Minor updates to documentation

git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@12318 c92efa57-630b-4861-b058-cf58834340f0

Doc/developer_man.tex

@@ -2246,6 +2246,10 @@ GIPAW http://qeforge.qe-forge.org/svn/qe-gipaw/trunk
 \section{Using git}
 \label{Sec:git}
 
+The following links conatin an introduction to \texttt{git}:\\
+https://git-scm.com/book/en/v2/Getting-Started-Git-Basics\\
+https://git-scm.com/course/svn.html
+
 \section{Bibliography}
 
 Fortran books:

TODO

@@ -1,35 +1,31 @@
 
-TODO (datafile & High throughput & reproducibility specific) - Jan 2016
+TODO (datafile & High throughput & reproducibility specific) - April 2016
 
-0) XML input: can it be improved?
 1) XML input in AIDA (what do we need to have these two working in harmony?)
 2) Datafile recording _all_ input info for reproducibility (some format decisions have to be made here) 
-3) Storing make.sys ? Does it make sense?
+3) Storing make.sys ? WanT trick is implemented in configure.
 4) Run time writing strategies at each scf step (do we really want this? can a new,optional "scf_history" file suffice? like bfgs history?)
 5) Datafile writing strategies for (vc)relax/md (data-file.0.xml 1.xml ...? giving the option to have the first and the last only)
 6) Finally, writing the output data in the datafile, fixing the redundant or missing pieces, and changing the language a bit so an outsider too can understand the content without too much suffering. 
 7) or better, writing a documentation for the tags used... 
 
-TODO LIST - May 2014
+TODO LIST
 
 0) Suspected bugs/problems:
   0.1  something happened to elf calculation between 4.1 to 4.2
-  0.2  nstep ignored in vc-relax and other cases
+  0.2  wf_collect and phonons on the grid + unneeded scf calculations
-  0.3  wf_collect and phonons on the grid + unneeded scf calculations
+  0.3  phonon restart should not recalculate the entire initialization
-  0.4  phonon restart should not recalculate the entire initialization
+  0.4  Small energy differences between PW and CP - maybe PP-related, 
-  0.5  Small energy differences between PW and CP - maybe PP-related, 
        but might also be a problem of Ewald calculation in CP ("raggio"?)
-  0.6  Numerical instabilities with: BLYP; TPSS; noncollinear GGA; LDA+U
+  0.5  Numerical instabilities with: BLYP; TPSS; noncollinear GGA; LDA+U
-  0.7  Strange numbers from phonon code in some specific cases
+  0.6  Strange numbers from phonon code in some specific cases
-  0.8  tqr results are "noisy"
+  0.7  XDM does not work with task groups
-  0.9  ntg + nbgrp incompatibility in at least one case
+  0.8  Bands with DFT+U should read U from data file, not from input
   1.0  "S matrix not positive definite"
 
 1) Organization
 1.0 Binary packages
   1.0.0 Debian compatibility:
-        - one directory per package (notable offender: PHonon/PlotPhon/QHA.
-          Move PlotPhon and QHA into PHonon or make separate packages?)
         - directory name and tarball name should be the same
         - No Java binaries (ColorCalculator)
 1.3 svn/packaging:
@@ -39,11 +35,6 @@ TODO LIST - May 2014
   1.4.1 Send monthly reminder? possibly with netiquette
   1.4.2 move to forums?
 1.7 Testing
-  1.7.1 The automated tests should be moved to a machine that can
-        send e-mail to q-e-commits
-  1.7.2 The automated tests should be performed only when something has
-        actually changed, for executables that have actually changed.
-        The current mechanism is way too rough.
   1.7.3 Many functionalities are still untested and there is not even an
         example. PP/ is a notable offender: there are a lot of possible
         calculations, most of which are never tested. Other untested
@@ -58,16 +49,7 @@ TODO LIST - May 2014
 
