~nickpapior/siesta/esm : changes

~nickpapior/siesta/esm » Changes from revision 515

From Revision 515 to 496

Rev	Summary	Authors	Date
515	When using ESM a citation is added When using ESM a citation is added	Nick Papior	7 years ago
514	Updated ESM code for better readability Updated ESM code for better readability - Only cosmetic changes	Nick Papior	7 years ago
513	Added inital ESM patch for 4.0-b2 Added inital ESM patch for 4.0-b2 - Through correspondance with: Minoru Otani, Yoshinari Takimoto and Osamu Sugino the ESM model has been fully included in siesta.	Nick Papior	7 years ago
512	Fixed OpenMP statement in mixer Fixed OpenMP statement in mixer - The default clause is not applicable to lone workshare constructs	Nick Papior	7 years ago
511	Fixed makefile for tbtrans Fixed makefile for tbtrans - The diagon changed routine name	Nick Papior	7 years ago
510	Redid all tests using r509 Redid all tests using r509 - r509 introduced the default DM.MixSCF1 .true. which in many cases improves on the convengence. - r509 also re-implemented the mixing routines which is one reason for the increased stability in the convergence. - All tests have been checked and they are deemed correct.	Nick Papior	7 years ago
509	Merge of ts-scf branch (BIG MERGE) Merge of ts-scf branch (BIG MERGE) - Fully re-implemented transiesta * N-terminal support in transiesta * Added different mechanisms for integration control of the contours in transiesta * Made the convergence of transiesta much better. This is accommodated by better handling of the Hartree potential. * Different ways of handling charge-reductions in SCF is enabled * All electrodes have settings _per electrode_ for full customization * Greatly reduced memory usage * Does not use xij as phases, enables skewed axis * Implemented MUMPS method for inversion * Implemented LAPACK for inversion * Implemented BTD method for inversion (extremely fast) * Implemented two different ways of calculation Gf.G.Gf MM * 12 different weighting schemes are available * Many different pivoting routines available * OpenMP threaded * Start directly from transiesta enabled * Temperature gradients as non-equilibrium a possibility - tbtrans fully reimplemented * EXTREME SCALE version (BTD-only) - Memory consumption _only_ dependent on "device" region * N-electrode support * region projections for transmission through "eigenstates" * Custom change of the self-energies * Enabled tight-binding using MPI-parallelised tbtrans (easily) * k -> k' transmissions * Interpolation of bias Hamiltonians * Bond-currents * DOS and bulk transmission for electrodes * Gf-DOS/spectral-DOS for device region - Special considerations for siesta * New and more robust mixing schemes (Pulay/Pulay-GR/Broyden) * Constraints are verbose and many new ways of using constraints exists * Added complete NetCDF4 file format for siesta (parallel IO) * LUA scripting for MD simulations - can also be used for regular constraints * Threading for a few routines in siesta * Phonon calculations now produces TSHS files more conveniently * Enabled gate-calculations (also for transiesta) - Charge gate - Hartree gate * Extended class objects for reference counting objects * Allowed fdf-flags on the command line: -fdf <flag>:<value>[:<unit>] only possible for non-blocks. * Changed default DM.MixSCF1 to .true. In many cases this is preferred, especially for restarts. * Will die if there are more processors than orbitals - Utilities * All make-files are now made to enable parallel builds - this makes compilation MUCH faster: make -j4 will compile using 4 cores. * Grimme utility - easy creation of FDF block for Grimme parameters Enables one to read an FDF file and print out the correct quantites * SpPivot, pivot sparsity pattern using several different routines * TS/** different utilities related to transiesta - All tests have been re-runned and checked against trunk	Nick Papior	7 years ago
508	Merged in spin-orbit coupling code from Ramon Merged in spin-orbit coupling code from Ramon - All tests have been runned to check consistency - This merge includes the full re-implementation of the spin-orbit coupling code implemented by Ramon Cuadrado - This merge also contains a fix for non-collinear GGA-XC. The fix corrects issues for calculations with vanishing density at certain grid points.	Nick Papior	7 years ago
507	Updated reference tests Updated reference tests - All tests have been re-runned. - The graphite_vdw_df test has been added more steps to actually make it converge.	Nick Papior	7 years ago
506	Fixes lp:1587060 Fixes lp:1587060 Fixes bug about de-allocation tracking (not per see a bug)	Nick Papior	7 years ago
505	Merged 4.0-496 Merged 4.0-496 Added comments about HSX derived type	Nick Papior	7 years ago
504	Update makefile in Util/Gen-basis after ldau inclusion Update makefile in Util/Gen-basis after ldau inclusion Some extra modules are needed in Gen-basis modified: Util/Gen-basis/Makefile	Alberto Garcia	7 years ago
