Merged trunk-540

Docs/Contributors.txt

@@ -38,11 +38,13 @@ Jaime Ferrer
 Chu-Chun Fu
 Sandra Garcia
 Victor M. Garcia-Suarez
+Georg Huhs
 Rogeli Grima
 Rainer Hoft
 Jorge Kohanoff
 Richard Korytar
 In-Ho Lee
+Lin Lin
 Nicolas Lorente
 Miquel Llunell
 Eduardo Machado
@@ -61,7 +63,7 @@ Andrew Walker
 Andrew Walkingshaw
 Toby White
 Francois Willaime
-
+Chao Yang
 
 O.F. Sankey, D.J. Niklewski and D.A. Drabold made the FIREBALL code
 available to P. Ordejon.  Although we no longer use the routines in

Docs/LitCode/README

+This directory contains html files produced directly from the .lit files in Src.
+These are written in emacs' org-mode, using the literate programming constructs.
+
+This is work in progress as the capabilities of the system are explored.

Docs/branch-changes/pexsi-bracket.CHANGES

+-------------------------------------------------------------------
+November 25, 2013   Alberto Garcia    trunk-447--pexsi-54--bracket-6
+Extra parameter for PEXSI "annealing"
+
+Use larger PEXSI temperatures when dDmax is far from convergence.
+This can remove instabilities for problematic systems.
+
+Options:
+
+  PEXSI.use-annealing T
+
+  PEXSI.annealing-preconditioner  {number} (default 1)
+  PEXSI.annealing-target-factor   {number} (default 10)
+
+  The effective PEXSI temperature (for solver and inertia-counts processing) is computed
+  as:
+
+   T = T_0 * ( 1 + precond* log(prevDmax/(target_factor*Dtol))  
+
+        (with maximum of T_0)
+
+  where 'Dtol' is the scf tolerance, 'prevDmax' is the previous iteration's maximum
+  deviation in DM (or H), 'target_factor' determines the level at which the nominal
+  temperature is reached in relation to the scf tolerance, and 'precond' is a scale
+  factor for the increase in temperature.
+
+  After the second iteration, the temperature decreases monotonically, regardless of
+  any large fluctuations in prevDmax, to avoid convergence oscillations.
+
+modified:
+  Src/m_pexsi_solver.F90
+
+-------------------------------------------------------------------
+November 22, 2013   Alberto Garcia    trunk-447--pexsi-54--bracket-5
+Implement PEXSI "annealing"
+
+Use larger PEXSI temperatures when dDmax is far from convergence.
+This can remove instabilities for problematic systems.
+
+Option:
+
+  PEXSI.use-annealing T
+  PEXSI.annealing-preconditioner  {number}
+
+  See code for details.
+
+modified:
+  Src/m_pexsi_solver.F90
+
+-------------------------------------------------------------------
+November 21, 2013   Alberto Garcia    trunk-447--pexsi-54--bracket-4
+Add more heuristics for bracketting
+
+Clarification of the workflow. Many more options to control the number
+of inertia count steps, the bracketting convergence, and the use of
+the information about the shift in Ef:
+
+
+* In numInertiaCounts is negative, it indicates a minimum number of ic
+  steps. There can be more, if the dDmax in the previous iteration is
+  above:
+
+  safe_dDmax_NoInertia = fdf_get("PEXSI.safe-dDmax-no-inertia",0.05)
+
+* Use of Ef shift:
+
+  If the dDmax in the previous iteration is above:
+
+  safe_dDmax_Ef_Inertia = fdf_get("PEXSI.safe-dDmax-ef-inertia",0.1)
+  safe_dDmax_Ef_solver = fdf_get("PEXSI.safe-dDmax-ef-solver",0.05)
+
+  the bracketting for IC and solver steps is controlled by
+
+  safe_width_ic = fdf_get("PEXSI.safe-width-ic-bracket",4.0_dp*eV,"Ry")
+ 
+  (half that width on either side of muLower and muUpper from the latest
+   inertia count step)
+
+  safe_width_solver = fdf_get("PEXSI.safe-width-solver-bracket",2.0_dp*eV,"Ry")
+
+  (half that width on either side of mu from the latest solver step)
+
+  If the dDmax is below the tolerance, the shift in Ef is used to move the
+  previous brackets for IC and the solver
+
+* Cosmetics
+
