[Pw_forum] Quantum ESPRESSO @ Exabyte.io
Timur Bazhirov
timur at exabyte.io
Fri Oct 7 21:03:38 CEST 2016
[In reply to Rolly Ng]
Hi Rolly,
We have a flexible pricing scheme starting at $0.02 per CPU-hour. You can
find more information at:
https://docs.exabyte.io/billing/pricing-and-service-levels/
Users willing to provide regular feedback and publish the results of their
work could explore our community programs:
https://docs.exabyte.io/other/community-programs/
Best,
Timur Bazhirov, Ph.D.
Founder/CEO | exabyte.io
1161 Mission street, suite 505
San Francisco, CA 94103
+1.510.473.7770
On Fri, Oct 7, 2016 at 3:00 AM, < 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. Re: Parallel Execution (Kanak Datta)
> 2. Re: Quantum ESPRESSO @ Exabyte.io (Rolly Ng)
> 3. (no subject) (Kanak Datta)
> 4. Re: (no subject) (stefano de gironcoli)
> 5. Re: (no subject) (Axel Kohlmeyer)
> 6. Re: Quantum ESPRESSO @ Exabyte.io (Suza W)
> 7. Simulation ends at forces greater than forc_conv_thr (quantum)
> 8. Help in cif file atomic positions (Krishnaiah Kallamadi)
> 9. Re: Help in cif file atomic positions (Andrius Merkys)
> 10. Re: Simulation ends at forces greater than forc_conv_thr
> (Giovanni Cantele)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 6 Oct 2016 10:09:33 -0400
> From: Kanak Datta < kanakeee08 at gmail.com>
> Subject: Re: [Pw_forum] Parallel Execution
> To: pw_forum at pwscf.org
> Message-ID:
> < CAPGf_QHDhkeyxMDneUbSksMbpNJzy6cigMb0uW_JbNWQNEFy5w at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi
>
> Reply to Manu Hedge:
>
> I have been using a windows platform computer. It is run on windows 7
> enterprise version.
>
> Reply to Dr. Axel Kohlmeyer:
>
> I faced no problem with mpich2 before. I am facing them now. I saw your
> documentation at QE website and followed the first command:
> m p i e x e c - l o c a l o n l y # p w . .
>
> I get the error: unknown option: -localonly
>
> Then I executed the second one:
>
> m p i e x e c - n p # p w . . .
>
> This time the process works, but the processes are serial, not parallel.
>
> I don't know where the problem is. My installed MPI version is:
>
> mpich2-1.4.1p1
>
> The same mpi version that I had used before.
>
> This is where currently things are.
>
> It would be really helpful to me if I could get some help in this issue.
> Thanks in advance
>
> --
> Kanak Datta
> Lecturer
> Department of Electrical and Electronic Engineering
> Bangladesh University of Engineering and Technology
> Dhaka-1205
> Website: https://sites.google.com/site/kanak0806085/home
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20161006/2d4
> de79f/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Fri, 7 Oct 2016 00:54:18 +0800
> From: Rolly Ng < rollyng at gmail.com>
> Subject: Re: [Pw_forum] Quantum ESPRESSO @ Exabyte.io
> To: PWSCF Forum < pw_forum at pwscf.org>
> Message-ID: < 30a8ab70-a406-1c4c-dd84-13c56e7dd7e5 at gmail.com>
> Content-Type: text/plain; charset="windows-1252"
>
> Hi Timur,
>
> Very interesting. May I know the cost of using the facility?
>
> Best,
>
> Rolly
>
>
> On 10/06/2016 02:09 PM, Timur Bazhirov wrote:
> > Fellow Quantum ESPRESSO users,
> >
> > Let me bring to your attention to exabyte.io <http://exabyte.io>: a
> > web-based materials simulations platform with full support for Quantum
> > ESPRESSO. A brief getting-started tutorial and more information is
> > available at:
> >
> > https://docs.exabyte.io/getting-started/run-first-simulation/
> >
> > We provide a comprehensive and convenient way to prototype new
> > materials, run large-scale simulations and analyze the results. We
> > previously focused on enterprise researchers, and are now ready to
> > release the beta version to the public. You can apply to try it in
> > action at:
> >
> > https://platform.exabyte.io/register
> >
> > New registration requests mentioning "QE-forum" will get $10 credit
> > upon approval. Users may invite friends and colleagues to get an
> > additional $10 for each new accepted registration.
> >
> > We look forward to your feedback.