 3) Pseudopotentials 
 
-3.1 Set up standard tests for all PPs
+3.3 Implement OEP PPs?
-3.3 Implement OEP PPs
-3.4 Standard recipe for generating reasonable PPs:
-    - Set of prescriptions for generation
-    - Criteria for portability
-    - Update PP table with PPs that follow the recipe
-3.5 Extend documentation in pseudo-gen.tex to the case of USPP
-    (eventually to PAW)
-3.6 Add default cutoff values as well as radii of augmented charge
-    in pseudopotential files (they are present in recent PP only)
 3.7 The intermediate hard NCPP is useless for PAW and should not be 
     done when generating a PAW set
 3.8 Finish merge of Meta-GGA (TPSS) code into atomic code
@@ -86,24 +68,17 @@ TODO LIST - May 2014
         to exx, using coulomb_vcut trick.
 
 4.1  New developments to be added (sooner or later):
-  4.1.1 new xml input/output
   4.1.2 XMCD in XSpectra
   4.1.3 Genetic Algorithm
-  4.1.4 LDA+U with Wannier functions
-  4.1.5 EPW (electron-phonon with Wannier stuff): released, 
-        has to be aligned with current version
   4.1.6 Converse NMR
-  4.1.7 QM-MM with MPI
-  4.1.8 Wannier-based exact-exchange in CP (available)
 
 4.2 Small new developments, desirable or to be added:
   4.2.0 Fermi energy in insulators (tetrahedron method) should either be 
         at the top of the valence band or in the middle of the gap; now
         it is sometimes at the bottom of the conduction band (Eduardo)
   4.2.1 configure issues:
-        - ifort+acml
+        - use environment variables MKL_* if available;
-        - ifort+mkl+scalapack troubles
+          guess MKL_ROOT otherwise, use it consistently
-        - add search for -lfftw3xf_intel 
   4.2.2 constraints should be implemented in all cases;
         a check should be added if constraints break the symmetry
   4.2.3 inversion symmetry should allow real hamiltonian and wavefunctions
@@ -177,7 +152,6 @@ TODO LIST - May 2014
         - seek for CG and DIIS algoritms that only use (H-eS)|psi>
           and not the two vector separately ... compute it in one single
           call. In this way S|psi> is inexpensive
-  4.3.2 Try the new "Density-Matrix-Based" diagonalization algorithm
   4.3.3 PH: use charge mixing instead of potential mixing
   4.3.4 D3: verify status of parallelization, clean it up if needed
 
@@ -225,7 +199,6 @@ TODO LIST - May 2014
   4.4.9 too many confusing error messages are still around
   4.4.10 Output should be more informative and less confused, better
          structured, and ready for automatic reading (.e.g by xcrysden)
-  4.4.11 any possibility to merge the various solve_* in PH ?
   4.4.12 Replace "use pwcom" with more "use" statements
   4.4.13 Move all plots requiring Fourier (or real-space) interpolation
          into pawplot.x, leaving in pp.x only gaussian cube and 3d xsf
@@ -259,10 +232,6 @@ TODO LIST - May 2014
   4.5.6 epsilon.x should be extended at least to have the nonlocal
         contribution included; there should be a pointer in the
         documentation explaining how to make a better calculation.
-  4.5.7 There should be a check on the FFT grid preventing a bad 
-        choice of Nr1,Nr2,Nr3 (e.g. different Nr for axis of the
-        same length or even worse related by symmetry): this is a
-        frequent source of trouble with electron-phonon calculations
   4.5.8 Still a few quirks with the atomic coordinate parser, if 
         DOS characters or tabulators are present (Lorenzo)
   4.5.9 Spin-polarized cases: input is clumsy, confusing, error-prone;
@@ -287,12 +256,6 @@ TODO LIST - May 2014
  5.4 Some inconsistencies between PW and CP in the xml file format
      (and inconsistencies with the documentation). Also: CP should
      behave like PW and create a directory if not existent
- 5.5 XML files:
-     1) removal of obsolete variables,
-     2) addition of variables that should be present,
-     3) possibility to reduce the number of files and directories
-     (hardcoded limit, more kpoints per directory, would replace
-     and extend lkpoint_dir)
  5.6 There should be a lock mechanism that prevents people from
      overwriting files of running processes. Should be done with
      care, or else every time a code crashes will make the following