+  The flow is now more clear.
+
+  See the code for a complete rundown of the changes. There are too many
+  to list at this stage.
+
+* New version of "memory" routine with basic MPI awareness.
+
+  The routine memory_all prints the maximum and minimum values of the
+  peak working set size accross the processors in the
+  communicator. Used only in the PEXSI routines for now.
+
+added:
+  Src/memory_all.F90
+modified:
+  Src/Makefile
+  Src/m_pexsi_solver.F90
+
+-------------------------------------------------------------------
+November 18, 2013   Alberto Garcia    trunk-447--pexsi-54--bracket-3
+Implement Ef shift estimation
+
+Using H for the current and the previous iterations, and the most recent DM,
+the program estimates the change in the band-structure energy, and from it
+(assuming a rigid shift), the change in Fermi level. This is passed to
+the PEXSI solver to modify the inherited brackets.
+
+added:
+  Src/compute_ebs_shift.F90
+modified:
+  Src/Makefile
+  Src/compute_dm.F
+  Src/m_pexsi_solver.F90
+  Src/setup_hamiltonian.F
+  Src/siesta_forces.F
+  Src/sparse_matrices.F
+  Src/state_init.F
+
+-------------------------------------------------------------------
+November 18, 2013   Alberto Garcia    trunk-447--pexsi-54--bracket-2
+Sync to trunk-pexsi-54
+
+Deallocate buffers in write_mat.
+
+(+ comment out initial memory snapshot in siesta.F -- no ionode yet)
+
+modified:
+  Src/m_matio.F90
+  Src/siesta.F
+
+-------------------------------------------------------------------
+November 16, 2013   Alberto Garcia    trunk-447--pexsi-53--bracket-2
+Monitoring of memory peaks by calls to getrusage()
+
+A simple, and crude for now, method to display the maximum resident
+size so far at several points in the program has been implemented, with
+file rusage.f90 (an interface to the C routine getrusage()) and 
+memory_snapshot.f90. This is not completely portable.
+
+added:
+  Src/memory_snapshot.f90
+  Src/rusage.f90
+modified:
+  Src/Makefile
+  Src/m_pexsi_solver.F90
+  Src/siesta.F
+  Src/siesta_forces.F
+
+-------------------------------------------------------------------
+November 6, 2013   Alberto Garcia    trunk-447--pexsi-53--bracket-1
+Implement an "expert" inertia-count driver and mu bracket heuristics
+
+(Work in progress)
+
+With the option
+
+  PEXSI.inertia-expert-driver T
+
+the program will call the inertia-count routine requesting a single
+iteration, and use the results in a loop to increase the number of
+criteria for convergence:
+
+-- Electron tolerance in the base interval.
+
+This reflects the basic heuristic that the integrated DOS should be more
+precise as the interval gets shorter.
+
+    PEXSI.inertia-num-electron-tolerance  [default 20]
+
+-- Workable electron tolerance in the base interval.
+
+    PEXSI.inertia-min-num-electron-tolerance  [default 10]
+
+There can be problems with the algorithm if the interval is too small. Hence this termination criterion.
+
+-- Mu tolerance
+
+If the chemical potential has changed by less than
+
+    PEXSI.inertia-mu-tolerance  [default a very small number] unit
+
+from one inertia-count iteration to the next, the cycle ends, and mu is passed
+on to the PEXSI solver.
+
+-- Energy width of the interval (deprecated, as it does not make sense
+   for gapped systems)
+
+
+When the inertia-count cycle ends, the bracket passed to the PEXSI solver is:
+
+  [muMinInertia, muMaxInertia]  (the refined interval)
+
+unless the user uses the option 
+
+   PEXSI.UseFixedMuBracket T
+
+in which case the bracket is
+
+ [muLower - delta/2, muUpper + delta/2]
+
+where delta is controlled by
+
+   PEXSI.FixedMuBracket [default 0.4 eV]
+
+added:
+  Src/m_interpolate.F90
+modified:
+  Src/Makefile
+  Src/m_pexsi_solver.F90
+
+
+

