<div dir="ltr"><img width="0" height="0" class="mailtrack-img" alt="" style="display:flex" src="https://mailtrack.io/trace/mail/3f2547da060686f46ad44615e8977f6c5820d239.png?u=1839753">Thanks for the reply. <div>Is it possible to read merged two output files in Xcrysden?</div><div>Looking forward to a reply.<br><br><br><br><div class="mt-signature">
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</div></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><span style="background-color:rgb(51,204,255)"><font size="2" face="arial, helvetica, sans-serif"><span style="background-color:rgb(0,0,0)"><span></span></span><span style="background-color:rgb(255,255,255)">Thanks and Regards<br>Dr. Anuja Chanana</span></font></span><div><span style="background-color:rgb(255,255,255)"><font size="2" face="arial, helvetica, sans-serif">Research Associate<br>Materials Theory Lab - Prof. Umesh Waghmare<br>Theoretical Sciences Unit,</font></span></div><div><span style="background-color:rgb(255,255,255)"><font size="2" face="arial, helvetica, sans-serif">Jawaharlal Nehru Centre for Advanced Scientific Research,</font></span></div><div><div><span style="background-color:rgb(255,255,255)"><font size="2" face="arial, helvetica, sans-serif">Jakkur Bangalore-560064<br></font></span></div><div><span style="background-color:rgb(255,255,255)"><font size="2" face="arial, helvetica, sans-serif"><a href="mailto:anuja@jncasr.ac.in" target="_blank">anuja@jncasr.ac.in</a></font></span></div><div><span style="background-color:rgb(255,255,255)"><font size="2"><font size="2"><font face="arial, helvetica, sans-serif"><a href="https://www.researchgate.net/profile/Anuja_Chanana" target="_blank">https://www.researchgate.net/profile/Anuja_Chanana</a></font><br></font></font></span></div><div><br></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Tue, Dec 19, 2017 at 4:30 PM, <span dir="ltr"><<a href="mailto:pw_forum-request@pwscf.org" target="_blank">pw_forum-request@pwscf.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Pw_forum mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. q2r not reading matdyn (A. Jain)<br>
2. Re: Unexpected error in NEB calculation (Paolo Giannozzi)<br>
3. Mailing list down (Paolo Giannozzi)<br>
4. Force is fluctuating for water system (Narendranath Ghosh)<br>
5. Optical properties: Real and imaginary part of dielectric<br>
function, Reflectivity, Energy loss function, Refractive index,<br>
dielectric constant, absorption spectrum (Sudha Priyanka)<br>
6. Merging output files (Anuja Chanana)<br>
7. error- dE0s is positive which should never happen (B S Bhushan)<br>
8. Re: Merging output files (Lorenzo Paulatto)<br>
<br>
<br>
------------------------------<wbr>------------------------------<wbr>----------<br>
<br>
Message: 1<br>
Date: Thu, 14 Dec 2017 12:13:49 +0000<br>
From: "A. Jain" <<a href="mailto:aj520@cam.ac.uk">aj520@cam.ac.uk</a>><br>
Subject: [Pw_forum] q2r not reading matdyn<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID: <<a href="mailto:7b7915f92c575a6f22355ecfd4445370@cam.ac.uk">7b7915f92c575a6f22355ecfd4445<wbr>370@cam.ac.uk</a>><br>
Content-Type: text/plain; charset=US-ASCII; format=flowed<br>
<br>
Hi all,<br>
<br>
I've successfully ran a phonon calculation on a 118 atom<br>
ruthenium-crystal system with P-1 symmetry over a 2x2x2 q-mesh. This<br>
results in 8 q-points. Due to the size of the system I followed the<br>
GRID_example layout, where each q-point was calculated independently<br>
using start_q and last_q. My ultimate aim is to obtain dispersion info<br>
and so I then tried to obtain IFCs using q2r.x. However it would read<br>
matdyn0 and matdyn1 without any issues but then stopped at matdyn2<br>
saying: BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES. The last<br>
few lines of the output are given below:<br>
<br>
na= 116<br>
0.01348 0.03651 -0.04974<br>
0.01943 0.02164 -0.18305<br>
-0.11583 -0.07468 -0.01909<br>
na= 117<br>
-0.08861 -0.09534 0.08548<br>
0.00377 0.05060 -0.05621<br>
0.04123 0.00009 0.12778<br>
na= 118<br>
-0.08861 -0.09534 0.08548<br>
0.00377 0.05060 -0.05621<br>
0.04123 0.00009 0.12778<br>
nqs= 1<br>
q= 0.00000000 0.00000000 0.00000000<br>
reading force constants from file matdyn2<br>
<br>
==============================<wbr>==============================<wbr>=======================<br>
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES<br>
= PID 26334 RUNNING AT cc061.cooley<br>
= EXIT CODE: 59<br>
= CLEANING UP REMAINING PROCESSES<br>
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES<br>
==============================<wbr>==============================<wbr>=======================<br>
<br>
<br>
Here is my input file for q2r.x:<br>
<br>
&input<br>
fildyn='matdyn',<br>
zasr='no',<br>
flfrc='dark_222.fc'<br>
/<br>
<br>
<br>
I have attempted the GRID_example using my 5.3.0 version of QE and it<br>
ran successfully without any issues. I'm still not vastly experienced<br>
with QE so I'm hoping this is an issue that others may have faced<br>
before. I initially thought my matdyn2 file may be corrupted and had a<br>
look but did not really see anything out of the ordinary. Please let me<br>
know if you all feel there are any changes I can make or if there is<br>
anymore information you may require.<br>
<br>
Apoorv Jain<br>
Department of Chemical Engineering and Biotechnology<br>
University of Cambridge<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 14 Dec 2017 14:06:10 +0100<br>
From: Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com">p.giannozzi@gmail.com</a>><br>
Subject: Re: [Pw_forum] Unexpected error in NEB calculation<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAPMgbCtHYcz7=<a href="mailto:r2J-m_gP-UuLTpez%2BaR1SzRwkTBwPifAhHaww@mail.gmail.com">r2J-m_gP-<wbr>UuLTpez+aR1SzRwkTBwPifAhHaww@<wbr>mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
On Thu, Dec 14, 2017 at 2:30 AM, jibiaoli <<a href="mailto:jibiaoli@foxmail.com">jibiaoli@foxmail.com</a>> wrote:<br>
<br>
I encountered a run error in NEB calculation. The error message is shown<br>
> below.<br>
><br>
<br>
it looks like a problem with your disk, not with the code itself<br>
<br>
Paolo<br>
<br>
--<br>
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
Phone <a href="tel:%2B39-0432-558216" value="+390432558216">+39-0432-558216</a>, fax <a href="tel:%2B39-0432-558222" value="+390432558222">+39-0432-558222</a><br>
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Message: 3<br>
Date: Mon, 18 Dec 2017 21:28:29 +0100<br>
From: Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com">p.giannozzi@gmail.com</a>><br>
Subject: [Pw_forum] Mailing list down<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>>, General discussion list for<br>
Quantum ESPRESSO developers <<a href="mailto:q-e-developers@qe-forge.org">q-e-developers@qe-forge.org</a>><br>
Cc: Quantum ESPRESSO Foundation <<a href="mailto:foundation@quantum-espresso.org">foundation@quantum-espresso.<wbr>org</a>><br>
Message-ID:<br>
<<a href="mailto:CAPMgbCui1yONgN4VG%2BqT_v-UuiscTo%2BfqXtkHY7bNQbDahBQQA@mail.gmail.com">CAPMgbCui1yONgN4VG+qT_v-<wbr>UuiscTo+fqXtkHY7bNQbDahBQQA@<wbr>mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Most <a href="http://qe-forge.org" rel="noreferrer" target="_blank">qe-forge.org</a> services, including mailing lists, have been unreachable<br>
since Dec.14 afternoon (CET time) due to a server problem and to a fialed<br>
restart. Now everything seems to be working again. Note however that the<br>
problem causing the crash (abnormal production of temporary files) is not<br>
solved, so mailing lists can be shut down any time to prevent further<br>
problems and will be moved soon to another hosting<br>
<br>
Paolo<br>
--<br>
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
Phone <a href="tel:%2B39-0432-558216" value="+390432558216">+39-0432-558216</a>, fax <a href="tel:%2B39-0432-558222" value="+390432558222">+39-0432-558222</a><br>
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<br>
Message: 4<br>
Date: Tue, 19 Dec 2017 09:16:07 +0530<br>
From: Narendranath Ghosh <<a href="mailto:ghosh.naren13@gmail.com">ghosh.naren13@gmail.com</a>><br>
