be slow compared to more direct
interfaces but I think it separates the slow stuff from the computations and?
can provide a better interface while preserving the intended performance.
In the c++ implementation, the base classes provided general features for
things like dumping citations to things you actually use or getting commentary
that would otherwise be too cumbersome to include in main code.?
If you are interesting in this general topic, see my posts on the libxc mail 
list.




> Ananya 
> 
> 
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[Pw_forum] external electric field in atomic all-electron calculations

[Mike Marchywka]

> Date: Tue, 4 Feb 2014 10:56:26 -0200 
> From: fabio.campolim at gmail.com 
> To: pw_forum at pwscf.org 
> Subject: [Pw_forum] external electric field in atomic all-electron 
> calculations 
> 
> Dear PW users, 
> 
> I would like to measure the effect of an external electrical field on 
> the wavefunctions of core electrons, like very small charge 
> displacements. 
> 
> I understand "atomic" calculates all-electron isolated atoms but I find 
> no options for external field on that one. 

For JDFTX anyway I just made fhi files with no pp/projectors :) Not sure
if that works here but it should be easy to modify if not ...



> 
> On the other hand, PW does include external field but as far as I know 
> only calculates (frozen-core) valence electron orbitals. 
> 
> Is this correct? Any suggestions? 
> 
> Thanks in advance, 
> Fabio Campolim 
> Ph.D. Student, 
> Nanosciences and Advanced Materials postgraduate program 
> UFABC - Universidade Federal do ABC, Brazil 
> 
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[Pw_forum] linking quantum espresso with ACML library

[Mike Marchywka]

If no one else has an answer, I would suggest using grep etc to find references 
to the missing symbols
and see if there is anything close in the library binaries or source. Sometimes 
putting the missing symbol
names into google is useful and sometimes libraries change API's. If there are 
lots of symbols missing,
this could be pointing to a wrong directory or something very simple like that 
but that will take a little
while to find.?



> Date: Mon, 28 Oct 2013 12:53:51 -0500
> From: gryko at jsu.edu
> To: pw_forum at pwscf.org
> Subject: [Pw_forum] linking quantum espresso with ACML library
>
>
>
> Hello,
>
> I would like to ask to clarify how to link Quantum Espresso with ACML library.
> I have no problem linking with fftw3, but when I try to link with the ACML,
> it cannot find all subroutines. There several posts on ACML on the Forum,
> but I still cannot link it. My PC is 8 core AMD 8350 Vishera with 32 GB 
> memory.
>
>
> Thank you very much,
> Jan Gryko
> Jacksonville, AL
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[Pw_forum] runtime error : [btl_tcp_endpoint.c:655:mca_btl_tcp_endpoint_complete_connect] connect() to 192.168.5.164 failed: Connection refused (111)

[Mike Marchywka]

If I just put that message into google it comes up as something to do witj MPI 
and
if I read it right it is complaining about port 111 which would be plausible 
for portmap
or some similar service. Any way, if it is unable to find port 111 did you try 
to use?
netstat or nmap to see if the expected service is running and observable from 
the other machines?

If you can find enough key words you can probably find something in your LAN or 
QE or some supporting servuce
to adjust.?