Docs/branch-changes/pexsi-gh-richer.CHANGES

+April 25, 2013  Georg Huhs trunk-434--pexsi-2--gh-richer-1
+Smarter interface with interval guessing by inertia counts
+
+This is the implementation by Georg Huhs of the new interface.
+
+There are now two entry points to PEXSI:
+
+f_ppexsi_inertiacount_interface
+f_ppexsi_solve_interface
+
+together with new parameters to determine the behavior of the code.
+Full documentation will be produced at the time of merging.
+
+(the dummy file pexsi_interface.F90, and the Makefile, was updated
+by A. Garcia)
+
+removed:
+  Src/pexsi.h
+added:
+  Docs/pexsi-gh-richer.CHANGES
+  Src/pexsi_inertia.h
+  Src/pexsi_solve.h
+modified:
+  Src/Makefile
+  Src/m_pexsi_solver.F90
+  Src/pexsi_interface.F90
+
+

Docs/branch-changes/pexsi-hio.CHANGES

+---------------------------------------------------------------
+October 14, 2013   Alberto Garcia    trunk-445--pexsi-46--hio-2
+Optionally read the Hamiltonian for analysis
+
+With the option
+
+   read-H-from-file T
+
+the program will attempt to read H from the file "H_IN". This is
+useful when performing analyses which only need H (and S), but not
+the DM. 
+
+For example, to compute bands, or (p)DOS:
+
+(... options for bands or (p)DOS...)
+max-scf-iterations 0
+read-H-from-file T
+
+Optionally, since the Fermi level is not computed in these cases, it
+can be set directly in the fdf file:
+
+   manual-fermi-level -3.05 eV
+
+The program might still attempt to initialize the DM, and print messages
+mentioning DM input. These are cosmetic issues, but the user should be
+aware that this options are to be used with care.
+
+
+modified:
+  Src/siesta_analysis.F
+
+---------------------------------------------------------------
+October 14, 2013   Alberto Garcia    trunk-445--pexsi-46--hio-1
+Save Hamiltonian and/or DM with proper filenames
+
+New file names:
+
+DM_MIXED: Useful for checkpointing
+DM_OUT:   Last DM computed
+
+H_MIXED:  Useful for checkpointing
+H_DMGEN:  Last H from which the electronic structure was computed
+
+The "mixed" files are produced only in the appropriate runs (MixDM
+(default), or MixHamiltonian).
+
+Other options affecting which files are written:
+
+- Checkpointing options:
+
+WriteDM
+WriteH
+
+- Analysis options:
+
+WriteDM.end.of.cycle
+WriteH.end.of.cycle
+
+- Backwards compatibility:
+
+SCF.MixAfterConvergence
+
+modified:
+  Src/Makefile
+  Src/m_iodm.F
+  Src/save_density_matrix.F
+  Src/siesta_forces.F
+  Src/siesta_options.F90