> >
> > Best,
> > Timur Bazhirov, Ph.D.
> > Founder/CEO | exabyte.io <http://exabyte.io>
> > 1161 Mission street, suite 505
> > San Francisco, CA 94103
> > +1.510.473.7770
> >
> > ? combinatorial screening of III-V semiconductors:
> > https://docs.exabyte.io/tutorials/combinatorial-screening/
> > ? 296 materials on 10,600 CPU in 38 hours:
> https://exabyte.io/#case-study
> > ? Quantum ESPRESSO benchmarking on exabyte.io <http://exabyte.io>:
> > https://exabyte.io/#case-study
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> PhD. Research Fellow,
> Dept. of Physics & Materials Science,
> City University of Hong Kong
> Tel: +852 3442 4000
> Fax: +852 3442 0538
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20161007/7f5
> c882a/attachment-0001.html
>
> ------------------------------
>
> Message: 3
> Date: Thu, 6 Oct 2016 14:01:12 -0400
> From: Kanak Datta < kanakeee08 at gmail.com>
> Subject: [Pw_forum] (no subject)
> To: pw_forum at pwscf.org
> Message-ID:
> < CAPGf_QG0bGJEpmryFae8xG7XehBGxDiHATeA--1JJtxphA9EnA at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear researchers
>
> Can Quantum Espresso 3.0 can be run with mpi distribution provided by
> microsoft i.e. MSMPI? In that case, will the command be the same?
>
> Best
> Kanak
>
> --
> Kanak Datta
> Lecturer
> Department of Electrical and Electronic Engineering
> Bangladesh University of Engineering and Technology
> Dhaka-1205
> Website: https://sites.google.com/site/kanak0806085/home
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20161006/ef2
> b36cc/attachment-0001.html
>
> ------------------------------
>
> Message: 4
> Date: Thu, 6 Oct 2016 20:08:33 +0200
> From: stefano de gironcoli < degironc at sissa.it>
> Subject: Re: [Pw_forum] (no subject)
> To: pw_forum at pwscf.org
> Message-ID: < 1566cb21-4040-65c5-f32e-426e418e4120 at sissa.it>
> Content-Type: text/plain; charset="windows-1252"
>
> don't really know anymore... Quantum ESPRESSO 6.0 has been just released.
> stefano
>
> On 06/10/2016 20:01, Kanak Datta wrote:
> > Dear researchers
> >
> > Can Quantum Espresso 3.0 can be run with mpi distribution provided by
> > microsoft i.e. MSMPI? In that case, will the command be the same?
> >
> > Best
> > Kanak
> >
> > --
> > Kanak Datta
> > Lecturer
> > Department of Electrical and Electronic Engineering
> > Bangladesh University of Engineering and Technology
> > Dhaka-1205
> > Website: https://sites.google.com/site/kanak0806085/home
> >
> >
> > _______________________________________________
> > 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/20161006/4cb
> 738d1/attachment-0001.html
>
> ------------------------------
>
> Message: 5
> Date: Thu, 6 Oct 2016 14:24:08 -0400
> From: Axel Kohlmeyer < akohlmey at gmail.com>
> Subject: Re: [Pw_forum] (no subject)
> To: PWSCF Forum < pw_forum at pwscf.org>
> Message-ID:
> < CADTmJ6H8KZWynYq651uY0jsKs0XX0BvYPh-+egzyCB3nE5oW0w at mail.g
> mail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Thu, Oct 6, 2016 at 2:08 PM, stefano de gironcoli < degironc at sissa.it>
> wrote:
> > don't really know anymore... Quantum ESPRESSO 6.0 has been just released.
>
> MS-MPI only supports MS Visual C++, which has no fortran support.
>
> axel
>
> > stefano
> >
> >
> > On 06/10/2016 20:01, Kanak Datta wrote:
> >
> > Dear researchers
> >
> > Can Quantum Espresso 3.0 can be run with mpi distribution provided by
> > microsoft i.e. MSMPI? In that case, will the command be the same?
> >
> > Best
> > Kanak
> >
> > --
> > Kanak Datta
> > Lecturer
> > Department of Electrical and Electronic Engineering
> > Bangladesh University of Engineering and Technology
> > Dhaka-1205
> > Website: https://sites.google.com/site/kanak0806085/home
> >
> >
> > _______________________________________________
> > 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
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 6 Oct 2016 12:55:40 -0700
> From: Suza W < suza.rri at gmail.com>
> Subject: Re: [Pw_forum] Quantum ESPRESSO @ Exabyte.io
> To: PWSCF Forum < pw_forum at pwscf.org>
> Message-ID:
> < CALN9FpQ78nost6S0pUee1hXNy8T8oKFyj+ErJAU0fOmG4zytCQ at mail.g
> mail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Very good news! thanks a lot Timur.