Subject: [Pw_forum] Force is fluctuating for water system<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:CAAadC28GKMdsG8K%2BVfQgrxmoOYExanP96yf-JnrL83inAqTR1g@mail.gmail.com">CAAadC28GKMdsG8K+<wbr>VfQgrxmoOYExanP96yf-<wbr>JnrL83inAqTR1g@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear all<br>
<br>
I am relaxing a system of 128 water molecule with extra electron.The force<br>
is fluctuating even after bfgs steps = 48.<br>
<br>
<br>
<br>
*Input:*<br>
<br>
&CONTROL<br>
calculation='relax',<br>
outdir='/share_home/hpc/<wbr>NEGATIVE_HYDRATED_ELECTRON/<wbr>OUTPUT',<br>
prefix='water-128-negative',<br>
pseudo_dir='/share_home/hpc/<wbr>RESEARCH_SCHOLAR/HYDRATED-<wbr>ELECTRON/pseudo',<br>
verbosity='high',<br>
restart_mode='restart',<br>
/<br>
&SYSTEM<br>
ibrav=0,<br>
celldm(1)=29.8576727681d0,<br>
nat=384,<br>
tot_charge=-1,<br>
ntyp=2,<br>
ecutwfc=70,<br>
ecutrho=280,<br>
input_dft='BLYP',<br>
occupations='smearing',<br>
degauss=0.05d0,<br>
/<br>
&ELECTRONS<br>
mixing_beta=0.500d0,<br>
electron_maxstep=500,<br>
/<br>
&IONS<br>
/<br>
ATOMIC_SPECIES<br>
O 16.0d0 O.blyp-mt.UPF<br>
H 1.0079d0 H.blyp-vbc.UPF<br>
<br>
K_POINTS {automatic}<br>
1 1 1 0 0 0<br>
CELL_PARAMETERS {alat}<br>
1.000000000000d0 0.000000000000d0 0.000000000000d0<br>
0.000000000000d0 1.000000000000d0 0.000000000000d0<br>
0.000000000000d0 0.000000000000d0 1.000000000000d0<br>
<br>
*Output*<br>
<br>
Total force = 0.030447 Total SCF correction = 0.001115<br>
Total force = 0.033732 Total SCF correction = 0.000223<br>
Total force = 0.042921 Total SCF correction = 0.000171<br>
Total force = 0.032971 Total SCF correction = 0.000165<br>
Total force = 0.032983 Total SCF correction = 0.000266<br>
Total force = 0.036132 Total SCF correction = 0.000252<br>
Total force = 0.040191 Total SCF correction = 0.000833<br>
Total force = 0.032897 Total SCF correction = 0.001663<br>
Total force = 0.025425 Total SCF correction = 0.000288<br>
Total force = 0.019869 Total SCF correction = 0.000279<br>
Total force = 0.020382 Total SCF correction = 0.000102<br>
Total force = 0.025164 Total SCF correction = 0.000109<br>
Total force = 0.027580 Total SCF correction = 0.000141<br>
Total force = 0.026211 Total SCF correction = 0.000188<br>
Total force = 0.023574 Total SCF correction = 0.000139<br>
Total force = 0.024877 Total SCF correction = 0.000103<br>
Total force = 0.027597 Total SCF correction = 0.000131<br>
Total force = 0.027563 Total SCF correction = 0.000169<br>
Total force = 0.023015 Total SCF correction = 0.000195<br>
Total force = 0.021111 Total SCF correction = 0.000109<br>
Total force = 0.021345 Total SCF correction = 0.000092<br>
Total force = 0.023793 Total SCF correction = 0.000129<br>
Total force = 0.024400 Total SCF correction = 0.000145<br>
Total force = 0.025073 Total SCF correction = 0.000243<br>
Total force = 0.022300 Total SCF correction = 0.000376<br>
Total force = 0.020060 Total SCF correction = 0.000097<br>
Total force = 0.021991 Total SCF correction = 0.000134<br>
Total force = 0.022541 Total SCF correction = 0.000132<br>
Total force = 0.023051 Total SCF correction = 0.000158<br>
Total force = 0.023734 Total SCF correction = 0.000168<br>
<br>
<br>
Total force = 0.023734 Total SCF correction = 0.000168<br>
number of scf cycles = 49<br>
number of bfgs steps = 48<br>
energy old = -4400.3520443575 Ry<br>
energy new = -4400.3528674259 Ry<br>
CASE: energy _new < energy _old<br>
new trust radius = 0.0602516409 bohr<br>
new conv_thr = 0.0000000591 Ry<br>
<br>
Please help me.<br>
<br>
*Dr. Narendra Nath Ghosh*<br>
<br>
*Research Associate*<br>
<br>
*University of Gour Banga*<br>
<br>
*Malda-732102*<br>
<br>
*India*<br>
<br>
*Phone No : 09126667601*<br>
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<br>
Message: 5<br>
Date: Tue, 19 Dec 2017 00:21:10 -0500<br>
From: Sudha Priyanka <<a href="mailto:sudhapriyanga24@gmail.com">sudhapriyanga24@gmail.com</a>><br>
Subject: [Pw_forum] Optical properties: Real and imaginary part of<br>
dielectric function, Reflectivity, Energy loss function, Refractive<br>
index, dielectric constant, absorption spectrum<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:CAMM%2BpcC83JXj-e6KN9YCoNMFeVtJPL1eeoBon1TyqS8cYHTW6A@mail.gmail.com">CAMM+pcC83JXj-<wbr>e6KN9YCoNMFeVtJPL1eeoBon1TyqS8<wbr>cYHTW6A@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Experts<br>