> Date: Wed, 3 Jul 2013 10:20:59 +0530 
> From: dhirendra22121987 at gmail.com 
> To: pw_forum at pwscf.org 
> Subject: Re: [Pw_forum] runtime error : 
> [btl_tcp_endpoint.c:655:mca_btl_tcp_endpoint_complete_connect] 
> connect() to 192.168.5.164 failed: Connection refused (111) 
> 
> Actually I am running pw.x through PBS using qsub. System admin says 
> passwardless ssh is taken care. I can run small parallel programs but 
> when I try to run pw.x it gives above error. 
> 
> 
> On Wed, Jul 3, 2013 at 8:17 AM, 
> mailto:foster362 at gmail.com>> wrote: 
> Can you ssh between nodes (node1 to node2) and server without having to 
> enter a password? 
> 
> On Jul 2, 2013, at 2:52 PM, DHIRENDRA VAIDYA 
> mailto:dhirendra22121987 at gmail.com>> 
> wrote: 
> 
> Dear PW_forum community, 
> 
> I am new to Quantum Espresso and I am trying to instal QE on our 
> institute cluster. Compilers are installed in some non-standard 
> directory and care is taken to include paths to variable PATH and 
> LD_LIBRARY_PATH. 
> 
> With this an espresso-5.0.1 is installed with gcc-4.8.1 and 
> openmpi-1.6.5. I tried to produce bandstructure of silicon (given in 
> one of the tutorials on web). By setting #PBS -l nodes=1:ppn=4 I get 
> the bandstructure of silicon, the problem is in when #PBS -l nodes=2(or 
> higher):ppn=2(anything here). The error I get is 
> 
> [compute-0-94.local][[63421,1],2][btl_tcp_endpoint.c:655:mca_btl_tcp_endpoint_complete_connect]
>  
> connect() to 192.168.5.164 failed: Connection refused (111) 
> [compute-0-94.local][[63421,1],3][btl_tcp_endpoint.c:655:mca_btl_tcp_endpoint_complete_connect]
>  
> connect() to 192.168.5.164 failed: Connection refused (111) 
> =>> PBS: job killed: walltime 607 exceeded limit 600 
> mpiexec: killing job... 
> 
> 
> Neither I nor our system admin doesnt know about this error. Can 
> someone please tell me what this error is about. There is very little 
> help on web about this error and solution to add --mca [with some 
> options] doesnt seem to work for me. 
> -- 
> Thanks a lot, 
> Dhirendra Vaidya, 
> IIT Bombay 
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> 
> 
> -- 
> Warm Regards, 
> Dhirendra Vaidya 
> 
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[Pw_forum] Periodicity

[Mike Marchywka]

> Date: Thu, 27 Jun 2013 06:06:37 +0200
> From: akohlmey at gmail.com
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] Periodicity
>
> On Thu, Jun 27, 2013 at 5:53 AM, Yantao Wu  wrote:
>> Dear Axel,
>>
>> Thank you very much for your reply. I understand that the energy wouldn't
>> exactly be doubled if you just put two identical systems together. But if QE
>> does treat the system as an infinite lattice, what is exactly the meaning of
>> the total energy in the output? How does QE obtain this output energy from
>> the calculated band energies in a manner that is proportional to the size of
>> the supercell. That is, I don't quite understand why you say
>>
>> "the reason that you *do* get exactly twice the energy if you double
>> the system (and reduce the kpoint grid corresspondingly) is exactly
>> proof of that."
>
> the total energy of an infinite system is ... infinity. so that is a
> pointless quantity.
> what you do get is the energy of _one unit cell_ *in* the infinite system.
> this one unit cell has interactions with its periodic neighbors (is
> the cell itself).
> perhaps you should look up how Ewald summation works to see how you
> can compute the energy of a unit cell in an intinitely large lattice.
>
> if you have an isolated unit cell, you have no interactions with
> periodic neighbors. so doubling the system, *significantly* changes
> the energy from double the single system. however, doubling a unit
> cell in a periodic system should give you exactly double the energy.
> the one thing that may make this not exactly double is k-point
> sampling you have to make sure that your sampling of k-space is the
> same, so you have to reduce the k-point grid, if you double the unit
> cell.
>
> if this still confuses you, you should look things up in a text book.
> there are several really good ones around that cover electronic
> structure calculations in condensed matter physics.


Many universities have good lecture notes online and of course full text?
theses on google scholar can provide a lot of introductory. citeseer has lots 
of math and computer
related academic work. I usually end up going to wikipedia
for many quick references- in fact I think I did just check them for Ewald sum 
and looking up how?
lattice vectors are?defined. You can not always assume it to be accurate but 
often it is fine.