>
> Science must be enjoyed by all and should not be limited only within the
> rich and big groups, who have money, power and control to buy large
> supercomputers. The exabyte platform would presumably help talented but
> unfortunate small groups.
>
> Is there anyone in Quantum ESPRESSO who could sell or rent his/her DFPT+U
> code? Is anyone aware of any DFPT+U version like the student version of
> Matlab or something? I know, VASP has DFPT+U option for the zone-center
> point, but it is super-expensive economically.
>
> Sincerely,
> Suza
>
> School of Physics and Electronic Sciences
> Changsha University of Science and Technology,
> Changsha, People?s Republic of China
>
>
> On Wed, Oct 5, 2016 at 11:09 PM, Timur Bazhirov < timur at exabyte.io>
> wrote:
>
> > Fellow Quantum ESPRESSO users,
> >
> > Let me bring to your attention to exabyte.io: a web-based materials
> > simulations platform with full support for Quantum ESPRESSO. A brief
> > getting-started tutorial and more information is available at:
> >
> > https://docs.exabyte.io/getting-started/run-first-simulation/
> >
> > We provide a comprehensive and convenient way to prototype new materials,
> > run large-scale simulations and analyze the results. We previously
> focused
> > on enterprise researchers, and are now ready to release the beta version
> to
> > the public. You can apply to try it in action at:
> >
> > https://platform.exabyte.io/register
> >
> > New registration requests mentioning "QE-forum" will get $10 credit upon
> > approval. Users may invite friends and colleagues to get an additional
> $10
> > for each new accepted registration.
> >
> > We look forward to your feedback.
> >
> > Best,
> > Timur Bazhirov, Ph.D.
> > Founder/CEO | exabyte.io
> > 1161 Mission street, suite 505
> > San Francisco, CA 94103
> > +1.510.473.7770
> >
> > ? combinatorial screening of III-V semiconductors:
> > https://docs.exabyte.io/tutorials/combinatorial-screening/
> > ? 296 materials on 10,600 CPU in 38 hours:
> https://exabyte.io/#case-study
> > ? Quantum ESPRESSO benchmarking on exabyte.io:
> > https://exabyte.io/#case-study
> >
> >
> > _______________________________________________
> > 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/20161006/cc4
> ea8ea/attachment-0001.html
>
> ------------------------------
>
> Message: 7
> Date: Fri, 07 Oct 2016 11:25:37 +0800 (CST)
> From: "quantum" < quantum at mail.ncyu.edu.tw>
> Subject: [Pw_forum] Simulation ends at forces greater than
> forc_conv_thr
> To: "pw_forum" < pw_forum at pwscf.org>
> Message-ID: < 1475810732.8196.quantum at mail.ncyu.edu.tw>
> Content-Type: text/plain; charset=utf-8
>
>
> Dear QE Friends:
>
> I am trying to optimize a crystal by allowing the atomic positions of
> hydrogens to relax. All other atoms of the crystal are held fixed. The QE
> input file is listed by the end of this message.
>
> QE starts with the self-consistent calculation using the initial guess of
> atomic positions. After the first scf cycle, QE prints out a new set of
> atomic positions, and ends without a new scf cycle with the new set of
> atomic positions. (Please see the QE output attached below.)
>
> The EQ output suggests that the forces acting on all hydrogen atoms are
> greater than "forc_conv_thr = 1.0D-4."
>
> Why does the simulation end with only one scf cycle?
>
> Thank you in advance.
>
>
> **** QE output file (partial) starts here ******************
>
> ! total energy = -1426.31830754 Ry
> Harris-Foulkes estimate = -1426.31830738 Ry
> estimated scf accuracy < 0.00000009 Ry
>
> The total energy is the sum of the following terms:
>
> one-electron contribution = -615.01611222 Ry
> hartree contribution = 407.92628821 Ry
> xc contribution = -287.90966771 Ry
> ewald contribution = -702.94572199 Ry
> Dispersion Correction = -0.28187072 Ry
> one-center paw contrib. = -228.09122311 Ry
>
> convergence has been achieved in 9 iterations
>
> Forces acting on atoms (Ry/au):
>
> atom 1 type 1 force = 0.00000104 -0.00894702 -0.00000051
> atom 2 type 1 force = -0.00000045 -0.00894443 -0.00000014
> ........
