[Pw_forum] QE-5.1.2: NEB.X Crashes with MPI errors
Dear All, I'm trying to submit a NEB calculation on the Mn3/4Co1/4PO4 system to calculate the Lithium energy barrier for diffusion. The baseline calculation on MnPO4 went fine. Inserting the cobalt atoms neb.x crashes during the calculation on the second image. No error is printed in the log but in the standard output I obtain: 2 2 INTERMEDIATE_IMAGE [t12node084:17231] 55 more processes have sent help message help-mpi-btl-openib.txt / reg mem limit low [t12node084:17231] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages [t12node082:28692] *** An error occurred in MPI_Bcast [t12node082:28692] *** on communicator MPI COMMUNICATOR 9 SPLIT FROM 7 [t12node082:28692] *** MPI_ERR_TRUNCATE: message truncated [t12node082:28692] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort -- mpiexec has exited due to process rank 31 with PID 28692 on node t12node082 exiting improperly. There are two reasons this could occur: 1. this process did not call "init" before exiting, but others in the job did. This can cause a job to hang indefinitely while it waits for all processes to call "init". By rule, if one process calls "init", then ALL processes must call "init" prior to termination. 2. this process called "init", but exited without calling "finalize". By rule, all processes that call "init" MUST call "finalize" prior to exiting or it will be considered an "abnormal termination" This may have caused other processes in the application to be terminated by signals sent by mpiexec (as reported here). -- [t12node084:17231] 8 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal Is my input in some way wrong, it's a problem of compilation of the code or it is a bug? My code is compiled with gcc/gfortran and OpenMPI. I'm reporting my input for reference below. Thanks lot in advance and best regards, Mauro Sgroi. Centro Ricerche FIAT, Italy. BEGIN BEGIN_PATH_INPUT restart_mode = 'from_scratch' string_method = 'neb', nstep_path= 200, ds= 1.D0, opt_scheme= "broyden2", num_of_images = 7, k_max = 0.3D0, k_min = 0.2D0, CI_scheme = "auto", path_thr = 0.1D0, first_last_opt= .true. / END_PATH_INPUT BEGIN_ENGINE_INPUT pseudo_dir='/data5/sgroi/DATABASE/ESPRESSO', prefix='mnpo4_121_gamma', outdir='/net/manager/remote/qespresso/mnpo4_121_gamma', wf_collect=.false., disk_io='none', / ibrav=8, nat=49, ntyp=5, ecutwfc=78, ecutrho=355, nbnd=240, occupations='smearing', degauss=1d-10, smearing='mv', nspin=2, starting_magnetization(1)=0.9, starting_magnetization(2)=0.9, lda_plus_u=.true., Hubbard_U(1)= 4.5, Hubbard_U(2)=5.695, celldm(1)=18.49395, celldm(2)=1.21346602537586616163, celldm(3)=0.49381770795314143273 / conv_thr=1.0d-9, electron_maxstep=200, mixing_beta=0.5, scf_must_converge=.false. / ATOMIC_SPECIES Mn 54.9381 Mn.pbesol-spn-kjpaw_psl.0.3.1.UPF Co 58.933195 Co.pbesol-n-kjpaw_psl.0.2.3.UPF P 30.9737 P.pbesol-n-kjpaw_psl.0.1.UPF O 15.9994 O.pbesol-n-kjpaw_psl.0.1.UPF Li 6.941 Li.pbesol-s-kjpaw_psl.0.2.1.UPF BEGIN_POSITIONS FIRST_IMAGE ATOMIC_POSITIONS { crystal } Li0.5 0.25 0.5 Co0.290725910.12500.91347261 Co0.290725910.62500.91347261 Mn0.709274090.87500.08652739 Mn0.709274090.37500.08652739 Mn0.209274090.87500.41347261 Mn0.209274090.37500.41347261 Mn0.790725910.12500.58652739 Mn0.790725910.62500.58652739 P0.100843650.12500.40451768 P0.100843650.62500.40451768 P0.899156350.87500.59548232 P0.899156350.37500.59548232 P0.399156350.87500.90451768 P0.399156350.37500.90451768 P0.600843650.12500.09548232 P0.600843650.62500.09548232 O0.123851740.12500.71580776 O0.123851740.62500.71580776 O0.876148260.87500.28419224 O0.876148260.37500.28419224 O0.376148250.87500.21580776 O0.376148250.37500.21580776 O0.623851740.12500.78419224 O0.623851740.62500.78419224 O0.446242230.12500.14543042 O0.446242230.62500.14543042 O0.553757770.87500.85456959 O0.553757770.37500.85456959 O0.053757770.87500.64543041 O0.053757770.37500.64543041 O0.946242230.12500.35456959 O0.946242230.62500.35456959 O0.829949470.474731250.74215029 O0.829949470.974731250.74215029 O
