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 an...@jncasr.ac.in https://www.researchgate.net/profile/Anuja_Chanana On Tue, Dec 19, 2017 at 4:30 PM, <pw_forum-requ...@pwscf.org> wrote: > Send Pw_forum mailing list submissions to > pw_forum@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-requ...@pwscf.org > > You can reach the person managing the list at > pw_forum-ow...@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" <aj...@cam.ac.uk> > Subject: [Pw_forum] q2r not reading matdyn > To: pw_forum@pwscf.org > Message-ID: <7b7915f92c575a6f22355ecfd4445...@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.gianno...@gmail.com> > Subject: Re: [Pw_forum] Unexpected error in NEB calculation > To: PWSCF Forum <pw_forum@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 <jibia...@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.gianno...@gmail.com> > Subject: [Pw_forum] Mailing list down > To: PWSCF Forum <pw_forum@pwscf.org>, General discussion list for > Quantum ESPRESSO developers <q-e-develop...@qe-forge.org> > Cc: Quantum ESPRESSO Foundation <foundat...@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.nare...@gmail.com> > Subject: [Pw_forum] Force is fluctuating for water system > To: PWSCF Forum <pw_forum@pwscf.org> > Message-ID: > <CAAadC28GKMdsG8K+VfQgrxmoOYExanP96yf- > jnrl83inaqt...@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 <sudhapriyang...@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@pwscf.org> > Message-ID: > <CAMM+pcC83JXj-e6KN9YCoNMFeVtJPL1eeoBon1TyqS8 > cyht...@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 <anujachanan...@gmail.com> > Subject: [Pw_forum] Merging output files > To: pw_forum@pwscf.org > Message-ID: > <CAAWKNTh1wxS3vL6-dYf1o6Z4RDvAMBg66JKQDdkwqWUEcO > a...@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 <ecebhus...@gmail.com> > Subject: [Pw_forum] error- dE0s is positive which should never happen > To: PWSCF Forum <pw_forum@pwscf.org> > Message-ID: > <CAK60_SYOVRnCT-ZM25kzmfm3LVd5ophn-L+ > lvmxbzx56+zd...@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 <paul...@gmail.com> > Subject: Re: [Pw_forum] Merging output files > To: PWSCF Forum <pw_forum@pwscf.org> > Message-ID: > <CAG+GtJd30sQTCsfNGq-ZvWmy0_+uUhjb3OikHa9FKmfqq+mJGw@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" <anujachanan...@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@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@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > End of Pw_forum Digest, Vol 125, Issue 13 > ***************************************** >
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