>
> axel.
>
> p.s.: the arguments also hold for classical interaction models of
> point charges and empirical potentials
>
>
>>
>> Thanks,
>> Yantao
>>
>>
>> On Wed, Jun 26, 2013 at 8:28 PM, Axel Kohlmeyer  
>> wrote:
>>>
>>> there is no contradiction.
>>>
>>> QE *does* treat your system as if it was periodic and thus a _unit
>>> cell of an infinite crystal_.
>>> the reason that you *do* get exactly twice the energy if you double
>>> the system (and reduce the kpoint grid corresspondingly) is exactly
>>> proof of that. if it would treat just the input system, the energy of
>>> the double size system would be the energy of the two halves *plus*
>>> the interaction energy between them.
>>>
>>> does that make sense?
>>> axel.
>>>
>>> On Thu, Jun 27, 2013 at 5:10 AM, Yantao Wu  wrote:
 Dear QE users,

 I have a general question on how QE treats periodicity of the system,
 e.g. a
 bcc lattice. I originally thought QE only calculates the wave function
 for
 the system you input into the program and enforce the Bloch periodic
 boundary condition of Psi(r+R) = exp(ikR)Psi(r) on the wave-functions,
 where
 R, the lattice constant, QE knows from the input of ibrav. In this case,
 QE
 doesn't "know" anything about the infinite lattice that may be inferred
 from
 the input system.

 But then I was told the other day that QE actually infers the infinite
 lattice from the input system and calculates the wave-function for the
 infinite system. Even though this sounds appealing to me, I'm still
 confused
 by one seeming paradox. That is, if I double the size of the input
 system
 but making sure that the infinite lattice inferred from this
 double-sized
 system be the same as the original system, then the energy calculated
 for
 the double-sized system will be almost precisely double of the energy of
 the
 original system. This makes me feel like that QE treats the system of
 interest to be just what the input system is.

 Can anyone clarify how exactly is periodicity treated in QE?

 Thank you much,
 Yantao Wu,
 Undergraduate Student,
 Harvey Mudd College 15'

 ___
 Pw_forum mailing list
 Pw_forum at pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>> ___
>>> Pw_forum 

[Pw_forum] graphene with Li input problem

[Mike Marchywka]

> Date: Sat, 15 Jun 2013 13:10:03 +0200
> From: akohlmey at gmail.com
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] graphene with Li input problem
>
> On Sat, Jun 15, 2013 at 12:48 PM, Mike Marchywka  
> wrote:
>> 
>>> Date: Sat, 15 Jun 2013 10:40:21 +0200
>>> From: akohlmey at gmail.com
>>> To: pw_forum at pwscf.org
>>> Subject: Re: [Pw_forum] graphene with Li input problem
>>>
>>>> If you have potentials and wavefunctions, how would you define bonds?
>>>
>>> that is what the DFT calculation is for. remember that bonds exist
>>
>> Yes but what techniques may you want to use to present these in
>> an artists conception that may be useful for either understanding the 
>> molecule or
>> debugging code and algorithm?
>
> this is why paolo commented, that you can make a career out of it.
> there *is* no unique and easy definition. if you want to have some

Yeah, I wasn't sure if there were libraries for this like there are for 
exchange-correlation
functionals. The link you give below
looks like it will help me look into some of these things when I have
something to visualize :) ?I'll check google scholar as I wait for my other code
to compile or run, just thought it was relevant to add to this thread. Thanks.?


> fun, get hold of a large group of organic chemists and start a
> discussion about aromaticity and how you can define and identify it,
> and particularly how you should draw the resulting structure. you
> probably need to run away quickly, because of the riot that will
> begin.
>
> if you look at this less religiously, there are some rather simplistic
> ways, that often work very well. e.g. you define an effective atom
> radius and then use a purely geometric criterion. that is how most
> molecular viz programs work. if they get things wrong, they often
> misidentify the element, or make assumptions about its oxidation
> state, that don't hold. remember, that bonds are typically important
> for organic molecules, where you have mostly the elements H, C, N, O
> where the simple geometric approach works quite well.
>
> beyond that, you can do (empirical) increment systems or charge
> equilibration and use that to assign "a bond order" based on the
> number of available valences. again, this is working ok, for as long
> as you have only s- and p- electrons to deal with.
>
> there also are electron density based methods like "atoms in
> molecules" and "ELF" that partition the electron density and allow to
> do some analysis based on that which can be used to assign (and
> compare) bonds. but those are not perfect either.
>
>> I guess if you were going to use some set of definitions you could write
>> a program to take dft output analyze it and output some bond or graphical
>> information to display in pymol or whatever. Not sure what formats
>> for input or output or how to contemplate a library of analysis methods to
>> find "bonds."
>
> see above. in my personal opinion, there are two choices: 1) you get
> religious about this and will either be never satisfied yourself or
> not be able to satisfy everybody or both or option 2) tell yourself
> that it is not that important and learn how to "futz it up", in case
> the simpleminded guess doesn't work.
> i have opted for the second option and spent my time rather to make
> the futzing simpler and wrote a VMD plugin for it (and for setting up
> topologies for classical MD)
> https://sites.google.com/site/akohlmey/software/topotools
>
> axel.
>
>
>> note new address
>> Mike Marchywka 2295 Collinworth Drive Marietta GA 30062.
>> formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)<- leave 
>> message 989-348-4796 (P)<- emergency
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
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>   

