[QE-users] Rotated Lattice defined by CELL_PARAMETERS
Dear all, Purely out of curiosity, I used a rotated simple cubic lattice with one atom at the origin to check the symmetry recognition of pw.x. I've read the trouble shooting section 5.0.0.19: if we rotate C60 molecule in its crystalline form, the symmetry elements of the molecule won't align with these of the underlying lattice, and then these symmetries will be discarded. This is reasonable. But the user guide is a bit ambiguous about the case when the underlying lattices is rotated relative to the Cartesian system. I tested a little bit. The lattice vectors are specified through CELL_PARAMETERS: 4 0 -3 0 5 0 3 0 4 This is a cubic lattice tilted a little bit around the v_2 vector (second lattice vector). It turns out only C4_h symmetries with 4-fold axis along v_2 vector are recognized. I attach my input and output for your reference. So my question is, does pw.x assume that the first principal axis (the symmetry axis of highest order of rotation) of the user-provided CELL_PARAMETERS always align with the z-axis of a global Cartesian coordinate system? An equivalent question is, does the c-vector of the conventional unit cell of the lattice defined by CELL_PARAMETERS always align with z-axis of the Cartesian coordinate system? Thanks for your patience in reading through this post! Best, Yunzhe Wang (Phil) Mueller Research Group Johns Hopkins University input Description: input stdout Description: stdout ___ Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] ibrav number check
The atomic positions you gave are not precise enough. Some symmetrical equivalent positions are determined as asymmetrical since internally, only positions matched up to 10^-5 are considered as equivalent. As you can imagine, if you put a basis with lower symmetry, then some symmetries of the lattice will be broken. Best, Yunzhe Wang Mueller Research Group, Johns Hopkins University Get Outlook for iOS<https://aka.ms/o0ukef> From: users on behalf of Giovanni Cantele Sent: Monday, November 19, 2018 5:02 PM To: Quantum Espresso users Forum Subject: Re: [QE-users] ibrav number check maybe you’re visualising the conventional, rather than the primitive unit cell. Try to set Display -> Primitive Cell Mode The bct unit cel should show up. Giovanni -- 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.cant...@spin.cnr.it<mailto:giovanni.cant...@spin.cnr.it> gcant...@gmail.com<mailto:gcant...@gmail.com> Phone: +39 081 676910 Skype contact: giocan74 Web page: https://sites.google.com/view/giovanni-cantele On 19 Nov 2018, at 19:38, Chan, Edmund mailto:thc...@exeter.ac.uk>> wrote: Dear all users, I am currently trying to relax a methylammonium lead iodide CH3NH3PbI3 structure which has tetragonal structure I4/mcm. Thus, in my input file, I select ibrav = 7 (body centred teragonal). However, as I visualise the input and output on Xcrysden, the unit cell becomes orthorhombic. Why is that? title = 'MAPI' , calculation = 'relax' , restart_mode = 'from_scratch' , outdir = './' , pseudo_dir = './' , prefix = 'CH3NH3PbI3' , / ibrav = 7, A = 8.83920, C = 12.6948, nat = 12, ntyp = 5, ecutwfc = 80 , ecutrho = 800, / electron_maxstep = 5000 , conv_thr = 1.0d-6 , mixing_beta = 0.3 , / ion_dynamics = 'bfgs' , / ATOMIC_SPECIES C 12.01070 c_pbesol_v1.2.uspp.F.UPF H1.00794 H.pbesol-rrkjus_psl.0.1.UPF N 14.00670 N.pbesol-theos.UPF Pb 207.2 Pb.pbesol-dn-kjpaw_psl.0.2.2.UPF I 126.90450 i_pbesol_v1.uspp.F.UPF ATOMIC_POSITIONS alat Pb 0.00.00.5 I 0.00.00.25000 I 0.294200.205800.5 I -0.29420 -0.207600.5 C 0.544000.921000.78400 H 0.609201.002100.76990 H 0.557300.845500.72460 H 0.551500.875200.86430 N 0.389000.987000.76700 H 0.324700.913900.73030 H 0.381401.068100.73430 H 0.339300.990800.83100 K_POINTS automatic 1 1 1 0 0 0 Thank you all. Kind regards, Edmund Chan Edmund Chan PhD Renewable Energy Student Environment & Sustainablity Institute College of Engineering, Mathematics and Physical Sciences University of Exeter, Penryn Campus Penryn, Cornwall United Kingdom TR10 9FE Tel: +44 (0)7455 235 701 Email: thc...@exeter.ac.uk<mailto:thc...@exeter.ac.uk> LinkedIn: https://uk.linkedin.com/in/edmundchan1 ___ users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] an error while installing quantum espresso
Hi Foudil, You don’t link against openmpi libraries. You can add additional flags using “./configure VARIABLES=VALUE” syntax. The examples can be found at the general user manual of QE. Best, Yunzhe Wang Mueller Research Group Johns Hopkins University Get Outlook for iOS<https://aka.ms/o0ukef> From: users on behalf of foudil zaabar Sent: Tuesday, November 20, 2018 5:45 AM To: users@lists.quantum-espresso.org Subject: [QE-users] an error while installing quantum espresso dear all I tried to install espresso-5.4.0 in parallel in our cluster following the next steps ~>./configure ~>make pw , I encountered this problem,: /usr/local/intel/composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a(BI_BlacsAbort.o): In function `BI_BlacsAbort': _BI_BlacsAbort.c:(.text+0x26): undefined reference to `ompi_mpi_comm_world' /usr/local/intel/composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a(BI_Pack.o): In function `BI_Pack': _BI_Pack.c:(.text+0x13): undefined reference to `ompi_mpi_byte' _BI_Pack.c:(.text+0x6b): undefined reference to `ompi_mpi_packed' /usr/local/intel/composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a(BI_GetMpiGeType.o): In function `BI_GetMpiGeType': _BI_GetMpiGeType.c:(.text+0x32): undefined reference to `ompi_mpi_byte' /usr/local/intel/composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a(BI_GetMpiTrType.o): In function `BI_GetMpiTrType': _BI_GetMpiTrType.c:(.text+0xa4): undefined reference to `ompi_mpi_byte' /usr/local/intel/composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a(BI_MPI_C_to_f77_trans_comm.o): In function `BI_MPI_C_to_f77_trans_comm': _BI_MPI_C_to_f77_trans_comm.c:(.text+0x6): undefined reference to `MPI_Comm_c2f' /usr/local/intel/composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a(sys2blacs_handle_.oo): In function `Csys2blacs_handle': _sys2blacs_handle_.c:(.text+0x21): undefined reference to `ompi_mpi_comm_null' _sys2blacs_handle_.c:(.text+0x98): undefined reference to `ompi_mpi_comm_world' _sys2blacs_handle_.c:(.text+0x166): undefined reference to `ompi_mpi_comm_world' /usr/local/intel/composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a(BI_MPI_F77_to_c_trans_comm.o): In function `BI_MPI_F77_to_c_trans_comm': _BI_MPI_F77_to_c_trans_comm.c:(.text+0x6): undefined reference to `MPI_Comm_f2c' make[2]: *** [pw.x] Erreur 1 make[2]: quittant le répertoire « /usr/users/iff_th1/rezo/espresso-5.4.0/PW/src » make[1]: *** [pw] Erreur 1 make[1]: quittant le répertoire « /usr/users/iff_th1/rezo/espresso-5.4.0/PW » make: *** [pw] Erreur 1 can any one help me to fix this problem, best regards foudil zaabar univarsity of bejaia algeria ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
