[Pw_forum] working neb example
Hi, Please have a look at example 17. HTH, Changru On 7 Oct, 2011, at 20:01, Hans Horn wrote: > Folks, > > could someone pls post a working (simple yet non-trivial) neb example > with output. > Thx a lot.! > > H. > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111007/b0e8e953/attachment.htm
[Pw_forum] cluster timing & delay -v.lousy way-
Dear Mona Elfadil, Q.E.3.0 was released on 2005. I would suggest you to try the newest version 4.3.2 first. You can find it here: http://www.quantum-espresso.org/download.php HTH, Changru On 21 Sep, 2011, at 17:19, Mona M.O. Elfadil wrote: > Dear all, >We had run an example -Q.E.3.0.1- from your package few days ago > on a linux cluster- CentOS 5-, and it worked although we had no > BLAS, LAPACK nor an FFTW packages previously installed - not > surprising,since you have said so in your user guide-. > Then we had tried an experimental data. It took a single CPU 10 min to get > the results. While, unfortunately, it took a 16 CPUs more than 40 min to > process the same data. > We had tried the following: > - Referring to your user guide: It needs a detailed physics background > which is unavailable at the moment. > - Downloading these mathematical packages: > FFTW 3.1.2-3 & FFTW 2.1.5-2 > LAPACK 3_0-2 > BLAS 3_0-2 > (RPM versions) > In the configuration phase of Q.E. it said that both LAPACK and FFTW are > not found although BLASS was successfully configured. > > We could not find FFTWND in our internet search(As a packet). But in your > archive you have said it is not an error. > > Assuming that all other factors are well, what could be the cause?? > > (P.S.: we are the system administrators) > > -- > Your sincerely, > Mona Elfadil > SudREN - Network Engineer > www.suin.edu.sd > +249911319113 > > > > > _______ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma ---
[Pw_forum] (no subject)
Dear Winfred, I just have a look at the input you provided. Are you sure this is TiO2 rutile? Please visualize the structure with a software like Xcrysden first. HTH, Changru On 7 Sep, 2011, at 14:22, Winfred Mulwa wrote: > Dear all > >I have tried doing a vc-relax on the attached TiO2 rutile supercell, > the calculations stop after a few minutes without giving any error. > What might be the problem? > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110907/0f1b7804/attachment.htm
[Pw_forum] Segmentation fault with pp.x
Dear Karthik, It's explained in the User Guide. 12.6.0.1 Why is my job crashing with ``segmentation fault''? Possible reasons: too much memory requested; executable or libraries fitted to a different hardware; code bug; compiler bug. The latter are typically not reproducible on different architectures or compilers; code bugs may sometimes be elusive, but typically yield a more reproducible, pattern of problems. Mysterious, unpredictable, erratic errors in parallel execution are almost always coming from bugs in the compiler or/and in the MPI libraries and sometimes even from flaky hardware. Sorry, not our fault. HTH, Changru On 5 Sep, 2011, at 08:51, vkarthik wrote: > Hi, > > I am using quantum espresso-4.3.2 and running some examples given at the > tutorial website on the quantum espresso > webpage.http://www.fisica.uniud.it/~giannozz/QE-Tutorial/ PWscf - Simple > examples > > I am trying to run a post process job to determine the charge density. > As mentioned in the slides when I run the command > prompt> espresso_dir/bin/pp.x < si.pp_rho.in > I get en error message > Program POST-PROC v.4.3.2 starts on 5Sep2011 at 12:13:38 > > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please cite > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); > URL http://www.quantum-espresso.org";, > in publications or presentations arising from this work. More details at > http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO > > Info: using nr1, nr2, nr3 values from input > > Info: using nr1s, nr2s, nr3s values from input > > G-vector sticks info > > sticks: dense smooth PW G-vecs:dense smooth PW > Sum 163 163 61 1459 1459 339 > > Segmentation fault > > any help would be appreciated. > best, > Karthik > > ___________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110905/9d133c90/attachment-0001.htm
[Pw_forum] usage of recover=.true.
No. What I suggested is exactly what you want. In the first calculation, set recover to false, the code will compute the first 105 modes for you. When it is working on the 106th mode, it stops as you said. Then you modify the input file, turn "recover" to true, run the calculation again and the code is able to recover what you have done and start from the 106th mode. I would suggest you to write to another output. In the output, you will see: ? Representation1 1 modes - Done ? Representation105 1 modes - Done Representation106 1 modes - To be done ? HTH Changru On 22 Aug, 2011, at 16:23, Elie Moujaes wrote: > Thanks a lot for the answer. The problem is I started calculating the phonons > at the Gamma point. In my system there are 180 modes and something went wrong > with the server so it stopped at the 106.I am doing the 180 in one go! Is > there a way to save the 106 ones already done! or u suggest that I calculate > each one of them in a separate fie and use recover=.true.? > > > Thanks > Elie > > From: crma at sissa.it > Date: Mon, 22 Aug 2011 16:17:17 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] usage of recover=.true. > > Dear Elie, > > In the document Doc/INPUT_PH.txt, variable "recover" is explained clearly: > >Variable: recover > >Type: LOGICAL >Default:.false. >Description:If .true. restart from an interrupted run. > > So set it to false in your first run and true in the second and the following > runs. > > HTH, > Changru > > On 22 Aug, 2011, at 16:06, Elie Moujaes wrote: > > Dear all, > > I am doing phonon calculations for a large system at the Gamma point (I have > 180 irreducible representations (modes) to work out). The server was shut for > a day. I have used in my input file recover=.true. I have reached > representation 106 before the server broke down. Does it mean that If I > executed the command ph.x again, the calculations will start from where it > was interrupted?if not, what can i do to not lose what has been done? > > Thanks > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Changru Ma > SISSA & Theory at Elettra group > email: crma at sissa.it > tel: +39 040 378 7870 > http://www.sissa.it/~crma > --- > > > ___ Pw_forum mailing list > Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/52bdda15/attachment.htm
[Pw_forum] usage of recover=.true.
Dear Elie, In the document Doc/INPUT_PH.txt, variable "recover" is explained clearly: Variable: recover Type: LOGICAL Default:.false. Description:If .true. restart from an interrupted run. So set it to false in your first run and true in the second and the following runs. HTH, Changru On 22 Aug, 2011, at 16:06, Elie Moujaes wrote: > Dear all, > > I am doing phonon calculations for a large system at the Gamma point (I have > 180 irreducible representations (modes) to work out). The server was shut for > a day. I have used in my input file recover=.true. I have reached > representation 106 before the server broke down. Does it mean that If I > executed the command ph.x again, the calculations will start from where it > was interrupted?if not, what can i do to not lose what has been done? > > Thanks > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/b461a2f8/attachment-0001.htm
[Pw_forum] Temperature rescaling in MD calculation
Dear Rui, On 12 Aug, 2011, at 16:12, DONG Rui wrote: > Hi, all, > > I am doing MD calculation in QuantumEspresso, and have a question now... > > here are some of the input list > &ions > ion_temperature = 'reduce-T', > tempw=10, > delta_t = 1, > nraise=10, > pot_extrapolation='second-order', > wfc_extrapolation='second-order', > / > > But I found the rescaling works only when delta_t is a negative number, which > is different from what the documentation tells me. In Doc/INPUT_PW.txt, I find the following lines: Variable: ion_temperature Type: CHARACTER 'reduce-T'reduce ionic temperature every "nraise" steps by the (negative) value "delta_t" and Variable: delta_t Type: REAL if ion_temperature='reduce-T': every 'nraise' steps the instantaneous temperature is reduced by -delta_T (.e. delta_t is added to the temperature) The instantaneous temperature is calculated at the end of every ionic move and BEFORE rescaling. This is the temperature reported in the main output. For delta_t < 0, the actual average rate of heating or cooling should be roughly C*delta_t/(nraise*dt) (C=1 for an ideal gas, C=0.5 for a harmonic solid, theorem of energy equipartition between all quadratic degrees of freedom). Why delta_t is a negative number is different from the document? > > Anyone has the same problem? And does anyone know how to heat the system up > use the method "reduce-T"? I think "reduce-T" is used to quench the system, it reduces ionic temperature every "nraise" steps by the (negative) value "delta_t". To heat the system up, I would suggest you to use other thermostats, like "rescaling", "rescale-v", "rescale-T", "berendsen" or "andersen". Best wishes, Changru > > Thank you guys! > > Rui ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110812/197a7de5/attachment.htm
[Pw_forum] CP simulation with ensemble-dft algorithm
Dear Pascal,
If you set ion_velocities = 'random' then the internal variable tcap will be
true. And if ion_temperature = 'nose', the internal variable tnosep is true.