[Pw_forum] AiiDA released - a new platform for materials' informatics
Dear Quantum ESPRESSO users, we are happy to announce that AiiDA - a materials' informatics Python platform to manage, store, organize, query and share large amounts of data, calculations, and workflows - has been recently released and can be freely downloaded from the website http://www.aiida.net. A preprint describing AiiDA is available on arXiv at http://arxiv.org/abs/1504.01163 while extensive code documentation for users and developers (installation instructions, tutorials, user and development manuals) is distributed with the code and available online at http://aiida-core.readthedocs.org/en/stable/ The core of the software ("aiida_core") is released under an open-source MIT license and can be freely downloaded (no registration necessary) from the AiiDA website or from BitBucket: http://www.aiida.net/?page_id=264 https://bitbucket.org/aiida_team/aiida_core "aiida_core" is complemented by an extended set of plugins; these are free and distributed with the code provided you belong to an academic institution. These plugins provide support for various simulation packages, including the Quantum ESPRESSO codes pw.x, cp.x, ph.x, matdyn.x, q2r.x. This extended version ("aiida_epfl", that includes "aiida_core") can be obtained from http://theossrv1.epfl.ch/aiida_download/ Hoping that you may find AiiDA useful for your research, Giovanni Pizzi on behalf of the AiiDA team (http://www.aiida.net/?page_id=34) -- Giovanni Pizzi Post-doctoral Research Scientist EPFL STI IMX THEOS MXC 340 (Bâtiment MXC) Station 12 CH-1015 Lausanne (Switzerland) Phone: +41 21 69 31124 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] cif to pwi
Dear all, please somebody help me get a supercell of 100 atoms in pwi format from the attached cif file. Kind regards Mulwa Winfred. D Phil Student, Computational Material Science Group, University of the Free State - QwaQwa, South Africa. win3.cif Description: application/vnd.multiad.creator.cif ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Pw_forum Digest, Vol 95, Issue 14
Re: Pw_forum Digest, Vol 95, Issue 11 ( total magnetization and absolute magnetization quenched) Dear Prof Paolo, Thank you for your swift response. Although I do not completely capture your response " they use different pseudopotentials and k-points" but am optimistic to learn more as to the reason for this strange change. In my relax calculation, the magnetic moment agrees well with the reported values and using QE pseudopotential with lesser number of k-points mesh, unfortunately, magnetic moment completely quenched in scf calculation and using the same QE pseudopotential at high k-points mesh. I will be happy to know the reason for the change with regards to their pseudo "http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.108.197207; (check here in) and what to modify to be able to repeat the same calculations: find below the input files for relax and scf calculations used RELAX CALCULATION calculation = 'relax' , title = 'C4N3' prefix='pbe1x1C4N3', restart_mode = 'from_scratch' , outdir = '/home/zuntu/yusuf/espresso-5.1.1/bin' pseudo_dir='/home/zuntu/yusuf/espresso-5.1.1/pseudo/upf_files' tstress = .true. , tprnfor = .true. , / ibrav=4, celldm(1)= 9.14623, celldm(3)= 3.22190083 nat= 7, ntyp= 2, ecutwfc =40.0, ecutrho = 270, tot_charge = 0.00, occupations = 'smearing' , degauss = 0.01 , smearing = 'mp' , nspin = 2 , starting_magnetization(1) = 0.3, / conv_thr = 1.D-6 , mixing_beta = 0.7D0 , / ion_dynamics = 'bfgs' , pot_extrapolation = 'second_order' , wfc_extrapolation = 'second_order' , / ATOMIC_SPECIES C 12.0107 C.pbe-n-kjpaw_psl.0.1.UPF N 14.0067 N.pbe-n-kjpaw_psl.0.1.UPF ATOMIC_POSITIONS angstrom C 0.0 0.0 2.0 C 1.21 0.64 2. N 2.42 0.00 2.00 C 3.63 0.674 2.0 N 3.63 2.022 2. C 2.42 2.68 2.00 N 1.21 2.022 2.0 K_POINTS automatic 4 4 1 1 1 1 SCF CALCULATION calculation = 'scf' , title = 'C4N3' prefix='pbe1x1C4N3', restart_mode = 'from_scratch' , outdir = '/home/zuntu/yusuf/espresso-5.1.1/bin' pseudo_dir='/home/zuntu/yusuf/espresso-5.1.1/pseudo/upf_files' verbosity='high' / ibrav=4, celldm(1)= 9.14623, celldm(3)= 3.22190083 nat= 7, ntyp= 2, ecutwfc =40.0, ecutrho = 270, tot_charge = 0.00, occupations = 'smearing' , degauss = 0.01 , smearing = 'mp' , nspin = 2 , starting_magnetization(1) = 0.6, / conv_thr = 1.D-6 , mixing_beta = 0.7D0 , / ATOMIC_SPECIES C 12.0107 C.pz-n-kjpaw_psl.0.1.UPF N 14.0067 N.pz-n-kjpaw_psl.0.1.UPF ATOMIC_POSITIONS (angstrom) C0.000169362 -0.049027525 2.01268 C1.246828369 0.669477960 2.01487 N2.420687939 0.008258827 1.96634 C3.593997961 0.670979132 2.02839 N3.579281825 2.018019377 1.98410 C2.419168269 2.703396539 2.03594 N1.259866274 2.016895690 1.95769 K_POINTS automatic 12 12 1 1 1 1 Thank you Yusuf Zuntu Postgraduate Student Universiti Sains Malaysia ---e On Mon, 6/15/15, pw_forum-requ...@pwscf.orgwrote: Subject: Pw_forum Digest, Vol 95, Issue 14 To: pw_forum@pwscf.org Date: Monday, June 15, 2015, 6:00 PM 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. Re: [*] Re: [qe-gpu] (Anubhav Kumar) 2. Re: Pw_forum Digest, Vol 95, Issue 13 (Umesh Roy) 3. Re: Bug (or not) with epsil = .false. in PH (trunk version) (Andrea Dal Corso) 4. Re: Pw_forum Digest, Vol 95, Issue 11 (Yusuf Zuntu) 5. Re: Pw_forum Digest, Vol 95, Issue 11 (Paolo Giannozzi) -- Message: 1 Date: Sun, 14 Jun 2015 15:57:41 +0530 From: "Anubhav Kumar" Subject: Re: [Pw_forum] [*] Re: [qe-gpu] To: "PWSCF Forum" Message-ID: <2447241701e01ab85061153de3e2d335.squir...@webmail.iitk.ac.in> Content-Type: text/plain;charset=iso-8859-1 Dear Filippo Thank you very much for your reply.I am new to parallel programming and cuda.So can you please explain in detail how to make changes suggested by you? > Dear Anubhav, > > run in parallel, 2 MPI and make sure CUDA_VISIBLE_DEVICES is set such > > MPI rank 0 -> GPU id 1 (K20) > MPI rank 1 -> GPU id 2 (K20) > > Those K20 GPU are active cooled cards, how many
[Pw_forum] Raman Spectra
Respected Sir/Mam, I am working on optical properties. I have run dynmat.x file and obtained the output below: # mode [cm-1][THz] IR Raman depol.fact 1 -487.60 -14.6178 37.7287 277.86090.6461 2 -0.00 -0.0.334597.41700.7437 3 -0.00 -0.0. 8113.29750.7291 4 -0.00 -0.0. 25779.90200.7455 5 0.000.0. 6417.84420.6634 6 0.000.0. 171.70540.6246 7 0.000.0. 29050.28080.7489 8 56.801.70284.4068273118.78750.7446 9160.494.8115 11.3630 55305.28850.7395 10223.346.69543.8373 91527.11270.7438 11327.829.82772.9918 21597.63730.7373 12351.66 10.54241.9769 1081889.82250.7431 13555.84 16.66373.8963 13013.88340.2450 14748.23 22.43159.1009 3164.22750.1576 15790.74 23.70595.1725 764.08950.5078. With the 2nd and 5th column i can form raman spectra, but output contains very few values which is giving abnormal plot. how can i plot a correct and smooth plot for raman spectra. please suggest me the correct path. -- Amreen Bano Department of Physics, Barkatullah University, Bhopal-462 026 INDIA +91-9993515955 banoamree...@gmail.com ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Projection of dos on to molecular orbitals