Docs/branch-changes/pexsi-matio.CHANGES

+-----------------------------------------------------------------
+October 24, 2013   Alberto Garcia    trunk-445--pexsi-50--matio-6
+Fix bug in dmbs2dm. Change name of argument to write_mat
+
+* A record was missing in the conversion to classic DM format by
+Util/DensityMatrix/dmbs2dm.
+
+* The optional argument to signal blocked operation in write_mat in
+module m_matio has been changed from "historical" to "compatible".
+
+modified:
+  Src/m_iodm.F
+  Src/m_matio.F90
+  Src/overlap.f
+  Src/save_density_matrix.F
+  Util/DensityMatrix/dmbs2dm.F90
+
+-----------------------------------------------------------------
+October 23, 2013   Alberto Garcia    trunk-445--pexsi-50--matio-5
+Write converter from blocked to non-blocked and deploy
+
+The newly re-organized DM and H information is now written
+to file in "blocked format" by default, unless the option
+
+       Use.Blocked.WriteMat F
+
+is used.
+
+The new format is not backwards compatible. A converter
+program (Util/DensityMatrix/dmbs2dm.F90) has been written
+to post-process those files intended for further analysis
+or re-use in Siesta. This is the best option for now, since
+it allows liberal checkpointing with a much smaller time
+consumption, and only incurs costs when re-using or analyzing
+files.
+
+Note that TranSiesta will continue to produce .DM files,
+in the old format (See save_density_matrix.F)
+
+( To test the new features, the option
+
+ S.Only T
+
+can be used. It will produce three files: a standard one,
+another one with optimized MPI communications, and a third,
+blocked one.
+)
+
+
+added:
+  Util/DensityMatrix/dmbs2dm.F90
+  Util/DensityMatrix/f2kcli.F90
+  Util/DensityMatrix/m_getopts.f90
+modified:
+  Src/Makefile
+  Src/m_iodm.F
+  Src/save_density_matrix.F
+  Util/DensityMatrix/makefile
+
+-----------------------------------------------------------------
+October 22, 2013   Alberto Garcia    trunk-445--pexsi-50--matio-4
+Use larger chunks for file writes
+
+The information in a whole "blocksize"-worth of data is now
+written to a single record on disk. This speeds up the I/O
+significantly.
+
+The new format is not backwards compatible. A new reading routine
+(possibly with on-the-fly blocksize changes) has to be written.
+
+modified:
+  Src/Makefile
+  Src/m_matio.F90
+  Src/overlap.f
+  Src/siesta_forces.F

Docs/branch-changes/pexsi-mixing.CHANGES

+------------------------------------------------------------
+September 30, 2013  A. Garcia   trunk-444--pexsi-42--mixing-6
+Documentation for latest features
+
+Merged trunk-mixing--6. See Mixing.CHANGES.
+
+------------------------------------------------------------
+September 20, 2013  A. Garcia   trunk-444--pexsi-42--mixing-5
+Fixes for TranSiesta continuation and scf loop logic
+
+Merged trunk-mixing--5. See Mixing.CHANGES.
+
+------------------------------------------------------------
+September 16, 2013  A. Garcia   trunk-444--pexsi-42--mixing-4
+Normalize the DM in the routines that handle it
+
+Merged trunk-mixing--4. See Mixing.CHANGES.
+
+------------------------------------------------------------
+September 13, 2013  A. Garcia   trunk-444--pexsi-42--mixing-3
+Optionally avoid mixing DM or H after scf-convergence
+
+Merged trunk-mixing--3. See Mixing.CHANGES.
+
+------------------------------------------------------------
+September 13, 2013  A. Garcia   trunk-444--pexsi-42--mixing-2
+(Sync patchlogs for H mixing)
+
+Merged trunk-mixing--2. See Mixing.CHANGES.
+No changes to the code needed.
+
+------------------------------------------------------------
+September 13, 2013  A. Garcia   trunk-444--pexsi-42--mixing-1
+More options for Pulay mixing
+
+Merged trunk-mixing--1. See Mixing.CHANGES.
+
+