[Pw_forum] graphene with Li input problem

[Mike Marchywka]

t;
>>> and this is what you get (* = in another cell):
>>>
>>> species: C - C 0.00 < D < 1.00
>>> atoms: 1 2 distance = 0.82197 A
>>> atoms: 3 5 distance = 0.82197 A
>>> atoms: 3 4 distance = 0.82197 A
>>> atoms: 5 6 distance = 0.82197 A
>>> atoms: 1 4* distance = 0.82197 A
>>> atoms: 2 6* distance = 0.82197 A
>>> atoms: 1 5 distance = 0.82198 A
>>> atoms: 2 3* distance = 0.82198 A
>>> atoms: 4 6* distance = 0.82198 A
>>> C 1: neighbors at 0.822 0.822 0.822
>>> d(center): 1.104 A angles : 120.0 120.0 120.0
>>> C 2: neighbors at 0.822 0.822 0.822
>>> d(center): 1.801 A angles : 120.0 120.0 120.0
>>> C 3: neighbors at 0.822 0.822 0.822
>>> d(center): 1.104 A angles : 120.0 120.0 120.0
>>> C 4: neighbors at 0.822 0.822 0.822
>>> d(center): 1.801 A angles : 120.0 120.0 120.0
>>> C 5: neighbors at 0.822 0.822 0.822
>>> d(center): 1.104 A angles : 120.0 120.0 120.0
>>> C 6: neighbors at 0.822 0.822 0.822
>>> d(center): 1.801 A angles : 120.0 120.0 120.0
>>> Li 7: neighbors at 2.466 2.466 2.466
>>> d(center): 6.092 A angles : 180.0 120.0 60.0
>>>
>>> P.
>>> --
>>> Paolo Giannozzi, Dept. Chemistry,
>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>>> Phone +39-0432-558216, fax +39-0432-558222
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum


note new address
Mike Marchywka 2295 Collinworth Drive Marietta GA 30062.
formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)<- leave 
message 989-348-4796 (P)<- emergency

[Pw_forum] graphene with Li input problem

[Mike Marchywka]

> From: paolo.giannozzi at uniud.it
> To: pw_forum at pwscf.org
> Date: Fri, 14 Jun 2013 18:06:37 +0200
> Subject: Re: [Pw_forum] graphene with Li input problem
>
> On Fri, 2013-06-14 at 16:55 +0200, yelena wrote:
>
>> So I have graphene
>
> or so you think (I don't, see below)
>
>> I don?t understand why all C atoms are connected
>> with every other C?
>
> because xcrysden, like most visualization tools, assumes
> that two atoms have a bond when they are closer than a
> typical bond length.

If you have potentials and wavefunctions, how would you define bonds?
Hydrogen bonds? etc. Is there something that could generate this?
And, using jdftx I had to write some code to translate binary potentials and
densities into xplor format to view. What is the eaisest way to get to pymol
from QE? ?I can probably look all of this up when I need to know but thought
it may help this thread :)?


>
> Many years ago I wrote a small code calculating interatomic
> distances from PWscf input data: PW/tools/dist.f . It reads
> the following input data, as explained in the file header:

I started to write code to generate polymers into xya files by specifying things
like a normal direction for a planar molecule ?and bond lengths and angles 
relative to last bond ,
presumably this could be extened to generate helicies etc.
I was debating about writing something to try to analyze a molecule collection
and regenerate from specifications like this but I was never sure
it was worth the effort or that I could specifiy the problem well engough to 
code :)

>
> 7 0 4.66 0.0 0.0 0.0 0.0 0.0 ! nat, ibrav, celldm(1-6)
> CELL_PARAMETERS (alat=4.6600){hexagonal}
> 0.84012 0.0 0.0
> -0.42006 0.866011558 0.0
> 0.0 0.0 12.188495864
> ATOMIC_POSITIONS (crystal)
> C 0.33000 -0.00730 -0.024511570
> C 0.65270 -0.00730 -0.024511570
> C 0.00730 0.33730 -0.024511570
> C 0.00730 0.66000 -0.024511570
> C 0.33000 0.33730 -0.024511570
> C 0.65270 0.66000 -0.024511570
> Li 0.33000 0.66000 0.197069420
>
> and this is what you get (* = in another cell):
>
> species: C - C 0.00 < D < 1.00
> atoms: 1 2 distance = 0.82197 A
> atoms: 3 5 distance = 0.82197 A
> atoms: 3 4 distance = 0.82197 A
> atoms: 5 6 distance = 0.82197 A
> atoms: 1 4* distance = 0.82197 A
> atoms: 2 6* distance = 0.82197 A
> atoms: 1 5 distance = 0.82198 A
> atoms: 2 3* distance = 0.82198 A
> atoms: 4 6* distance = 0.82198 A
> C 1: neighbors at 0.822 0.822 0.822
> d(center): 1.104 A angles : 120.0 120.0 120.0
> C 2: neighbors at 0.822 0.822 0.822
> d(center): 1.801 A angles : 120.0 120.0 120.0
> C 3: neighbors at 0.822 0.822 0.822
> d(center): 1.104 A angles : 120.0 120.0 120.0
> C 4: neighbors at 0.822 0.822 0.822
> d(center): 1.801 A angles : 120.0 120.0 120.0
> C 5: neighbors at 0.822 0.822 0.822
> d(center): 1.104 A angles : 120.0 120.0 120.0
> C 6: neighbors at 0.822 0.822 0.822
> d(center): 1.801 A angles : 120.0 120.0 120.0
> Li 7: neighbors at 2.466 2.466 2.466
> d(center): 6.092 A angles : 180.0 120.0 60.0
>
> P.
> --
> Paolo Giannozzi, Dept. Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> ___
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>   

[Pw_forum] A few questions about MD simulations

[Mike Marchywka]

> To: pw_forum at pwscf.org
> From: akohlmey at gmail.com
> Date: Sat, 1 Jun 2013 17:50:07 +
> Subject: Re: [Pw_forum] A few questions about MD simulations
>
> Nevertheless significant compression should be possible using some knowledge 
> of the physics, e.g. through projecting on atomic wavefunctions. Mind you, 
> this is a lossy compression if a minimal basis is used. I've seen pretty good 
> compression and a decent completeness for example by projecting on an STO-6G 
> basis for example. That was with a different coff though, but still using 
> plane waves and DFT.

Well, the wave functions are hardly random or uniformly distributed over the 
full range of numeric values and simple things like smoothness can be exploited 
for somec ompression that is ?easy and
fairly fast. Getting exact results from floating point algorithms can be 
difficult but if you can tolerate a few
changed LSB's or want to put some thought into it it may be something to 
consider :)



>
> Axel
> --Original Message--
> From: Paolo Giannozzi
> Sender: pw_forum-bounces at pwscf.org
> To: PWSCF Forum
> ReplyTo: PWSCF Forum
> Subject: Re: [Pw_forum] A few questions about MD simulations
> Sent: Jun 1, 2013 7:36 PM
>
> On Sat, 2013-06-01 at 10:06 -0400, Mike Marchywka wrote:
>
>> Don't ignore the possibility of adding compression code,
>> something like gzip
>
> large data files are written in binary format, so there
> is little to be gained from compression.
>
> P.
> --
> Paolo Giannozzi, Dept. Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> --
> Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>
> ___
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>   