Dear QE users, I want to project the density of states of complete system (molecule adsorbed on a surface) on to molecular orbitals of adsorbate and find population of different molecular orbitals. If I understood correctly there is an post-processing tool molecularpdos.x in quantum ESPRESSO v 5.1.2 which does this job. If I am mistaken please correct me. ( http://www.quantum-espresso.org/wp-content/uploads/Doc/pp_user_guide/node8.html ) Statement 1) >From /espresso-5.1.2/PP/Doc/INPUT_molecularpdos.html " *Then the eigenvectors of the full system are projected onto the ones of the part. For example, to decompose the PDOS of an adsorbed molecule into its molecular orbital, as determined by a gas-phase calculation*" I don't understand what is meant by decomposition of pdos while in first part it says eigenvectors of full system are used. Statement 2) "*The atomic wavefunctions identified by the ranges i_atmwfc_beg_full:i_atmwfc_end_full (full system) and i_atmwfc_beg_part:i_atmwfc_end_part (molecular part) should correspond to the same atomic states. See the header of the output of projwfc.x for more information*." I feel the above statement slightly confusing as in statement 1 it is said that "*Then the eigenvectors of the full system are projected onto the ones of the part*" Hope that things are conveyed well. With regards Vasudevan M V JNCASR Bangalore ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Pw_forum Digest, Vol 95, Issue 11
On Mon, Jun 15, 2015 at 10:56 AM, Yusuf Zuntuwrote: Input files for relax and scf attached. > they use different pseudopotentials and k-points P. -- Paolo Giannozzi, Dept. Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy hone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Pw_forum Digest, Vol 95, Issue 11
Topic: total magnetization and absolute magnetization quenched. Dear Quantum Espresso users, Can some one bail me out of this problem. In trying to repeat some calculations of this article "http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.108.197207;, an unexpected magnetic behavior manifest between relax and scf calculations. Below are the details of the output: Relax calculation the Fermi energy is-3.1983 ev !total energy =-158.20644301 Ry Harris-Foulkes estimate =-158.20644301 Ry estimated scf accuracy< 3.5E-09 Ry total all-electron energy = -633.159253 Ry The total energy is the sum of the following terms: one-electron contribution =-664.83395884 Ry hartree contribution = 338.58658021 Ry xc contribution = -32.69935803 Ry ewald contribution= 252.19023776 Ry one-center paw contrib. = -51.45032393 Ry smearing contrib. (-TS) = 0.00037981 Ry total magnetization = 1.00 Bohr mag/cell absolute magnetization= 1.08 Bohr mag/cell convergence has been achieved in 5 iterations Forces acting on atoms (Ry/au): negative rho (up, down): 3.821E-04 3.015E-04 atom1 type 1 force =-0.00036461 -0.000342330.0075 atom2 type 1 force =-0.000629030.000154880.0019 atom3 type 2 force =-0.000134860.00026628 -0.0034 atom4 type 1 force = 0.00046437 -0.00072125 -0.0023 atom5 type 2 force = 0.00015269 -0.4785 -0.0012 atom6 type 1 force = 0.000255660.00039710 -0.0008 atom7 type 2 force = 0.000255780.00029316 -0.0017 Total force = 0.001377 Total SCF correction = 0.000117 entering subroutine stress ... negative rho (up, down): 3.821E-04 3.015E-04 total stress (Ry/bohr**3) (kbar) P= -1.16 -0.1005 0.0007 -0. -1.48 0.01 -0.00 0.0007 -0.1037 0. 