TACC Lonestar 6 notes
 Our group directory on LS6 is
/work/04255/yow5110/group
Here you’ll find shared data and selfcompiled codes.  On LS6 you will need the following before running ABINIT.
#For dynamic libraries
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/work/04255/yow5110/group/src/netcdffortran4.5.3/build/lib:/work/04255/yow5110/group/src/netcdfc4.8.1/build/lib:/work/04255/yow5110/group/src/local/lib#For finding binaries in the ABINIT suite
export PATH=$PATH:/work/04255/yow5110/group/src/abinit9.6.2/build/bin/#For most builtin tests and tutorials from Abinit
export ABI_PSPDIR=/work/04255/yow5110/group/src/abinit9.6.2/tests/Psps_for_tests
#change this to your own directory for pseudopotentials when running your projects#To run abinit
mpirun abinit [inputfile] >& log
VASP
 Turn off symmetry when using EFIELD (VASP detects symmetry based only on geometry).
 When using LDIPOL, the compensating planar dipole is always sitting at the cell boudary (not affected by DIPOL, at least for v5.2), so make sure slabs don’t cross boundaries.
 Use LVHAR when plotting local potential for faster convergence towards vacuum level.
 Isolated atoms. Use a very small smearing, e.g. 0.1 meV. To avoid slow convergence, use NUPDOWN to constrain the net spin. Always check ground state electron configuration with experiments, keeping in mind that LDA/GGA energies are more likely to be off quantitatively.
 Use KPAR level parallelization when applicable.
 LOPTICS only gives interband contributions. A Drude term needs to be put in later for metals.
 Optical matrix elements can be obtained by uncommenting the line regarding ‘WAVEDERF’; a ‘WAVEDERF’ file will appear after a LOPTICS run. These are <irj>, not <ipj>. Same for BerkeleyGW.
 Phonon dispersions and quasiharmonic treatments from Phonopy.
 Phonon lifetimes and lattice thermal conductivities from Phono3py.
 Abinitio MD too slow? See if advanced rare event sampling methods work for you.
 Implementation of noncollinear magnetism in VASP: Phys. Rev. B 62, 11556 (2000)
 The spectral representation trick (LSPECTRAL) in VASP (and similar KK or Hilbert transform tricks in other codes): Phys. Rev. B 74, 035101 (2006)
 How to calculate band structures with hybrid functionals, here.
 Many other tips here
QE / Wannier90 / EPW
 To see how you can split phonon calculations, check the last section of the ph.x documentation
 nk level parallelization is very efficient for small systems.
 official FAQ for phonons
 How to construct highquality Wannier functions. But read this first.
Abinit
 Very well written documentation and tutorial and version information.
 Use version 7.4 onwards for calculating linear and nonlinear optical properties – two bugs related to symmetry were present in versions before that.
 The input for nonlinear optical calculations supports scissor shifts to remedy band gap problems. Unlike linear optics, adding scissor shifts in nonlinear optics do not simply rigidly shift the spectrum.
 Photon polarization is controlled by gw_qlwl, the “small” q vector that describes the q>0 limit of the head and wings of the dielectric matrix.
 MBPT features:
 Supports dense kpoint interpolatino for BSE using “bs_interp_mode”, but only works for Haydock as of now (v8.10).
 Extrapolar (active) and Effective Eneregy Technique (discontinued as of v8.0) to accelerate convergence with respect to band summation.
 Bug associated with gwcomp reported here.
 Allows splitq, splitk and splitbands calculaitons in plasmonpole model, using nqptdm+qptdm and nkptgw+kptgw+bdgw. Mrgscr tool to collect.
 Supports Coulomb interaction cutoff to accelerate convergence with respect to cell size, using “icutcoul” and “vcutgeo”. The the surface/2D case, “rcut” is automatically set to half the cell height Lz/2 (see m_vcoul/cutoff_surface).
 Distributed empty bands and reduced memory demand using the “gwpara=2” parallelization level. More on MBPT parallellization techniques in this tutorial.
 When generating hundreds/thousands of empty bands, the highest computed ones might be degenerate (with not computed ones) and difficult to converge, as one might expericence with other codes. To work around this problem, nbdbuf excludes a portion of the empty bands from the convergence criteria. From this tutorial: “As a rule of thumb use 10% of nband or even more in complicated systems. This can really make a huge difference at the level of the wall time.”
 prtvol >= 3 to monitor nscf progress (for kptopt == 1)
 use max_ncpus to estimate memory usage and scaling before doing GW routines (a forum post here).
BerkeleyGW
 BerkeleyGW workshop materials for 2013, 2014, and 2018
 Optical matrix elements are obtained from wavefunctions and thus have arbitrary phases. Special care is needed when calculating cross terms, e.g. epsilon_xy.
 ch_converge.dat to check the convergence of Coulombhole term of the electron selfenergy with respect to emtpy bands.
 MBPT features:
 BSE routines with dense kpoint interpolation and nonuniform sampling schemes.
 Static remainder and SAPO to ease convergences with respect to band summation.
 Allows splitq and splitk calculaitons in plasmonpole model. wfnmerge.x and epsmat_merge tool to collect.
 Supports Coulomb interaction cutoff to accelerate convergence with respect to cell size, using “cell_****_truncation”
 The QE/BerkeleyGW interface pw2bgw.x allows control over whether semicore states are included in the charge density in the HLGPP model, through “rhog_nvmin”.
VMD
 Quick and easy visualization, also with advanced rendering options. Depth of field can be controlled after rendering script is generated, e.g. for Tachyon under “Camera” specify “projection perspective_dof” and “aperture [number]”
 VMD color palette https://www.ks.uiuc.edu/Research/vmd/plugins/palettetool/
Evernote
 “Search notes” seems to be broken? Try recreating full search index.
Mac / Keynote notes
 Pasting following the present local format: Shift + Option + Cmd + V
 Hate rightclickmovetofront? Just cut and paste.
 Handdrawn curves curving weirdly? Rightclick on editable point and make Bezier point.
 Cropping with irregular shape: Draw irregular shape over image – select both – Format>Image>Mask with selection
Talon 3 cluster notes
 Ready built: QE, LAMMPS, jdftx, mkl, hdf5
 SLURM user guide
ROAR cluster notes
 Exclusive nodes. “qsub n” guarantees exclusive nodes. The scheduler finds the minimum number of nodes that grants you exclusivity, e.g. gives you 2 exclusive nodes if you request 20 cores (without specifying topology) on and 16corepernode system.

$PBS_NODEFILE to check all running nodes. See also other $PBS_xxx variables and the “pbsnodes” command.
 Email notification. #PBS m [options]. Used with #PBS M [email adress]
 Memory monitoring using a script, without ‘top’. Find process # in ‘ps’, then look in /proc/#/status. Vsize and Vrss are the requested and active memory.

Specify a node: #PBS l nodes=[node name], e.g. node name = lionxg93
 After a job starts, you are allowed to ssh to that compute node, e.g. to check memory use.
 Want to save an interactive job session? Use the “screen” utility to allow attachment/detachment for an interactive session. See gnu page or here for details.
 For different mpi flavors, use libmkl_blacs_[flavor]_lp64.a, where flavor can be intelmpi, openmpi …
 Module load mkl and find all libraries under $MKLROOT.
 Make sure the MKL version is compatible with the compiler version.