[Pw_forum] A few questions about MD simulations

[Mike Marchywka]

> From: paolo.giannozzi at uniud.it
> To: pw_forum at pwscf.org
> Date: Sat, 1 Jun 2013 15:49:34 +0200
> Subject: Re: [Pw_forum] A few questions about MD simulations
>
> On Fri, 2013-05-31 at 12:49 -0400, Robert Hembree wrote:
>
>> I noticed that upon completion of the simulation that the
>> wavefunction files seem to have disappeared.
>
> wavefunctions do not "disappear", but only those at the last step
> (or the last two, or three, if wavefunctionn interpolation is used)
> are kept
>
>> Is there an easy way to access this information? Or would it require
>> large changes to the code base?
>
> it would require a lot of disk space. It should be relatively easy
> to modify the code in such a way that it saves all wavefunctions.
> Please look into the code that performs wavefunction interpolation,
> "update_wfc", for inspiration. Or, you can do the simulation one
> step at the time, save wavefunction files under a different name.

I've run into this issue on my lap top with JDFTX. Don't ignore the posibility
of adding compression code, something like gzip that could use the statistical
properties of the wavefunction values. ?Offhand I don't know if adding gzip to
the code would help but the time and effort spent on reducing size could be 
paid back
in a few disk transfers. It also may be interesting to try to write a lossless 
( exactly invertible ) compression
algorithm for wavefunctions, or potentials for that matter, as compression 
relies on?
statistics or properties of the data. In theory of course, your PW input file 
is the most concise
way to describe your wavefunction but "decompression" relies on starting the 
simulation from
scratch again LOL. The point being that it may be an interesting problem to 
consider for a number
of reasons.?

>
>> Third: In the source files where does the MD simulation start? For
>> example, an scf cycle is handled in the file electrons.f90.
>
> look into "move_ions.f90". The MD code is unfortunately very confusing.
>
>> is the correct way to access the planewave expansion coefficients
>> through the
>> USE wavefunctions_module, ONLY : psic
>
> no. Wavefunctions are contained in variable evc(i,j), i=plane-wave
> index, j=band index
>
> P.
>



> --
> Paolo Giannozzi, Dept. Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum


note new address
Mike Marchywka 2295 Collinworth Drive Marietta GA 30062.
  

[Pw_forum] local and global minimums in relaxation

[Mike Marchywka]

Thanks, I thought I looked there must have just missed it :)


http://qe-forge.org/pipermail/pw_forum/2012-December/100661.html

Usually I just use google and don't have a problem but it doesn't seem these
are posted anywhere is sees them. Anyway, I thought the water article posted
on LinkedIn comp chem board was rather thought provoking about
limitations of static ground state.?



> From: giannozz at democritos.it
> Date: Fri, 15 Feb 2013 09:20:53 +0100
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] local and global minimums in relaxation
>
>
> On Feb 15, 2013, at 2:34 , Mike Marchywka wrote:
>
> >
> > btw, where are old posts archived
>
> in the archive: http://www.quantum-espresso.org/ => Contacts => link
> (http://www.qe-forge.org/mailman/listinfo/pw_forum) to archives
> >
>
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
  

[Pw_forum] local and global minimums in relaxation

[Mike Marchywka]

> From: giannozz at democritos.it
> Date: Fri, 15 Feb 2013 09:20:53 +0100
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] local and global minimums in relaxation
>
>
> On Feb 15, 2013, at 2:34 , Mike Marchywka wrote:
>
> >
> > btw, where are old posts archived
>
> in the archive: http://www.quantum-espresso.org/ => Contacts => link
> (http://www.qe-forge.org/mailman/listinfo/pw_forum) to archives

Thanks, I found at least two place prior to posting that but none contained
my old posts :) There seemed to be some confusion as IIRC one redirected
or something. I'll check again.?


> >
>
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
  

[Pw_forum] local and global minimums in relaxation

[Mike Marchywka]

btw, where are old posts archived, I wanted to post these comments on Linked In
Computational chemistry group to explain my reaction to a post someone
else made there earlier ( see link to water model below).?