These two logic variables can't be both true since the code rejects
(CPV/cplib.f90 line 441).
HTH,
Changru
On 16 Jun, 2011, at 20:53, pascal boulet wrote:
> Dear all,
>
> It seems that my first post was completely unreadable (html). Sorry for
> that. Here is the content.
>
> I am trying to run a CP simulation (cp.x) of a molecule in contact with
> a small metallic cluster of atoms.
>
>
> First here is the input file of my test job:
>
> &CONTROL
> title = 'MD',
> calculation = 'cp',
> dt= 20.d0,
> isave = 5,
> nstep = 10,
> etot_conv_thr = 5.d-7,
> prefix= 'test',
> pseudo_dir= '/opt/espresso-4.3.1/pseudo',
> restart_mode = 'from_scratch',
> verbosity = 'high',
> iprint= 1
> /
> &SYSTEM
> ibrav = 0,
> celldm(1) = 34.015084,
> nat = 4,
> ntyp= 2,
> ecutwfc = 25.,
> ecutrho = 200.,
> occupations = 'ensemble',
> smearing= 'fd',
> degauss = 0.02,
> input_dft = 'PBE',
> nbnd= 30,
> assume_isolated = 'makov-payne'
> /
> &ELECTRONS
> conv_thr= 5.d-7,
> mixing_beta = 0.4d0,
> startingwfc = 'random',
> tcg = .TRUE.,
> electron_velocities = 'zero',
> electron_temperature = 'nose',
> fnosee = 300.,
> ekincw = 0.001,
> orthogonalization = 'Gram-Schmidt'
> /
> &IONS
> ion_dynamics= 'verlet',
> ion_temperature = 'nose',
> ion_velocities = 'random',
> remove_rigid_rot = .TRUE.,
> tempw = 623.d0,
> ndega = -6,
> nhpcl = 1,
> fnosep = 24.,
> /
> ATOMIC_SPECIES
> Ag 107.8682 Ag.pbe-d-rrkjus.UPF
> N14.0067N.pbe-rrkjus.UPF
>
> ATOMIC_POSITIONS angstrom
> Ag 6.467294548 12.585619859 10.268802850
> Ag 6.293658753 10.453834050 12.214668134
> N4.165456080 10.433924294 8.842653616
> N3.807795851 10.451920023 9.956290174
>
> CELL_PARAMETERS {cubic}
> 1. 0. 0.
> 0. 1. 0.
> 0. 0. 1.
>
>
>
> If I run the above input file, I get the following error message:
>
> %%
> from ions_print_info : error # 1
> tcap and tnosep both true
> %%
>
> What is the meaning of the variables tcap and tnosep?
>
> It seems they are not adjustable variables through the input file since
> they are not referenced in the manual. Indeed, if I set tcap=.false. in
> the input file I get the following:
>
>
> %%%%%%
> from read_namelists : error #19
> reading namelist ions
> %%
>
> So, is there any contradiction in my input file?
>
>
> Thank you for your help
>
> Best regards
> Pascal
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Changru Ma
SISSA & Theory at Elettra group
email: crma at sissa.it
tel: +39 040 375 8713 (Elettra)
+39 040 378 7870 (SISSA)
http://www.sissa.it/~crma
---
[Pw_forum] How to restart md calculation using pw.x
Dear Will, You can just simply set restart_mode = 'restart', in CONTROL namelist. With the same "prefix" and "outdir", atomic positions are read from directory $outdir/$prefix.save, which is the last configuration in the previous calculation. Best wishes, Changru On 17 May, 2011, at 18:05, willy kohn wrote: > Dear Pwscf Users: > > I'm trying to use the "md" option in the pw.x to do some > Born-Oppenheimer molecular dynamics calculation, but found that there > is no way to restart the md calculation from the last configuration > (including both positions and velocities) of atoms in a properly > finished running. I'm wondering if there is a simple solution for > that. > > Best, > > Will > > student of Gatech > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 375 8713 (Elettra) +39 040 378 7870 (SISSA) http://www.sissa.it/~crma ---
[Pw_forum] Hello, I have some problemof QE.
Dear YHHo,
nelup and neldw are number of spin-up and spin-down electrons, respectively.
The sum must yield nelec that must also be specified explicitly in this case.
