[Pw_forum] Pw_forum Digest, Vol 125, Issue 13
Anuja Chanana
anujachanana26 at gmail.com
Wed Dec 20 04:42:50 CET 2017
Thanks for the reply.
Is it possible to read merged two output files in Xcrysden?
Looking forward to a reply.
<https://mailtrack.io/> Sent with Mailtrack
<https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality>
Thanks and Regards
Dr. Anuja Chanana
Research Associate
Materials Theory Lab - Prof. Umesh Waghmare
Theoretical Sciences Unit,
Jawaharlal Nehru Centre for Advanced Scientific Research,
Jakkur Bangalore-560064
anuja at jncasr.ac.in
https://www.researchgate.net/profile/Anuja_Chanana
On Tue, Dec 19, 2017 at 4:30 PM, <pw_forum-request at pwscf.org> wrote:
> Send Pw_forum mailing list submissions to
> pw_forum at pwscf.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://pwscf.org/mailman/listinfo/pw_forum
> or, via email, send a message with subject or body 'help' to
> pw_forum-request at pwscf.org
>
> You can reach the person managing the list at
> pw_forum-owner at pwscf.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
> 1. q2r not reading matdyn (A. Jain)
> 2. Re: Unexpected error in NEB calculation (Paolo Giannozzi)
> 3. Mailing list down (Paolo Giannozzi)
> 4. Force is fluctuating for water system (Narendranath Ghosh)
> 5. Optical properties: Real and imaginary part of dielectric
> function, Reflectivity, Energy loss function, Refractive index,
> dielectric constant, absorption spectrum (Sudha Priyanka)
> 6. Merging output files (Anuja Chanana)
> 7. error- dE0s is positive which should never happen (B S Bhushan)
> 8. Re: Merging output files (Lorenzo Paulatto)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 14 Dec 2017 12:13:49 +0000
> From: "A. Jain" <aj520 at cam.ac.uk>
> Subject: [Pw_forum] q2r not reading matdyn
> To: pw_forum at pwscf.org
> Message-ID: <7b7915f92c575a6f22355ecfd4445370 at cam.ac.uk>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Hi all,
>
> I've successfully ran a phonon calculation on a 118 atom
> ruthenium-crystal system with P-1 symmetry over a 2x2x2 q-mesh. This
> results in 8 q-points. Due to the size of the system I followed the
> GRID_example layout, where each q-point was calculated independently
> using start_q and last_q. My ultimate aim is to obtain dispersion info
> and so I then tried to obtain IFCs using q2r.x. However it would read
> matdyn0 and matdyn1 without any issues but then stopped at matdyn2
> saying: BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES. The last
> few lines of the output are given below:
>
> na= 116
> 0.01348 0.03651 -0.04974
> 0.01943 0.02164 -0.18305
> -0.11583 -0.07468 -0.01909
> na= 117
> -0.08861 -0.09534 0.08548
> 0.00377 0.05060 -0.05621
> 0.04123 0.00009 0.12778
> na= 118
> -0.08861 -0.09534 0.08548
> 0.00377 0.05060 -0.05621
> 0.04123 0.00009 0.12778
> nqs= 1
> q= 0.00000000 0.00000000 0.00000000
> reading force constants from file matdyn2
>
> ============================================================
> =======================
> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> = PID 26334 RUNNING AT cc061.cooley
> = EXIT CODE: 59
> = CLEANING UP REMAINING PROCESSES
> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> ============================================================
> =======================
>
>
> Here is my input file for q2r.x:
>
> &input
> fildyn='matdyn',
> zasr='no',
> flfrc='dark_222.fc'
> /
>
>
> I have attempted the GRID_example using my 5.3.0 version of QE and it
> ran successfully without any issues. I'm still not vastly experienced
> with QE so I'm hoping this is an issue that others may have faced
> before. I initially thought my matdyn2 file may be corrupted and had a
> look but did not really see anything out of the ordinary. Please let me
> know if you all feel there are any changes I can make or if there is
> anymore information you may require.
>
> Apoorv Jain
> Department of Chemical Engineering and Biotechnology
> University of Cambridge
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 14 Dec 2017 14:06:10 +0100
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> Subject: Re: [Pw_forum] Unexpected error in NEB calculation
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAPMgbCtHYcz7=r2J-m_gP-UuLTpez+aR1SzRwkTBwPifAhHaww@
> mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Thu, Dec 14, 2017 at 2:30 AM, jibiaoli <jibiaoli at foxmail.com> wrote:
>
> I encountered a run error in NEB calculation. The error message is shown
> > below.
> >
>
> it looks like a problem with your disk, not with the code itself
>
> 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20171214/
> 6c468c5c/attachment-0001.html
>
> ------------------------------
>
> Message: 3
> Date: Mon, 18 Dec 2017 21:28:29 +0100
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> Subject: [Pw_forum] Mailing list down
> To: PWSCF Forum <pw_forum at pwscf.org>, General discussion list for
> Quantum ESPRESSO developers <q-e-developers at qe-forge.org>
> Cc: Quantum ESPRESSO Foundation <foundation at quantum-espresso.org>
> Message-ID:
> <CAPMgbCui1yONgN4VG+qT_v-UuiscTo+fqXtkHY7bNQbDahBQQA@
> mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Most qe-forge.org services, including mailing lists, have been unreachable
> since Dec.14 afternoon (CET time) due to a server problem and to a fialed
> restart. Now everything seems to be working again. Note however that the
> problem causing the crash (abnormal production of temporary files) is not
> solved, so mailing lists can be shut down any time to prevent further
> problems and will be moved soon to another hosting
>
> 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20171218/
> c1c5d0aa/attachment-0001.html
>
> ------------------------------
>
> Message: 4
> Date: Tue, 19 Dec 2017 09:16:07 +0530
> From: Narendranath Ghosh <ghosh.naren13 at gmail.com>
> Subject: [Pw_forum] Force is fluctuating for water system
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAAadC28GKMdsG8K+VfQgrxmoOYExanP96yf-
> JnrL83inAqTR1g at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all
>
> I am relaxing a system of 128 water molecule with extra electron.The force
> is fluctuating even after bfgs steps = 48.
>
>
>
> *Input:*
>
> &CONTROL
> calculation='relax',
> outdir='/share_home/hpc/NEGATIVE_HYDRATED_ELECTRON/OUTPUT',
> prefix='water-128-negative',
> pseudo_dir='/share_home/hpc/RESEARCH_SCHOLAR/HYDRATED-ELECTRON/pseudo',
> verbosity='high',
> restart_mode='restart',
> /
> &SYSTEM
> ibrav=0,
> celldm(1)=29.8576727681d0,
> nat=384,
> tot_charge=-1,
> ntyp=2,
> ecutwfc=70,
> ecutrho=280,
> input_dft='BLYP',
> occupations='smearing',
> degauss=0.05d0,
> /
> &ELECTRONS
> mixing_beta=0.500d0,
> electron_maxstep=500,
> /
> &IONS
> /
> ATOMIC_SPECIES
> O 16.0d0 O.blyp-mt.UPF
> H 1.0079d0 H.blyp-vbc.UPF
>
> K_POINTS {automatic}
> 1 1 1 0 0 0
> CELL_PARAMETERS {alat}
> 1.000000000000d0 0.000000000000d0 0.000000000000d0
> 0.000000000000d0 1.000000000000d0 0.000000000000d0
> 0.000000000000d0 0.000000000000d0 1.000000000000d0
>
> *Output*
>
> Total force = 0.030447 Total SCF correction = 0.001115
> Total force = 0.033732 Total SCF correction = 0.000223
> Total force = 0.042921 Total SCF correction = 0.000171
> Total force = 0.032971 Total SCF correction = 0.000165
> Total force = 0.032983 Total SCF correction = 0.000266
> Total force = 0.036132 Total SCF correction = 0.000252
> Total force = 0.040191 Total SCF correction = 0.000833
> Total force = 0.032897 Total SCF correction = 0.001663
> Total force = 0.025425 Total SCF correction = 0.000288
> Total force = 0.019869 Total SCF correction = 0.000279
> Total force = 0.020382 Total SCF correction = 0.000102
> Total force = 0.025164 Total SCF correction = 0.000109
> Total force = 0.027580 Total SCF correction = 0.000141
> Total force = 0.026211 Total SCF correction = 0.000188
> Total force = 0.023574 Total SCF correction = 0.000139
> Total force = 0.024877 Total SCF correction = 0.000103
> Total force = 0.027597 Total SCF correction = 0.000131
> Total force = 0.027563 Total SCF correction = 0.000169
> Total force = 0.023015 Total SCF correction = 0.000195
> Total force = 0.021111 Total SCF correction = 0.000109
> Total force = 0.021345 Total SCF correction = 0.000092
> Total force = 0.023793 Total SCF correction = 0.000129
> Total force = 0.024400 Total SCF correction = 0.000145
> Total force = 0.025073 Total SCF correction = 0.000243
> Total force = 0.022300 Total SCF correction = 0.000376
> Total force = 0.020060 Total SCF correction = 0.000097
> Total force = 0.021991 Total SCF correction = 0.000134
> Total force = 0.022541 Total SCF correction = 0.000132
> Total force = 0.023051 Total SCF correction = 0.000158
> Total force = 0.023734 Total SCF correction = 0.000168
>
>
> Total force = 0.023734 Total SCF correction = 0.000168
> number of scf cycles = 49
> number of bfgs steps = 48
> energy old = -4400.3520443575 Ry
> energy new = -4400.3528674259 Ry
> CASE: energy _new < energy _old
> new trust radius = 0.0602516409 bohr
> new conv_thr = 0.0000000591 Ry
>
> Please help me.