> From: marchywka at hotmail.com
> To: pw_forum at pwscf.org
> Date: Thu, 27 Dec 2012 11:44:44 -0500
> Subject: Re: [Pw_forum] local and global minimums in relaxation
>
>
>
>
>
> > Date: Mon, 24 Dec 2012 23:20:34 -0500
> > From: correlation at tut.by
> > To: pw_forum at pwscf.org
> > Subject: Re: [Pw_forum] local and global minimums in relaxation
> >
> > I see..
> > Thank you!
>
> Well as I understand the situation, normally you have a molecule that you 
> want to
> optimize and hope your original structure is close enough that the "forces" 
> the minimizer
> sees get it to the right answer. Most molecules are not in some global 
> minimum configuration
> of atoms right? You could take atoms infinitely far apart I guess and see 
> what you get.
>
> Personally though I did have a related question and that is what is neglected 
> by trying to
> find a static ground state and ignoring any fluctuations? This is probably 
> not yet
> relevant compared to errors in getting static result but curious if anyone 
> wanted to comment.
>

This was just posted on the linked in Computational Chemistry group, showing 
importance
of fluctuation in understanding water, thought it was relevant to my earlier 
comment LOL

http://www.rsc.org/chemistryworld/2013/02/water-structure-tetrahedral-controversy-xas-xafs



>
>
>
> >
> > Sergey
> >
> > On 12/21/2012 3:47 PM, Paolo Giannozzi wrote:
> > > On Dec 21, 2012, at 20:01 , Sergey wrote:
> > >
> > >> when I do relaxation (using bfgs algorithm), I end up with the
> > >> system in
> > >> one of the minimums. It can be local one or it can be global one. And
> > >> there is probably several other possible local minimums in the system.
> > >> How can I publish such a result? As I see in the papers no one usually
> > >> describe this issue. Usually it is just - 'we performed structural
> > >> optimization (relaxation) and here is the result.'
> > >>
> > >> How to deal with this matter?
> > > if you find a better way to deal with this matter, your future career is
> > > guaranteed. It is a well-known problem. That's way smart people
> > > have invented simulating annealing, genetic algorithms,
> > > metadynamics, ...
> > >
> > > P.
> > > ---
> > > Paolo Giannozzi, Dept of Chemistry,
> > > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> > > Phone +39-0432-558216, fax +39-0432-558222
> > >
> > >
> > >
> > >
> > > ___
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://pwscf.org/mailman/listinfo/pw_forum
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> ___
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
  

[Pw_forum] setting grid size and memory management for pw scf

[Mike Marchywka]

> From: giannozz at democritos.it
> Date: Fri, 11 Jan 2013 23:01:13 +0100
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] setting grid size and memory management for pw scf
>
>
> On Jan 11, 2013, at 17:06 , Mike Marchywka wrote:
>
> > Sorry if there is a simple answer but I could not immediately
> > figure out the
> > issues with setting fft grid size or the actual parameters to set
> > in the input file
>
> which issues?

http://www.quantum-espresso.org/wp-content/uploads/Doc/pw_user_guide/node19.html
Manually setting the FFT grids to a desired value is possible, but slightly 
tricky, using input variables?nr1,?nr2,?nr3?and?nr1s,?nr2s,?nr3s. The code will 
still increase them if not acceptable. Automatic FFT grid dimensions are 
slightly overestimated, so one may try?very carefully?to reduce them a little 
bit. The code will stop if too small values are required, it will waste CPU 
time and memory for too large values.


In any case using CG diagonalization got it to run much faster, presumably 
making the point that memory can be more important in speed than just
counting operations ( I understand the default is faster with infinite memory). 
?Could not bracket Fermi level though, I'll have to check the
other settings for this. The system is just all trans retinoic acid with a 
single Fe atom either near the COOH or out of plane of the chain.
It I started with a a random placement and did structure optimization with 
jdftx but wanted to compare to QE and get more insight.
I'm not even sure this system has physical meaning ( the pseudopotentials are 
the first ones I found without a lot of consideration and I have
to come up with some "known" results for comparison yet).?


Thanks.