503	Merged fix lp:1582978 (from rel-4.0) Merged fix lp:1582978 (from rel-4.0)	Nick Papior	7 years ago
502	Revise mentions to now-standalone ATOM program. Revert Tests... Revise mentions to now-standalone ATOM program. Revert Tests/test.mk. * The ATOM program is not bundled with Siesta due to licensing differences. Mentions to it throughout the documentation and example files have been updated accordingly. * The file Tests/test.mk has been reverted to the revno 488 version. Note that the proper way to run the tests for a given version is to descend into the 'Tests' directory directly below the compilation directory ('Obj' or other) rather than going to the top-level 'Tests'. * Syntax changes for compiler complaints reported by Mariella Ippolito from CINECA. * Completion of changes to licensing headers. modified: Docs/siesta.tex Examples/README Examples/Vps/README Src/SiestaXC/vv_vdwxc.F90 Src/fsiesta_mpi.F90 Src/write_inp_wannier.F90 Src/ldau.F Src/ldau_specs.f Tests/test.mk + Header changes in a number of files	Alberto Garcia	7 years ago
501	Fix in 'fat' utility. Write spin info in 'eigfat2plot' Fix in 'fat' utility. Write spin info in 'eigfat2plot' The 'fat' program in Util/COOP computes the projections of specific band states onto sets of orbitals. Due to an error, the program did not function correctly when a subset of upper bands was selected with the '-b' and '-B' flags. The 'eigfat2plot' utility in Util/Bands now prints an extra field giving the spin of the state. modified: Util/Bands/eigfat2plot.f90 Util/COOP/fat.f90 Util/COOP/main_vars.f90	Alberto Garcia	7 years ago
500	Fix for handling of geometry info in bands/wfns calculation Fix for handling of geometry info in bands/wfns calculation The computation of bands and/or wavefunctions in 'siesta_analysis' requires an initial setup of the k-point sets involved. These are input in ad-hoc fdf blocks with two possible options for the scaling: 'pi/a' and 'ReciprocalLatticeVectors'. The 'pi/a' option needs a lattice constant, which is determined by issuing an 'fdf_get' call, whereas the reciprocal lattice vector option triggers a call to 'redcel' to determine the unit cell. An immediate problem is the absence of lattice constant or unit-cell information in the fdf file. This may happen, for example, when the 'use-struct-file' or 'use-save-xv' options are in effect. The program would either stop when not finding the lattice constant, or, worse, would implicitly compute a zero unit cell and crash later with linear-algebra related errors such as faulty Cholesky decompositions. (The zero-unit-cell case is an unfortunate consequence of the implicit convention that an absent unit cell means that the user wants an automatic one.) A second problem is that, even if the required geometry information is given in the fdf file, the band/wfn calculation might be happening at the end of a cell relaxation or MD run, so the actual unit cell is not that in the fdf file. This should be considered bad practice, but it might happen. The minimal solution adopted (encoded in routine get_kpoints_scale) consists of attempting to read the lattice constant for the 'pi/a' case, as before, but to use the unit-cell information in the 'siesta_geom' module for the reciprocal-lattice-vectors case. This information is not enough for the 'pi/a' option, since no record is kept of any centering options for cubic systems, so 'a' cannot be directly determined from the volume of the unit cell. Note that the setup information is handled at the beginning of the run (during the initialization in 'siesta_init'. A message is printed to warn the user about possible inconsistencies if the unit-cell changes by the end of the run. In any case, the practice of computing bands or wavefunctions at the end of a geometry-changing run should be discouraged. added: Src/get_kpoints_scale.f90 modified: Src/Makefile Src/bands.F Src/writewave.F	Alberto Garcia	7 years ago
499	Allowed neglecting KB projectors with LDA+U Allowed neglecting KB projectors with LDA+U - The LDA+U projectors are now not dependent on the NeglNonOverlapInt option which only deals with KB projectors. - Streamlined calculation of rmaxo/rmaxkb in hsparse, ldau, nlefsm, Basically they looped over the entire structure to find only the species orbital/projector ranges. Thus it is more efficient in those routines. modified: Src/Makefile Src/hsparse.F Src/ldau.F Src/nlefsm.f Src/siesta_init.F Src/state_init.F	Nick Papior	7 years ago
498	Fixed imports Fixed imports modified: Src/ldau_specs.f Src/m_cite.F90	Nick Papior	7 years ago
497	Added LDA+U citation of the implementation paper Added LDA+U citation of the implementation paper modified: Src/ldau_specs.f Src/m_cite.F90	Nick Papior	7 years ago
496	Fixed Makefile dependencies Fixed Makefile dependencies modified: Src/Makefile	Nick Papior	7 years ago

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