>
> *Dr. Narendra Nath Ghosh*
>
> *Research Associate*
>
> *University of Gour Banga*
>
> *Malda-732102*
>
> *India*
>
> *Phone No : 09126667601*
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20171219/
> d771c77c/attachment-0001.html
>
> ------------------------------
>
> Message: 5
> Date: Tue, 19 Dec 2017 00:21:10 -0500
> From: Sudha Priyanka <sudhapriyanga24 at gmail.com>
> Subject: [Pw_forum] Optical properties: Real and imaginary part of
> dielectric function, Reflectivity, Energy loss function, Refractive
> index, dielectric constant, absorption spectrum
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAMM+pcC83JXj-e6KN9YCoNMFeVtJPL1eeoBon1TyqS8
> cYHTW6A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Experts
> How to compute Optical properties of the material such as Real and
> imaginary part of the dielectric function, Reflectivity, Energy loss
> function, Refractive index, dielectric constant, absorption spectrum by
> using qe-6.1? Is there any example files in current and previous version?
> When I am trying with epsilon.x it shows some error related to
> pseudopotential ie.,"USPP is not implemented". Is there any other option to
> calculate the optical properties with USPP?
> I need your guidance in this regards. Thanks in advance.
>
>
> With warm regards
> Sudha Priyanka G
> Assistant Professor,
> Lady Doak College,
> Madurai, Tamilnadu, India.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20171219/
> 20386ead/attachment-0001.html
>
> ------------------------------
>
> Message: 6
> Date: Tue, 19 Dec 2017 13:57:09 +0530
> From: Anuja Chanana <anujachanana26 at gmail.com>
> Subject: [Pw_forum] Merging output files
> To: pw_forum at pwscf.org
> Message-ID:
> <CAAWKNTh1wxS3vL6-dYf1o6Z4RDvAMBg66JKQDdkwqWUEcO
> AWwA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear QE,
> Is there a way to merge various output files in espresso and observe the
> results of the merged output file in Xcrysden?
>
> Looking forward to a reply.
>
> Thanks and Regards
> Dr. Anuja Chanana
> Research Associate
> Jawaharlal Nehru Centre for Advanced Scientific Research,
> Jakkur Bangalore-560064
>
>
>
>
>
> <https://mailtrack.io/> Sent with Mailtrack
> <https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/
> ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_
> medium=signature&utm_campaign=signaturevirality>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20171219/
> b50f4820/attachment-0001.html
>
> ------------------------------
>
> Message: 7
> Date: Tue, 19 Dec 2017 15:08:26 +0530
> From: B S Bhushan <ecebhushan at gmail.com>
> Subject: [Pw_forum] error- dE0s is positive which should never happen
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAK60_SYOVRnCT-ZM25kzmfm3LVd5ophn-L+
> LVmXbZX56+Zd8Vw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear experts...
>
> I have received this following error when I was trying to optimize a doped
> graphene sheet.
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%
> Error in routine bfgs (1):
> dE0s is positive which should never happen
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%%
>
> Please suggest me.... how to avoid this error.
>
> Thank you very much for your precious time and knowledge.
>
> Sincerely,
> B S Bhushan,
> Ph.D Scholar,
> ABV-IIITM Gwalior, India.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20171219/
> cc053919/attachment-0001.html
>
> ------------------------------
>
> Message: 8
> Date: Tue, 19 Dec 2017 11:17:32 +0100
> From: Lorenzo Paulatto <paulatz at gmail.com>
> Subject: Re: [Pw_forum] Merging output files
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAG+GtJd30sQTCsfNGq-ZvWmy0_+uUhjb3OikHa9FKmfqq+mJGw at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> cat file1 file2 > file_merged
>
> Kind regards
>
> --
> Lorenzo Paulatto
> Written on a virtual keyboard with real fingers
>
> On Dec 19, 2017 10:14, "Anuja Chanana" <anujachanana26 at gmail.com> wrote:
>
> > Dear QE,
> > Is there a way to merge various output files in espresso and observe the
> > results of the merged output file in Xcrysden?
> >
> > Looking forward to a reply.
> >
> > Thanks and Regards
> > Dr. Anuja Chanana
> > Research Associate
> > Jawaharlal Nehru Centre for Advanced Scientific Research,
> > Jakkur Bangalore-560064
> >
> >
> >
> >
> >
> > <https://mailtrack.io/> Sent with Mailtrack
> > <https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/
> ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_
> medium=signature&utm_campaign=signaturevirality>
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20171219/
> c5c230d8/attachment-0001.html
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
> End of Pw_forum Digest, Vol 125, Issue 13
> *****************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20171220/1530293a/attachment.html>
More information about the users
mailing list