> atom 33 type 4 force = -0.01684128 -0.06271162 0.16881369
> atom 34 type 4 force = -0.01684137 -0.06271191 0.16881443
> atom 35 type 4 force = -0.01684128 0.06271162 0.16881368
> atom 36 type 4 force = -0.01684137 0.06271191 0.16881444
> atom 37 type 4 force = 0.01684128 -0.06271162 -0.16881368
> atom 38 type 4 force = 0.01684137 -0.06271191 -0.16881444
> atom 39 type 4 force = 0.01684128 0.06271162 -0.16881369
> atom 40 type 4 force = 0.01684137 0.06271191 -0.16881443
> atom 41 type 4 force = 0.05926419 0.21504962 -0.01148228
> atom 42 type 4 force = 0.05926450 0.21505075 -0.01148234
> atom 43 type 4 force = 0.05926419 -0.21504962 -0.01148228
> atom 44 type 4 force = 0.05926450 -0.21505072 -0.01148234
> atom 45 type 4 force = -0.05926419 0.21504962 0.01148228
> atom 46 type 4 force = -0.05926450 0.21505072 0.01148234
> atom 47 type 4 force = -0.05926419 -0.21504962 0.01148228
> atom 48 type 4 force = -0.05926450 -0.21505075 0.01148234
>
> ...........
>
> Total force = 2.613470 Total SCF correction = 0.000031
>
> Total Dispersion Force = 0.007543
>
> ...........
>
> BFGS Geometry Optimization
>
> number of scf cycles = 1
> number of bfgs steps = 0
>
> energy new = -1426.3183075352 Ry
>
> new trust radius = 0.5000000000 bohr
> new conv_thr = 0.0000001000 Ry
>
>
> **** QE input file starts here ***********************************
> &control
> title = 'Gypsum (CaSO4.2H20 Z=4)'
> prefix = 'gypsum-SSSP_acc_PBE-exp0.56G'
> outdir = '/work2/u2equa02/tempdir/gypsum-SSSP_acc_PBE-exp0.56G'
> pseudo_dir = '/home/u2equa02/quantumhome/pseudo'
> calculation = 'relax'
> restart_mode = 'from_scratch'
> disk_io = 'low'
> verbosity = 'high'
> tstress = .true.
> tprnfor = .true.
> nstep = 1
> etot_conv_thr = 1.0D-5
> forc_conv_thr = 1.0D-4
> iprint = 1
> /
> &system
> ibrav = 0
> ntyp = 4
> nat = 48
> ecutwfc = 100
> ecutrho = 800
> vdw_corr = 'grimme-d2'
> /
> &electrons
> electron_maxstep = 200
> conv_thr = 1.0D-7
> diago_thr_init = 1.0D-4
> startingpot = 'atomic'
> startingwfc = 'atomic+random'
> mixing_mode = 'plain'
> mixing_beta = 0.5
> mixing_ndim= 8
> diagonalization = 'david'
> /
> &ions
> ion_dynamics = 'bfgs'
> /
>
> ATOMIC_SPECIES
> Ca 40.0780000000 Ca_pbe_v1.uspp.F.UPF
> S 32.0650000000 S_pbe_v1.2.uspp.F.UPF
> O 15.9994000000 O.pbe-n-kjpaw_psl.0.1.UPF
> H 1.0079000000 H.pbe-rrkjus_psl.0.1.UPF
>
> ATOMIC_POSITIONS crystal
> Ca 0.00000000000000 0.17110000000000 0.25000000000000 0 0 0
> Ca 0.50000000000000 0.67110000000000 0.25000000000000 0 0 0
> Ca 0.00000000000000 0.82890000000000 0.75000000000000 0 0 0
> Ca 0.50000000000000 0.32890000000000 0.75000000000000 0 0 0
> S 0.00000000000000 0.32880000000000 0.75000000000000 0 0 0
> S 0.50000000000000 0.82880000000000 0.75000000000000 0 0 0
> S 0.00000000000000 0.67120000000000 0.25000000000000 0 0 0
> S 0.50000000000000 0.17120000000000 0.25000000000000 0 0 0
> O 0.08200000000000 0.27600000000000 0.59100000000000 0 0 0
> O 0.58200000000000 0.77600000000000 0.59100000000000 0 0 0
> O 0.08200000000000 0.72400000000000 0.09100000000000 0 0 0
> O 0.58200000000000 0.22400000000000 0.09100000000000 0 0 0
> O 0.91800000000000 0.27600000000000 0.90900000000000 0 0 0
> O 0.41800000000000 0.77600000000000 0.90900000000000 0 0 0