I also have a look at your molecule with XCrysden, are you sure it is a
molecule?
The new release, v.4.3, of the Quantum ESPRESSO distribution is available for
download. I suggest you to use the newest version.
Next time please specify your question explicitly in the subject of the mail.
Best wishes,
Changru
On 4 May, 2011, at 09:33, yhho wrote:
> Hello,
> Because I want to calculate my molecule by cp.x, I build the input file as
> espresso-4.0.3/example/example29.
> But I got many error massages like this:
>
> from system_checkin : error # 1
> nelup out of range
> I think that's coused by my wrong setting of nelup in input file.
> But although I tried to change the value of nelup, there's still the same
> error when I run cp.x
>
> The version I used QE is 4.0.3.
>
> Here's my input file.
> Please give me some suggestions about nelup setting. Thank you very much.
>
> &CONTROL
> calculation = 'cp',
> restart_mode = 'from_scratch',
> nstep = 5,
> iprint = 10,
> isave = 10,
> tstress = .TRUE.,
> tprnfor = .TRUE.,
> dt= 10.0d0,
> prefix = 'Glu43',
> pseudo_dir = '$PSEUDO_DIR/',
> outdir='$TMP_DIR/'
>
> /
>
> &SYSTEM
> ibrav =0,
> celldm(1) = 1.0D0,
> nat =41,
> ntyp =6,
> ecutwfc = 30,
> ecutrho = 300.0,
> occupations ='smearing',
> smearing='fd',
> degauss =0.02,
> nr1b=20,nr2b=20,nr3b=20
> nspin=2,
> nelup=6,
> neldw=1,
> /
> &ELECTRONS
> emass = 1000.d0,
> emass_cutoff = 4.d0,
> orthogonalization = 'Gram-Schmidt',
> startingwfc = 'random',
> ampre = 0.02,
> n_inner = 8,
> tcg = .true.,
> passop=0.3,
> maxiter = 250,
> conv_thr=1.d-6
> /
> ion_dynamics = 'damp',
> ion_damping = 0.,
> ion_positions = 'from_input',
> greasp=1.0,
> ion_radius(1) = 0.8d0,
> ion_temperature = 'not_controlled',
> /
>
> ATOMIC_SPECIES
> C 12.01 C.pbe-van_ak.UPF
> N 14.01 N.pbe-van_ak.UPF
> Fe 55.85 Fe.pbe-sp-van_ak.UPF
> Cl 35.45 Cl.pbe-n-van.UPF
> O 16.00 O.pbe-van_ak.UPF
> H 1.008 H.pbe-van_ak.UPF
> ATOMIC_POSITIONS (crystal)
> Fe 4.1641719 -0.5471554 -0.5471554
> Cl 4.5964120 -0.9816182 -1.5908458
> C 0.000 0.000 0.000
> C 1.2973805 0.000 -0.3758962
> C 1.2525726 -0.0289989 1.8170181
> C 2.1350316 -4.1256236 2.1865112
> C 2.9221888 -3.0442425 2.4078019
> C 2.8226321 -3.3447077 0.2413133
> C 6.2923254 -0.8182676 2.5823989
> C 5.2510634 -0.2023719 3.4131521
> C 5.5088329 0.0750602 4.8865937
> C 4.907 0.8379462 5.5071409
> C 4.5779602 1.2229945 6.9527704
> N 0.000 0.000 1.3847892
> N 2.0542695 0.0002705 0.7687871
> N 2.1102671 -4.3058679 0.8117062
> N 3.3274628 -2.5693481 1.1859156
> O 7.3914426 -1.1172282 3.0850061
> O 6.0627468 -0.9981431 1.3551644
> O 4.1575035 0.0273619 2.9063284
> O 3.6274812 1.7187097 7.6151903
> O 5.6844234 0.9906742 7.4543204
> O 6.3046402 -3.3176420 -0.4637370
> O 4.8477761 1.5314745 0.3194472
> H -0.8142000 0.0187705 1.9653079
> H 1.6667575 0.0001924 -1.3801718
> H 1.5611887 -0.0697114 2.8404880
> H 1.6328039 -5.0405899 0.3297794
> H 3.1807154 -2.6355708 3.3623162
> H 2.9657556 -3.2174549 -0.8109516
> H 5.5447595 -0.8771014 5.3743575
> H 6.3541964 0.7303920 4.9296487
> H 3.5103975 0.1546553 5.5181216
> H 4.2582631 1.7576717 4.9649696
> H 5.4053363 -3.2956001 -0.7980536
> H 6.3150255 -3.0172862 0.4481679
> H 3.9484722 1.5535164 -0.0148694
> H 4.8581614 1.8318303 1.2313521
> H -0.8951512 0.0338588 -0.5859376
> H 1.6443833 -4.7879056 2.8685623
> H 2.8399482 1.1827425 7.4958090
>
> CELL_PARAMETERS {cubic}
> 20.000 0. 0.
> 0. 20.000 0.
> 0. 0. 20.000
>
>
> Best regards,
> YHHo, IAMS in Taiwan
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
---
Changru Ma
SISSA & Theory at Elettra group
email: crma at sissa.it
tel: +39 040 375 8713 (Elettra)
+39 040 378 7870 (SISSA)
http://www.sissa.it/~crma
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[Pw_forum] CVS Version download link
Dear Madan, Anonymous CVS Access This project's CVS repository can be checked out through anonymous (pserver) CVS with the following instruction set. The module you wish to check out must be specified as the modulename. When prompted for a password for anonymous, simply press the Enter key. cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e login cvs -d :pserver:anonymous at scm.qe-forge.org:/cvsroot/q-e checkout espresso Best wishes, Changru On 10 Mar, 2011, at 18:45, Madan Mithra. L. M wrote: > Hello, > > I was able to download the CVS Version from qe-forge site earlier. Now the > link is missing. Could you please direct me to the correct link ? > > Thank you > > - Madan > > > Madan Mithra .L.M > Senior Research Fellow > Dept.of Physics > Indian Institute of Science > Bangalore - 560 012 > INDIA > . > e-mail : mit at physics.iisc.ernet.in >: snd2mra at yahoo.com > Phone : 91-80-22932313(Lab) > FAX: (080) 360 2602 > - > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 375 8713 (Elettra) +39 040 378 7870 (SISSA) http://www.sissa.it/~crma --- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110310/cd9712e2/attachment-0001.htm
[Pw_forum] projwfc.x error
Dear Yuyang, Please read user guide, page 56. On 23 Feb, 2011, at 05:13, YY wrote: > Dear All, > > After the scf calculation, I try to use projwfc.x to calculate the PDOS, but > get an error message like this: > Calling projwave > > %% > from davcio : error #10 > error while reading from file > > %% > > I am sure the inputfile is right and the related files exists, because I can > calculate total DOS by dos.x correctly. > I search the archive of this forum, the same problem was report several > times, but no clear answer. > I compiled pw.x and projwfc.x from the same version source code (v4.2.1). > No matter I use 1 CPU or the same number CPUs as used in pw.x, I get the same > error message. Either use wf_collect = .t. or use the same number CPUs as used in pw.x I suggest you to check if outdir and prefix are the same first. Best wishes, Changru --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 375 8713 (Elettra) +39 040 378 7870 (SISSA) http://www.sissa.it/~crma --- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110223/7f34870d/attachment.htm
[Pw_forum] classical potential MD simulation
Dear sakthi kumaran, It's not possible to perform classical molecular dynamics in Quantum Espresso now. QE can do ab-initio molecular dynamics: Car-Parrinello Molecular Dynamics and Born-Oppenheimer Molecular Dynamics. PS. Next time please take a few seconds to sign your post with your affiliation. Best wishes, Changru On 19 Feb, 2011, at 07:28, sakthi kumaran wrote: > Dear all, > Is it possible to compute the interaction between two capped > nanotubes facing each other using classical LJ12 potential using Molecular > dynamics technique in Quantum espresso.If possible what is the procedure for > doing so. > > Thank you guys in advance > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 375 8713 (Elettra) +39 040 378 7870 (SISSA) http://www.sissa.it/~crma ---
[Pw_forum] Energy calculation for single carbon atom
Hi Tram,
Please have a look at the User's Guide first:
http://www.quantum-espresso.org/user_guide/node50.html#SECTION0001110240
Best wishes,
Changru
> Hi Everyone,
> I'm trying to run the total energy calculation for a simple cubic of
> carbon, in which i'm using the lattice constant of 40 Bohrs (a.u) and the
> E
> cut off of 30 Ryd. this should be a very simple calculation. when I used
> K-points of 10x10x10, the calculation worked fine. However, I then wanna
> try
> with the K point of {gamma} and it kept giving me the error of " 1
> eigensvalue is not converged". So my question is would you look at the
> input
> file and the (not-finished) out put file and let me know what might have
> been my mistakes?