>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
  

[Pw_forum] setting grid size and memory management for pw scf

[Mike Marchywka]

Sorry if there is a simple answer but I could not immediately figure out the
issues with setting fft grid size or the actual parameters to set in the input 
file
( I think I found n1r and n1rs or something similar in a troubleshooting guide 
?but not in user's
guide right away ). The troubleshooting guide said that the program could
override the selection in any case IIRC. Is there a single place this is 
documented?

I'm try do dft on about 24 atoms using laptop and the thing runs out of real 
memory.
I set diagnolaization to cg which may have solved the immediate problem but 
curious
on what other things I can do.
Thanks.



note new address
Mike Marchywka 2295 Collinworth Drive Marietta GA 30062.

  

[Pw_forum] what code actually loads xplor files? The edmplugin does not seem to execute and I can't find a py file.

[Mike Marchywka]

sorry wrong address arrgggh can you please delete that...




> From: marchywka at hotmail.com
> To: pw_forum at pwscf.org
> Subject: what code actually loads xplor files? The edmplugin does not seem to 
> execute and I can't find a py file.
> Date: Wed, 2 Jan 2013 10:59:13 -0500
>
>
>
> I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I 
> wanted to debug the
> problem but can't get my debug statements to execute. The only thing that 
> greps for "xplor"
> is a few pymol modules and plugin called edmplugin. If I rebuild the plugin 
> and relink pymol
> nothing seems to change. Is this the right code? I also wanted to add a 
> loader for other
> formats of density or vector fields and maybe do some rendering ( I have an 
> old viewer I wrote
> with glut and thought I may be able to salvage parts of that for use here).
>
> Thanks.
>
>
>
> note new address
> Mike Marchywka 2295 Collinworth Drive Marietta GA 30062.
> formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)<- leave 
> message 989-348-4796 (P)<- emergency
>
>
>
  

[Pw_forum] what code actually loads xplor files? The edmplugin does not seem to execute and I can't find a py file.

[Mike Marchywka]

I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I 
wanted to debug the
problem but can't get my debug statements to execute. The only thing that greps 
for "xplor"
is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and 
relink pymol
nothing seems to change. Is this the right code? I also wanted to add a loader 
for other
formats of density or vector fields and maybe do some rendering ( I have an old 
viewer I wrote
with glut and thought I may be able to salvage parts of that for use here).

Thanks.



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Mike Marchywka 2295 Collinworth Drive Marietta GA 30062.
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[Pw_forum] local and global minimums in relaxation

[Mike Marchywka]

> Date: Mon, 24 Dec 2012 23:20:34 -0500
> From: correlation at tut.by
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] local and global minimums in relaxation
>
> I see..
> Thank you!

Well as I understand the situation, normally you have a molecule that you want 
to
optimize and hope your original structure is close enough that the "forces" the 
minimizer
sees get it to the right answer. Most molecules are not in some global minimum 
configuration
of atoms right? You could take atoms infinitely far apart I guess and see what 
you get.

Personally though I did have a related question and that is what is neglected 
by trying to
find a static ground state and ignoring any fluctuations? This is probably not 
yet
relevant compared to errors in getting static result but curious if anyone 
wanted to comment.




>
> Sergey
>
> On 12/21/2012 3:47 PM, Paolo Giannozzi wrote:
> > On Dec 21, 2012, at 20:01 , Sergey wrote:
> >
> >> when I do relaxation (using bfgs algorithm), I end up with the
> >> system in
> >> one of the minimums. It can be local one or it can be global one. And
> >> there is probably several other possible local minimums in the system.
> >> How can I publish such a result? As I see in the papers no one usually
> >> describe this issue. Usually it is just - 'we performed structural
> >> optimization (relaxation) and here is the result.'
> >>
> >> How to deal with this matter?
> > if you find a better way to deal with this matter, your future career is
> > guaranteed. It is a well-known problem. That's way smart people
> > have invented simulating annealing, genetic algorithms,
> > metadynamics, ...
> >
> > P.
> > ---
> > Paolo Giannozzi, Dept of Chemistry,
> > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> > Phone +39-0432-558216, fax +39-0432-558222
> >
> >
> >
> >
> > ___
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>
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