> O 0.91800000000000 0.72400000000000 0.40900000000000 0 0 0
> O 0.41800000000000 0.22400000000000 0.40900000000000 0 0 0
> O 0.20300000000000 0.38700000000000 0.91700000000000 0 0 0
> O 0.70300000000000 0.88700000000000 0.91700000000000 0 0 0
> O 0.20300000000000 0.61300000000000 0.41700000000000 0 0 0
> O 0.70300000000000 0.11300000000000 0.41700000000000 0 0 0
> O 0.79700000000000 0.38700000000000 0.58300000000000 0 0 0
> O 0.29700000000000 0.88700000000000 0.58300000000000 0 0 0
> O 0.79700000000000 0.61300000000000 0.08300000000000 0 0 0
> O 0.29700000000000 0.11300000000000 0.08300000000000 0 0 0
> O 0.78700000000000 0.06900000000000 0.91800000000000 0 0 0
> O 0.28700000000000 0.56900000000000 0.91800000000000 0 0 0
> O 0.78700000000000 0.93100000000000 0.41800000000000 0 0 0
> O 0.28700000000000 0.43100000000000 0.41800000000000 0 0 0
> O 0.21300000000000 0.06900000000000 0.58200000000000 0 0 0
> O 0.71300000000000 0.56900000000000 0.58200000000000 0 0 0
> O 0.21300000000000 0.93100000000000 0.08200000000000 0 0 0
> O 0.71300000000000 0.43100000000000 0.08200000000000 0 0 0
> H 0.74200000000000 0.08700000000000 0.76600000000000 1 1 1
> H 0.24200000000000 0.58700000000000 0.76600000000000 1 1 1
> H 0.74200000000000 0.91300000000000 0.26600000000000 1 1 1
> H 0.24200000000000 0.41300000000000 0.26600000000000 1 1 1
> H 0.25800000000000 0.08700000000000 0.73400000000000 1 1 1
> H 0.75800000000000 0.58700000000000 0.73400000000000 1 1 1
> H 0.25800000000000 0.91300000000000 0.23400000000000 1 1 1
> H 0.75800000000000 0.41300000000000 0.23400000000000 1 1 1
> H 0.75600000000000 0.02000000000000 0.92300000000000 1 1 1
> H 0.25600000000000 0.52000000000000 0.92300000000000 1 1 1
> H 0.75600000000000 0.98000000000000 0.42300000000000 1 1 1
> H 0.25600000000000 0.48000000000000 0.42300000000000 1 1 1
> H 0.24400000000000 0.02000000000000 0.57700000000000 1 1 1
> H 0.74400000000000 0.52000000000000 0.57700000000000 1 1 1
> H 0.24400000000000 0.98000000000000 0.07700000000000 1 1 1
> H 0.74400000000000 0.48000000000000 0.07700000000000 1 1 1
>
> K_POINTS automatic
> 12 6 18 0 0 0
>
> CELL_PARAMETERS bohr
> 11.83535471815098 0.00000000000000 0.00000000000000
> 0.00000000000000 28.65391722678003 0.00000000000000
> -4.39283675093634 0.00000000000000 9.75628273508813
>
>
>
>
>
> Tsung-Lung Li, Ph. D.
> Professor
> Department of Applied Physics
> National Chia-Yi University
> 300 Hsueh-Fu Road, Chiayi 60004, Taiwan
> Phone: 886-5-2717904. FAX: 886-5-2717909.
> E-mail:quantum at mail.ncyu.edu.tw
> URL:http://web.ncyu.edu.tw/~quantum
>
>
>
> ------------------------------
>
> Message: 8
> Date: Fri, 7 Oct 2016 11:00:57 +0530
> From: Krishnaiah Kallamadi < krishnsustain at gmail.com>
> Subject: [Pw_forum] Help in cif file atomic positions
> To: PWSCF Forum < pw_forum at pwscf.org>
> Message-ID:
> < CAKfmqB6xdyOX3Z-N-wKovF4CV29QcyfHAsrrvR98EZfrauOBvw at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear friends,
>
> In a *cif* file attached below, two different atoms have same atomic
> positions with occupancy of 0.5. Due to this i am not able to generate *
> scf.in
> <http://scf.in>* file from cif2cell program. Please help me.
>
> N1 N 1.0000 1.0000 0.21657(2) 0.36(10) Uani 0.5 6 d S T P C 2
>
> C1 C 1.0000 1.0000 0.21657(2) 0.36(10) Uani 0.5 6 d DS T P A 1
>
>
> --
> Thanks and Regards,
>
> K.Krishna
> PhD Student, MSE-Department
> IIT Kanpur
> India
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20161007/1b6
> 58114/attachment-0001.html
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: c5cc10455f2.rtf
> Type: application/rtf
> Size: 16246 bytes
> Desc: not available
> Url : http://pwscf.org/pipermail/pw_forum/attachments/20161007/1b6
> 58114/attachment-0001.rtf
>
> ------------------------------
>
> Message: 9
> Date: Fri, 7 Oct 2016 09:03:29 +0300
> From: Andrius Merkys < andrius.merkys at gmail.com>
> Subject: Re: [Pw_forum] Help in cif file atomic positions
> To: PWSCF Forum < pw_forum at pwscf.org>
> Message-ID: < f4c4b94a-3f47-0746-2c50-5c48b539e77e at gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Krishna,
>
>
> On 07/10/16 08:30, Krishnaiah Kallamadi wrote:
> > In a *cif* file attached below, two different atoms have same atomic
> > positions with occupancy of 0.5. Due to this i am not able to generate
> > *scf.in <http://scf.in>* file from cif2cell program. Please help me.
>
> you have to account for a joint 0.5N+0.5C site at this position. I am
> not sure if/how such thing is possible at QE input, but AFAIK, people
> are dealing with such models.
>
> HTH,
> Andrius
>
> --
> Andrius Merkys
> PhD student at Vilnius University Institute of Biotechnology, Saul?tekio
> al. 7
> LT-10223 Vilnius, Lithuania
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20161007/e88
> 2bad7/attachment-0001.html
>
> ------------------------------
>
> Message: 10
> Date: Fri, 7 Oct 2016 09:34:48 +0200
> From: Giovanni Cantele < giovanni.cantele at spin.cnr.it>
> Subject: Re: [Pw_forum] Simulation ends at forces greater than
> forc_conv_thr
> To: PWSCF Forum < pw_forum at pwscf.org>
> Message-ID: < 33B7A576-28E9-4311-ADAD-5BBC72796E37 at spin.cnr.it>
> Content-Type: text/plain; charset="us-ascii"
>
> from: http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT
> _PW.html#idm6452736 <http://www.quantum-espresso.o
> rg/wp-content/uploads/Doc/INPUT_PW.html#idm6452736>
>
> nstep -> number of molecular-dynamics or structural optimization steps
> performed in this run
>
> So if you set nstep=1 just one optimisation step is carried out.
>
> Giovanni
>
>
>
> > On 7 Oct 2016, at 05:25, quantum < quantum at mail.ncyu.edu.tw> wrote:
> >
> >
> > Dear QE Friends:
> >
> > I am trying to optimize a crystal by allowing the atomic positions of
> hydrogens to relax. All other atoms of the crystal are held fixed. The QE
> input file is listed by the end of this message.
> >
> > QE starts with the self-consistent calculation using the initial guess
> of atomic positions. After the first scf cycle, QE prints out a new set of
> atomic positions, and ends without a new scf cycle with the new set of
> atomic positions. (Please see the QE output attached below.)
> >
> > The EQ output suggests that the forces acting on all hydrogen atoms are
> greater than "forc_conv_thr = 1.0D-4."
> >
> > Why does the simulation end with only one scf cycle?
> >
> > Thank you in advance.
> >
> >
> > **** QE output file (partial) starts here ******************
> >
> > ! total energy = -1426.31830754 Ry
> > Harris-Foulkes estimate = -1426.31830738 Ry
> > estimated scf accuracy < 0.00000009 Ry
> >
> > The total energy is the sum of the following terms:
> >
> > one-electron contribution = -615.01611222 Ry
> > hartree contribution = 407.92628821 Ry
> > xc contribution = -287.90966771 Ry
> > ewald contribution = -702.94572199 Ry
> > Dispersion Correction = -0.28187072 Ry
> > one-center paw contrib. = -228.09122311 Ry
> >
> > convergence has been achieved in 9 iterations
> >
> > Forces acting on atoms (Ry/au):
> >
> > atom 1 type 1 force = 0.00000104 -0.00894702
> -0.00000051
> > atom 2 type 1 force = -0.00000045 -0.00894443
> -0.00000014
> > ........