Docs/branch-changes/pexsi-v0.7.CHANGES

+------------------------------------------------------------
+December 22, 2014  A. Garcia        trunk-464--pexsi-v0.7-14
+Clarifications in the manual. Non-square np-per-pole.
+
+Made some clarifications in the manual on the basis of feedback from
+Lin Lin.
+
+- The restriction of being a perfect square for np-per-pole has been lifted. 
+
+- New default of 1 for PEXSI.np-symbfact.
+
+- Clearer labeling for different ways of computing the band-structure
+  energy (displayed when verbosity >= 2)
+
+modified:
+  Docs/siesta.tex
+  Src/m_pexsi.f90
+  Src/m_pexsi_dos.F90
+  Src/m_pexsi_driver.F90
+  Src/m_pexsi_local_dos.F90
+
+------------------------------------------------------------
+December 17, 2014  A. Garcia        trunk-464--pexsi-v0.7-13
+Some more documentation. Update of PEXSI tests.
+
+added:
+  Tests/sih-pexsi/
+  Tests/sih-pexsi/makefile
+  Tests/sih-pexsi/sih-pexsi.fdf
+  Tests/sih-pexsi/sih-pexsi.pseudos
+modified:
+  Docs/siesta.tex
+  Src/obj_setup.sh
+  Tests/si64-pexsi/si64-pexsi.fdf
+
+------------------------------------------------------------
+December 17, 2014  A. Garcia        trunk-464--pexsi-v0.7-12
+Sync to trunk-464. More documentation on sparse-matrix i/o.
+
+Improve the documentation of the new framework for H and DM output.
+Add Util/DensityMatrix/dmUnblock.F90
+
+464:  Merge fixes from rc-4.0: constr. forces, MPI compilation, mm.potentials
+463:  Added restart file for smooth continuation of annealing runs (F. Corsetti)
+462:  Improved MPI version of siesta as a subroutine (J.M.Soler)
+461:  %files added to Util/JobList options (J.M.Soler)
+460:  New GGA and VDW functionals (M.Fritz & J.M.Soler)
+
+added:
+  Docs/gga.CHANGES
+  Docs/rc-4.0.CHANGES
+  Src/SiestaXC/Testers/Reference/
+  Src/SiestaXC/Testers/test6.f90
+  Src/SiestaXC/Testers/test6.m
+  Tests/anneal-cont/
+  Tests/anneal-cont/README
+  Tests/anneal-cont/makefile
+  Tests/anneal-cont/script.sh
+  Util/DensityMatrix/dmUnblock.F90
+  Util/JobList/Examples/Ice/dummyFile
+  Util/SiestaSubroutine/ProtoNEB/
+renamed:
+  Src/SiestaXC/Testers/test2.f90 => Src/SiestaXC/Testers/test2.F90
+modified:
+  Docs/CHANGES
+  Docs/siesta.tex
+  Pseudo/atom/Docs/atom.tex
+  Pseudo/atom/pseudoXML.f
+  Pseudo/atom/pxf.F90
+  Pseudo/atom/velect.f
+  Pseudo/atom/version.h
+  Src/MPI/Makefile
+  Src/SiestaXC/Testers/makefile
+  Src/SiestaXC/Testers/test1.f90
+  Src/SiestaXC/Testers/test3.F90
+  Src/SiestaXC/Testers/test4.F90
+  Src/SiestaXC/Testers/test5.f90
+  Src/SiestaXC/atomxc.F90
+  Src/SiestaXC/cellxc.F90
+  Src/SiestaXC/ggaxc.f
+  Src/SiestaXC/ldaxc.f
+  Src/SiestaXC/makefile
+  Src/SiestaXC/siestaxc.F90
+  Src/SiestaXC/vdwxc.F90
+  Src/SiestaXC/vv_vdwxc.F90
+  Src/SiestaXC/xcmod.f90
+  Src/atom.F
+  Src/dynamics.f
+  Src/fsiesta_mpi.F90
+  Src/molecularmechanics.F90
+  Src/write_subs.F
+  Src/xc.f
+  Util/DensityMatrix/README
+  Util/DensityMatrix/makefile
+  Util/JobList/Examples/Ice/iceChecks.jobs
+  Util/JobList/README
+  Util/JobList/Src/jobList.f90
+  Util/SiestaSubroutine/README
+  Src/SiestaXC/Testers/test2.F90
+
+
+----------------------------------------------------------------
+December 16, 2014  A. Garcia        trunk-459--pexsi-59--v0.7-11
+More documentation. Cosmetic changes in output
+
+Improve the documentation of some features. 
+Remove very low-level output and wrap other according to verbosity levels
+(work in progress).
+
+modified:
+  Docs/siesta.tex
+  Src/m_pexsi_dos.F90
+  Src/m_pexsi_driver.F90
+  Src/m_pexsi_local_dos.F90
+  Src/m_redist_spmatrix.F90
+
+----------------------------------------------------------------
+December 15, 2014  A. Garcia        trunk-459--pexsi-59--v0.7-10
+Document the PEXSI features and update interface to v0.7.3