How to compute Optical properties of the material such as Real and<br>
imaginary part of the dielectric function, Reflectivity, Energy loss<br>
function, Refractive index, dielectric constant, absorption spectrum by<br>
using qe-6.1? Is there any example files in current and previous version?<br>
When I am trying with epsilon.x it shows some error related to<br>
pseudopotential ie.,"USPP is not implemented". Is there any other option to<br>
calculate the optical properties with USPP?<br>
I need your guidance in this regards. Thanks in advance.<br>
<br>
<br>
With warm regards<br>
Sudha Priyanka G<br>
Assistant Professor,<br>
Lady Doak College,<br>
Madurai, Tamilnadu, India.<br>
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<br>
Message: 6<br>
Date: Tue, 19 Dec 2017 13:57:09 +0530<br>
From: Anuja Chanana <<a href="mailto:anujachanana26@gmail.com">anujachanana26@gmail.com</a>><br>
Subject: [Pw_forum] Merging output files<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<<a href="mailto:CAAWKNTh1wxS3vL6-dYf1o6Z4RDvAMBg66JKQDdkwqWUEcOAWwA@mail.gmail.com">CAAWKNTh1wxS3vL6-<wbr>dYf1o6Z4RDvAMBg66JKQDdkwqWUEcO<wbr>AWwA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear QE,<br>
Is there a way to merge various output files in espresso and observe the<br>
results of the merged output file in Xcrysden?<br>
<br>
Looking forward to a reply.<br>
<br>
Thanks and Regards<br>
Dr. Anuja Chanana<br>
Research Associate<br>
Jawaharlal Nehru Centre for Advanced Scientific Research,<br>
Jakkur Bangalore-560064<br>
<br>
<br>
<br>
<br>
<br>
<<a href="https://mailtrack.io/" rel="noreferrer" target="_blank">https://mailtrack.io/</a>> Sent with Mailtrack<br>
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Message: 7<br>
Date: Tue, 19 Dec 2017 15:08:26 +0530<br>
From: B S Bhushan <<a href="mailto:ecebhushan@gmail.com">ecebhushan@gmail.com</a>><br>
Subject: [Pw_forum] error- dE0s is positive which should never happen<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:CAK60_SYOVRnCT-ZM25kzmfm3LVd5ophn-L%2BLVmXbZX56%2BZd8Vw@mail.gmail.com">CAK60_SYOVRnCT-<wbr>ZM25kzmfm3LVd5ophn-L+<wbr>LVmXbZX56+Zd8Vw@mail.gmail.com</a><wbr>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear experts...<br>
<br>
I have received this following error when I was trying to optimize a doped<br>
graphene sheet.<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
%%%%%%%%%%%%%%%%%%<br>
Error in routine bfgs (1):<br>
dE0s is positive which should never happen<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
%%%%%%%%%%%%%%%%%%%<br>
<br>
Please suggest me.... how to avoid this error.<br>
<br>
Thank you very much for your precious time and knowledge.<br>
<br>
Sincerely,<br>
B S Bhushan,<br>
Ph.D Scholar,<br>
ABV-IIITM Gwalior, India.<br>
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Message: 8<br>
Date: Tue, 19 Dec 2017 11:17:32 +0100<br>
From: Lorenzo Paulatto <<a href="mailto:paulatz@gmail.com">paulatz@gmail.com</a>><br>
Subject: Re: [Pw_forum] Merging output files<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:CAG%2BGtJd30sQTCsfNGq-ZvWmy0_%2BuUhjb3OikHa9FKmfqq%2BmJGw@mail.gmail.com">CAG+GtJd30sQTCsfNGq-ZvWmy0_+<wbr>uUhjb3OikHa9FKmfqq+mJGw@mail.<wbr>gmail.com</a>><br>
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<br>
cat file1 file2 > file_merged<br>
<br>
Kind regards<br>
<br>
--<br>
Lorenzo Paulatto<br>
Written on a virtual keyboard with real fingers<br>
<br>
On Dec 19, 2017 10:14, "Anuja Chanana" <<a href="mailto:anujachanana26@gmail.com">anujachanana26@gmail.com</a>> wrote:<br>
<br>
> Dear QE,<br>
> Is there a way to merge various output files in espresso and observe the<br>
> results of the merged output file in Xcrysden?<br>
><br>
> Looking forward to a reply.<br>
><br>
> Thanks and Regards<br>
> Dr. Anuja Chanana<br>
> Research Associate<br>
> Jawaharlal Nehru Centre for Advanced Scientific Research,<br>
> Jakkur Bangalore-560064<br>
><br>
><br>
><br>
><br>
><br>
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