> > atom 33 type 4 force = -0.01684128 -0.06271162
> 0.16881369
> > atom 34 type 4 force = -0.01684137 -0.06271191
> 0.16881443
> > atom 35 type 4 force = -0.01684128 0.06271162
> 0.16881368
> > atom 36 type 4 force = -0.01684137 0.06271191
> 0.16881444
> > atom 37 type 4 force = 0.01684128 -0.06271162
> -0.16881368
> > atom 38 type 4 force = 0.01684137 -0.06271191
> -0.16881444
> > atom 39 type 4 force = 0.01684128 0.06271162
> -0.16881369
> > atom 40 type 4 force = 0.01684137 0.06271191
> -0.16881443
> > atom 41 type 4 force = 0.05926419 0.21504962
> -0.01148228
> > atom 42 type 4 force = 0.05926450 0.21505075
> -0.01148234
> > atom 43 type 4 force = 0.05926419 -0.21504962
> -0.01148228
> > atom 44 type 4 force = 0.05926450 -0.21505072
> -0.01148234
> > atom 45 type 4 force = -0.05926419 0.21504962
> 0.01148228
> > atom 46 type 4 force = -0.05926450 0.21505072
> 0.01148234
> > atom 47 type 4 force = -0.05926419 -0.21504962
> 0.01148228
> > atom 48 type 4 force = -0.05926450 -0.21505075
> 0.01148234
> >
> > ...........
> >
> > Total force = 2.613470 Total SCF correction = 0.000031
> >
> > Total Dispersion Force = 0.007543
> >
> > ...........
> >
> > BFGS Geometry Optimization
> >
> > number of scf cycles = 1
> > number of bfgs steps = 0
> >
> > energy new = -1426.3183075352 Ry
> >
> > new trust radius = 0.5000000000 bohr
> > new conv_thr = 0.0000001000 Ry
> >
> >
> > **** QE input file starts here ***********************************
> > &control
> > title = 'Gypsum (CaSO4.2H20 Z=4)'
> > prefix = 'gypsum-SSSP_acc_PBE-exp0.56G'
> > outdir = '/work2/u2equa02/tempdir/gypsum-SSSP_acc_PBE-exp0.56G'
> > pseudo_dir = '/home/u2equa02/quantumhome/pseudo'
> > calculation = 'relax'
> > restart_mode = 'from_scratch'
> > disk_io = 'low'
> > verbosity = 'high'
> > tstress = .true.
> > tprnfor = .true.
> > nstep = 1
> > etot_conv_thr = 1.0D-5
> > forc_conv_thr = 1.0D-4
> > iprint = 1
> > /
> > &system
> > ibrav = 0
> > ntyp = 4
> > nat = 48
> > ecutwfc = 100
> > ecutrho = 800
> > vdw_corr = 'grimme-d2'
> > /
> > &electrons
> > electron_maxstep = 200
> > conv_thr = 1.0D-7
> > diago_thr_init = 1.0D-4
> > startingpot = 'atomic'
> > startingwfc = 'atomic+random'
> > mixing_mode = 'plain'
> > mixing_beta = 0.5
> > mixing_ndim= 8
> > diagonalization = 'david'
> > /
> > &ions
> > ion_dynamics = 'bfgs'
> > /
> >
> > ATOMIC_SPECIES
> > Ca 40.0780000000 Ca_pbe_v1.uspp.F.UPF
> > S 32.0650000000 S_pbe_v1.2.uspp.F.UPF
> > O 15.9994000000 O.pbe-n-kjpaw_psl.0.1.UPF
> > H 1.0079000000 H.pbe-rrkjus_psl.0.1.UPF
> >
> > ATOMIC_POSITIONS crystal
> > Ca 0.00000000000000 0.17110000000000 0.25000000000000 0 0
> 0
> > Ca 0.50000000000000 0.67110000000000 0.25000000000000 0 0
> 0
> > Ca 0.00000000000000 0.82890000000000 0.75000000000000 0 0
> 0
> > Ca 0.50000000000000 0.32890000000000 0.75000000000000 0 0
> 0
> > S 0.00000000000000 0.32880000000000 0.75000000000000 0 0 0
> > S 0.50000000000000 0.82880000000000 0.75000000000000 0 0 0
> > S 0.00000000000000 0.67120000000000 0.25000000000000 0 0 0
> > S 0.50000000000000 0.17120000000000 0.25000000000000 0 0 0
> > O 0.08200000000000 0.27600000000000 0.59100000000000 0 0 0
> > O 0.58200000000000 0.77600000000000 0.59100000000000 0 0 0
> > O 0.08200000000000 0.72400000000000 0.09100000000000 0 0 0