>
> Thank you and have a great week,
>
>
>
> --
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
> ___
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>
--
Changru Ma, PhD Student
SISSA and Theory at Elettra Group
email: crma at sissa.it
SISSA Webmail https://webmail.sissa.it/
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[Pw_forum] Mean Square Displacement (MSD) of atoms
Dear Bertrand, The mean square displacement of atoms in a simulation can be easily computed by its definition MSD = < (r(t) - r(0)) ** 2.0 > Be careful when you compute r(t) - r(0), as Giovanni La Penna mentioned. You's better post process .pos to .xsf by cppp.x first and then calculate MSD from .xsf file. "Mean square Displacement" printed every isave step in the output file is the mean square displacement of each ionic specie. It's calculated in Modules/ions_base.f90, subroutine ions_displacement(). What you want is "to collect the MSD of each ions during the dynamics". So you have to calculate it yourself. Best wishes, Changru > Dear Changru > > Thank very much for your answer. > > The routines in Daan Frenkel and Berend Smit's book is are not suitable > for postprocessing the *.pos file. Maybe these could give an idea, but I > would like to have a routine that could help in postprocessing the *.pos > file. > > Secondly, what about the "Means square Displacement" printed every "isave" > step in the *.out file? I though one could collect all the printed MSDs in > one file to build the total MSD for all ions. Is this correct? > > Thank once again for your help > > > > Bertrand SITAMTZE YOUMBI, PhD > Laboratory of Material Sciences > University of Yaounde I-Cameroon > * > > --- En date de?: Lun 17.1.11, Changru Ma a ?crit?: > > De: Changru Ma > Objet: Re: [Pw_forum] Mean Square Displacement (MSD) of atoms > ?: "PWSCF Forum" > Date: Lundi 17 janvier 2011, 23h15 > > Dear Bertrand, > Positions of each ions during the dynamics will be written in > $outdir/prefix.pos every iprint steps. They are sorted by specie, and > converted to real a.u. coordinates. > You have to write a code yourself to calculate the MSD.?Understanding > molecular simulation: from algorithms to applications by Daan Frenkel and > Berend Smit page 91 and page 95 might be helpful. > Best wishes,Changru > On 17 Jan, 2011, at 18:06, Bertrand SITAMTZE wrote: > Dear all, > > I have performed ab-initio Molecular Dynamics within the CP code and I > would like to collect the MSD of each ions during the dynamics. > > Please could somebody tell me how to proceed from QE output? > > Thanks very much for your answers > > > Bertrand SITAMTZE YOUMBI, PhD > Laboratory of Material Sciences > University of Yaounde I-Cameroon > * > > > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Changru Ma > SISSA & Theory at Elettra group > email:?crma at sissa.it > tel: +39 040 375 8713 (Elettra) > ?? ? ?+39 040 378 7870 (SISSA) > http://www.sissa.it/~crma > --- > > > > -La pi?ce jointe associ?e suit- > > _______ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Changru Ma, PhD Student SISSA and Theory at Elettra Group email: crma at sissa.it SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/
[Pw_forum] Mean Square Displacement (MSD) of atoms
Dear Bertrand, Positions of each ions during the dynamics will be written in $outdir/prefix.pos every iprint steps. They are sorted by specie, and converted to real a.u. coordinates. You have to write a code yourself to calculate the MSD. Understanding molecular simulation: from algorithms to applications by Daan Frenkel and Berend Smit page 91 and page 95 might be helpful. Best wishes, Changru On 17 Jan, 2011, at 18:06, Bertrand SITAMTZE wrote: > Dear all, > > I have performed ab-initio Molecular Dynamics within the CP code and I would > like to collect the MSD of each ions during the dynamics. > > Please could somebody tell me how to proceed from QE output? > > Thanks very much for your answers > > > Bertrand SITAMTZE YOUMBI, PhD > Laboratory of Material Sciences > University of Yaounde I-Cameroon > * > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 375 8713 (Elettra) +39 040 378 7870 (SISSA) http://www.sissa.it/~crma --- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110117/0842b955/attachment.htm
