Siesta

lp:~nickpapior/siesta/4.1-md-supercell

Created by Nick Papior and last modified
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Owner:
Nick Papior
Project:
Siesta
Status:
Merged

Recent revisions

989. By Nick Papior

Updated Makefiles

988. By Nick Papior

Re-added the copy-supercell routines which may be useful in some utilities

For now they are removed from the actual code via pre-processor statements.

987. By Nick Papior

Applied patch for fixing folding into 000 supercells

This change has surfaced from discussion with Alberto (his fix).
This change stores the 000 element in the supercell DM, and if
this element does not exist it will store a "random" supercell DM
element. This has some problems for very small unit-cells, however,
we expect this problem to be insignificant compared to the problems it
solves.

986. By Nick Papior

Merged Alberto's fixes for DM folding

985. By Nick Papior

Merged Alberto's documentation updates (clarifications)

984. By Nick Papior

Implemented auxiliary cell to Gamma-only sparse pattern folding mechanism

When starting from a DM originating from a supercell calculation, and
performing a Gamma-only calculation, then connections may be doubled when
io,jo == io,io where jo is the supercell orbital.
This should equate to summing the DM contributions for all equal orbitals.

This is now implemented and tested for the si64 system
1. no auxiliary cell
2. auxiliary, init with DM from 1.
3. no auxiliary, init with DM from 2.

983. By Nick Papior

Implemented a Gamma-only sparse pattern extrapolator

When starting from a DM originating from a Gamma-only calculation the only elements that
exists are elements that "looks" like they exist in the primary unit cell. However,
they in fact correspond to supercell connections. Now the code will try and unfold
the Gamma-only calculation DM elements to the supercell format by copying the elements
multiple times (this comes from the fact that the DM is a Gamma-only with auxiliary cell
has the same DM elements for all orbital connections).

There are cases where this does not hold, e.g. when users create their own initial DM, in those
cases one can use the flag: DM.Init.Unfold false to disable the unfolding.

982. By Nick Papior

Updated description in the code for the correction of the supercell

981. By Nick Papior

Added doxygen creation (using Ford files)

The documentation created by doxygen is now very limited.
However, it may be used to check that code-documentation is
ford-doxygen compatible!
Indeed the sparse_matrices.f90

There are some major difficulties in implementation for both:

- ford accepts markdown-like links with specific entries for the
  pages site, i.e.: [see here](|page|/.../page.html).
  These are not used by Doxygen
- Doxygen uses \* commands for creating specific entries etc.
  These are not used by ford

Bottomline, continue using FORD, but iff documentation is added
in the code files, check that it runs using Doxygen.

980. By Nick Papior

Finalized a few more details in the ford documentation styles.

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