> > O 0.58200000000000 0.22400000000000 0.09100000000000 0 0 0
> > O 0.91800000000000 0.27600000000000 0.90900000000000 0 0 0
> > O 0.41800000000000 0.77600000000000 0.90900000000000 0 0 0
> > O 0.91800000000000 0.72400000000000 0.40900000000000 0 0 0
> > O 0.41800000000000 0.22400000000000 0.40900000000000 0 0 0
> > O 0.20300000000000 0.38700000000000 0.91700000000000 0 0 0
> > O 0.70300000000000 0.88700000000000 0.91700000000000 0 0 0
> > O 0.20300000000000 0.61300000000000 0.41700000000000 0 0 0
> > O 0.70300000000000 0.11300000000000 0.41700000000000 0 0 0
> > O 0.79700000000000 0.38700000000000 0.58300000000000 0 0 0
> > O 0.29700000000000 0.88700000000000 0.58300000000000 0 0 0
> > O 0.79700000000000 0.61300000000000 0.08300000000000 0 0 0
> > O 0.29700000000000 0.11300000000000 0.08300000000000 0 0 0
> > O 0.78700000000000 0.06900000000000 0.91800000000000 0 0 0
> > O 0.28700000000000 0.56900000000000 0.91800000000000 0 0 0
> > O 0.78700000000000 0.93100000000000 0.41800000000000 0 0 0
> > O 0.28700000000000 0.43100000000000 0.41800000000000 0 0 0
> > O 0.21300000000000 0.06900000000000 0.58200000000000 0 0 0
> > O 0.71300000000000 0.56900000000000 0.58200000000000 0 0 0
> > O 0.21300000000000 0.93100000000000 0.08200000000000 0 0 0
> > O 0.71300000000000 0.43100000000000 0.08200000000000 0 0 0
> > H 0.74200000000000 0.08700000000000 0.76600000000000 1 1 1
> > H 0.24200000000000 0.58700000000000 0.76600000000000 1 1 1
> > H 0.74200000000000 0.91300000000000 0.26600000000000 1 1 1
> > H 0.24200000000000 0.41300000000000 0.26600000000000 1 1 1
> > H 0.25800000000000 0.08700000000000 0.73400000000000 1 1 1
> > H 0.75800000000000 0.58700000000000 0.73400000000000 1 1 1
> > H 0.25800000000000 0.91300000000000 0.23400000000000 1 1 1
> > H 0.75800000000000 0.41300000000000 0.23400000000000 1 1 1
> > H 0.75600000000000 0.02000000000000 0.92300000000000 1 1 1
> > H 0.25600000000000 0.52000000000000 0.92300000000000 1 1 1
> > H 0.75600000000000 0.98000000000000 0.42300000000000 1 1 1
> > H 0.25600000000000 0.48000000000000 0.42300000000000 1 1 1
> > H 0.24400000000000 0.02000000000000 0.57700000000000 1 1 1
> > H 0.74400000000000 0.52000000000000 0.57700000000000 1 1 1
> > H 0.24400000000000 0.98000000000000 0.07700000000000 1 1 1
> > H 0.74400000000000 0.48000000000000 0.07700000000000 1 1 1
> >
> > K_POINTS automatic
> > 12 6 18 0 0 0
> >
> > CELL_PARAMETERS bohr
> > 11.83535471815098 0.00000000000000 0.00000000000000
> > 0.00000000000000 28.65391722678003 0.00000000000000
> > -4.39283675093634 0.00000000000000 9.75628273508813
> >
> >
> >
> >
> >
> > Tsung-Lung Li, Ph. D.
> > Professor
> > Department of Applied Physics
> > National Chia-Yi University
> > 300 Hsueh-Fu Road, Chiayi 60004, Taiwan
> > Phone: 886-5-2717904. FAX: 886-5-2717909.
> > E-mail:quantum at mail.ncyu.edu.tw
> > URL:http://web.ncyu.edu.tw/~quantum
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> e-mail: giovanni.cantele at spin.cnr.it
> Phone: +39 081 676910
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20161007/405
> 7a18e/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 111, Issue 7
> ****************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20161007/251164a8/attachment.html>
More information about the users
mailing list