0.01 -1.53 0.00 -0. 0. -0.0322 -0.00 0.00 -0.47 bfgs converged in 7 scf cycles and 6 bfgs steps (criteria: energy < 1.0E-04, force < 1.0E-03) End of BFGS Geometry Optimization Final energy =-158.2064430134 Ry Begin final coordinates ATOMIC_POSITIONS (angstrom) C0.000169362 -0.049027525 2.01268 C1.246828369 0.669477960 2.01487 N2.420687939 0.008258827 1.96634 C3.593997961 0.670979132 2.02839 N3.579281825 2.018019377 1.98410 C2.419168269 2.703396539 2.03594 N1.259866274 2.016895690 1.95769 End final coordinates. SCF calculation: the Fermi energy is-3.3467 ev !total energy =-110.83170176 Ry Harris-Foulkes estimate =-110.83170172 Ry estimated scf accuracy< 0.0008 Ry The total energy is the sum of the following terms: one-electron contribution =-665.86218544 Ry hartree contribution = 338.49928445 Ry xc contribution = -35.54208467 Ry ewald contribution= 252.07341919 Ry smearing contrib. (-TS) = -0.00013530 Ry total magnetization =-0.00 Bohr mag/cell absolute magnetization= 0.00 Bohr mag/cell convergence has been achieved in 14 iterations. Input files for relax and scf attached. Yusuf Zuntu Postgraduate Student Universiti Sains Malaysia On Fri, 6/12/15, pw_forum-requ...@pwscf.orgwrote: Subject: Pw_forum Digest, Vol 95, Issue 11 To: pw_forum@pwscf.org Date: Friday, June 12, 2015, 6:00 PM 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. Re: total magnetization and absolute magnetization (Elham) 2. Re: total magnetization and absolute magnetization (Arles V. Gil Rebaza) 3. looking for optimal k-point sampling specific to monoclinic cells (Manuel P?rez Jigato) 4. spin polarization (Tayebeh Roohande) 5. Re: PLUMED and Quantum-ESPRESSO (Paolo Giannozzi) 6. Re: spin polarization (Mostafa Youssef) -- Message: 1 Date: Thu, 11 Jun 2015 14:49:51 +0430 From: Elham
Re: [Pw_forum] Bug (or not) with epsil = .false. in PH (trunk version)
On Sat, 2015-06-13 at 16:38 +0100, Samuel Poncé wrote: > Dear all, > > I found out that it was impossible de make a phonon calculation without > calculating the Born effective charge in a semi-conductor even if we set > epsil = .false. > > This is due to the routine prepare_q.f90 that is called inside do_phonon.f90 > In the routine there is > IF ( lgamma ) THEN > ! > IF ( .NOT. lgauss ) THEN >! >! ... in the case of an insulator at q=0 one has to calculate >! ... the dielectric constant and the Born eff. charges >! ... the other flags depend on input >! >epsil = .TRUE. >zeu = .TRUE. >zue = .TRUE. > > > This means that if we compute q=Gamma and if we do not have > gaussian-smearing (i.e. an semi-cond or insulator), then epsil is > automatically set to TRUE. > > I know that physically one should have such LO/TO splitting but the user > should be able to choose. > > Maybe this forcing could be reported in the input variable ? or simply put > the default value to .TRUE. instead of false and not enforcing that rule? > > What do you think? This is true only when ldisp=.TRUE.. If you do a phonon calculation at gamma with ldisp=.FALSE. you can set/unset the dielectric constant calculation with the flag epsil. It has to be like this, otherwise the dispersion would show a jump at gamma and the interpolation would not work. HTH, Andrea > > Best, > > Samuel Ponce, > Department of Materials, University of Oxford > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Andrea Dal CorsoTel. 0039-040-3787428 SISSA, Via Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalco...@sissa.it ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum