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

[Nick Papior]

Fixing MD/supercell changes to the sparsity pattern, add initial developer documentation template

This fixes the remaining issue of changing the sparsity pattern while using DM extrapolation.
I.e. now the DM_history sparse matrices are aligned with the current MD-steps sparse pattern.
Additionally this change also allows reading *any* DM file which is then converted to the intrinsic
sparse pattern used by siesta. This brings forth a nice platform for creating better initial guesses
based on simpler models (e.g. use sisl to create a better guess).

Secondly, Alberto created an initial template for doing developer documentation in Siesta.
Now FORD (doxygen for testing purposes) may be used to generate documentation of the full
Siesta code!
Indeed this is extremely valuable to point new-comers to internal details in Siesta.

[Alberto Garcia (albertog)]

For now, just a heads-up on a misbehavior of "correct_supercell" when nsc_read=(1,1,1), and a request for clarification of what the code is doing in the routine.

[Alberto Garcia (albertog)]

A followup to the folding corrrection. Perhaps it is useful to save also S in the DM file (it is just another "data string" which can go at the end of the file.

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

982. By Nick Papior on 2018-09-03

Updated description in the code for the correction of the supercell

[Nick Papior (nickpapior)]

1) Is it a calculation with folding that you want to initialize from? I.e. the nsc_read = (1,1,1) in this case?

2) I agree, this would be the best, to handle the overlap matrix, however, in cases where one wan't to create an initial DM from previously (separate) calculated DM it becomes too elaborate. In the end I think this is mainly a good idea from a perspective of doing manual interpolation and/or manual initialization.

As for the nsc_read == 1, I can successfully run the script I send (privately) with nsc_read == 1, without problems?
Secondly, where do you want the extra clarification to be put, in the dev-docs, or the source?
Could you check out the new commit?

[Alberto Garcia (albertog)]

> On 3 Sep 2018, at 10:21, Nick Papior <email address hidden> wrote:
>
> 1) Is it a calculation with folding that you want to initialize from? I.e. the nsc_read = (1,1,1) in this case?

Yes. Assume a user has run a calculation without k-points (and without an auxcell), and then wants to use the DM to initialize a
k-point calculation. This is what happens in the si64 example:

—————————————
Initializing Density Matrix...

Attempting to read DM from file... Succeeded...
DM from file:
<dSpData2D:IO-DM: si64.DM
  <sparsity:IO-DM: si64.DM
    nrows_g=256 nrows=136 sparsity=.4275 nnzs=28016, refcount: 1>
  <dData2D:(new from dSpData2D) n=28016 m=1, refcount: 1>
refcount: 1>
Note: For starting DM, Qtot, Tr[D*S] = 256.00000000 229.72632220
—————————————

This is a calculation with “normal” folding, i.e. only edge image interactions, but no direct diagonal images, so that S(i,i) = 1.0.

The missing norm is coming (or not coming…) from the zeros in the supercell DM.

Later on:

———————————
        iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
   scf: 1 10293.156932 -1324.422347 -1324.455994 3.337586 -3.198437142.619752
timer: Routine,Calls,Time,% = IterSCF 1 4.132 80.76
   scf: 2 35111.572145 3756.559710 3756.553850 4.416191 -2.224851288.324694
   scf: 3 -1549.974918 444.670819 444.641579 3.270160 -2.128185164.985102
   scf: 4 -5371.294656 -2706.434665 -2706.485243 1.485187 -2.565191125.811367
   scf: 5 18837.075132 -728.224618 -728.241614 4.270983 -3.174556153.635637
   scf: 6 -8033.559239 -5034.599795 -5034.645848 2.447968 -2.942511 88.795877
   scf: 7 -7165.186747 -6839.938924 -6839.938924 2.852955 -2.675640 4.831900
   scf: 8 -6836.790121 -6839.363374 -6839.363374 0.078137 -2.668903 4.867
…..
————————

Note that, for k=0, even in extreme folding cases, the DM has a very simple structure, and is NOT folded. Only H and S are actually folded. ALL the image elements of the DM are the same as those in the unit-cell square matrix. This is the code in diagg:

                do j = 1,numd(io)
                  ind = listdptr(io) + j
                  jo = listd(ind)
                  jo = MODP(jo,nuotot) ! To allow auxiliary supercells
                  Dnew(ind,ispin) = Dnew(ind,ispin) + qei*paux(jo)
                  Enew(ind,ispin) = Enew(ind,ispin) + eei*paux(jo)
                enddo

So all the entries (arbitrary “ind”) have the same value as those in the “fold-to” corner of the rectangular DM.

To get back the missing norm approximately in the nsc_read= (1,1,1) case, one then could do:

  foreach non-zero extended S entry “ind_new” in the new, full-nsc supercell:
       find the io,jo entry in the read DM, and copy the entry to the new DM.

It might be easier to reverse the logic and just “un-fold” the read DM, with a loop very similar to the above.

Of course, it is simpler to run the k=0 calculation with “force-auxcell”, but this change looks simple, and will add functionality.

The handling of intermediate cases, when nsc_read is a “s...

[Nick Papior (nickpapior)]

I am not sure everything is as easy as it seems.

1) For the si64 case you say that the connections are all "singly counted", i.e. there are no connections that are summed twice. In this case the missing charges are most likely coming from the periodic charge distribution. However, what if the user changes the basis range which then adds more interactions? I.e. how does Siesta knows if the generated sparse pattern is not generated as the primary unit-cell charge *only*? For now I have added a flag called DM.Init.Unfold which is default to true. If one knows the DM stems from a different initialization field one can set this to false.

2) As for MD simulations, yes, this is another problem...

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

983. By Nick Papior on 2018-09-03

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.

[Nick Papior (nickpapior)]

I have added the fix for 1). Now si64 runs very nice when changing from no-auxcell to force-auxcell.

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

984. By Nick Papior on 2018-09-05

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.

985. By Nick Papior on 2018-09-05

Merged Alberto's documentation updates (clarifications)

[Nick Papior (nickpapior)]

Bump thread :)

[Nick Papior (nickpapior)]

Marked lp:~albertog/siesta/4.1-supercell-docs as merged! Revert mark if dev is continued there. :)

[Alberto Garcia (albertog)]

We have clarified offline the issue of "folding" to a 111 supercell. What we need is actually 'copying'. A patch is going to be applied, and the merge request is approved.

review: Approve

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

986. By Nick Papior on 2018-09-12

Merged Alberto's fixes for DM folding

987. By Nick Papior on 2018-09-12

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.

988. By Nick Papior on 2018-09-12

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.

989. By Nick Papior on 2018-09-12

Updated Makefiles

=== added directory 'Docs/developer'
=== added file 'Docs/developer/doxygen-siesta'
--- Docs/developer/doxygen-siesta	1970-01-01 00:00:00 +0000
+++ Docs/developer/doxygen-siesta	2018-09-12 13:10:27 +0000
@@ -0,0 +1,2484 @@
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+# to NO, structs, classes, and unions are shown on a separate page (for HTML and
+# Man pages) or section (for LaTeX and RTF).
+# The default value is: NO.
+
+INLINE_SIMPLE_STRUCTS  = NO
+
+# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically be
+# useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+# The default value is: NO.
+
+TYPEDEF_HIDES_STRUCT   = NO
+
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can be
+# an expensive process and often the same symbol appears multiple times in the
+# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
+# doxygen will become slower. If the cache is too large, memory is wasted. The
+# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
+# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
+# symbols. At the end of a run doxygen will report the cache usage and suggest
+# the optimal cache size from a speed point of view.
+# Minimum value: 0, maximum value: 9, default value: 0.
+
+LOOKUP_CACHE_SIZE      = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
+# documentation are documented, even if no documentation was available. Private
+# class members and static file members will be hidden unless the
+# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
+# Note: This will also disable the warnings about undocumented members that are
+# normally produced when WARNINGS is set to YES.
+# The default value is: NO.
+
+EXTRACT_ALL            = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
+# be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PRIVATE        = NO
+
+# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
+# scope will be included in the documentation.
+# The default value is: NO.
+
+EXTRACT_PACKAGE        = NO
+
+# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
+# included in the documentation.
+# The default value is: NO.
+
+EXTRACT_STATIC         = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
+# locally in source files will be included in the documentation. If set to NO,
+# only classes defined in header files are included. Does not have any effect
+# for Java sources.
+# The default value is: YES.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# This flag is only useful for Objective-C code. If set to YES, local methods,
+# which are defined in the implementation section but not in the interface are
+# included in the documentation. If set to NO, only methods in the interface are
+# included.
+# The default value is: NO.
+
+EXTRACT_LOCAL_METHODS  = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base name of
+# the file that contains the anonymous namespace. By default anonymous namespace
+# are hidden.
+# The default value is: NO.
+
+EXTRACT_ANON_NSPACES   = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
+# undocumented members inside documented classes or files. If set to NO these
+# members will be included in the various overviews, but no documentation
+# section is generated. This option has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_MEMBERS     = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy. If set
+# to NO, these classes will be included in the various overviews. This option
+# has no effect if EXTRACT_ALL is enabled.
+# The default value is: NO.
+
+HIDE_UNDOC_CLASSES     = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
+# (class|struct|union) declarations. If set to NO, these declarations will be
+# included in the documentation.
+# The default value is: NO.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
+# documentation blocks found inside the body of a function. If set to NO, these
+# blocks will be appended to the function's detailed documentation block.
+# The default value is: NO.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation that is typed after a
+# \internal command is included. If the tag is set to NO then the documentation
+# will be excluded. Set it to YES to include the internal documentation.
+# The default value is: NO.
+
+INTERNAL_DOCS          = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
+# names in lower-case letters. If set to YES, upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+# The default value is: system dependent.
+
+CASE_SENSE_NAMES       = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
+# their full class and namespace scopes in the documentation. If set to YES, the
+# scope will be hidden.
+# The default value is: NO.
+
+HIDE_SCOPE_NAMES       = NO
+
+# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
+# append additional text to a page's title, such as Class Reference. If set to
+# YES the compound reference will be hidden.
+# The default value is: NO.
+
+HIDE_COMPOUND_REFERENCE= NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
+# the files that are included by a file in the documentation of that file.
+# The default value is: YES.
+
+SHOW_INCLUDE_FILES     = YES
+
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC  = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
+# files with double quotes in the documentation rather than with sharp brackets.
+# The default value is: NO.
+
+FORCE_LOCAL_INCLUDES   = NO
+
+# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
+# documentation for inline members.
+# The default value is: YES.
+
+INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
+# (detailed) documentation of file and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order.
+# The default value is: YES.
+
+SORT_MEMBER_DOCS       = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
+# descriptions of file, namespace and class members alphabetically by member
+# name. If set to NO, the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
+# The default value is: NO.
+
+SORT_BRIEF_DOCS        = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
+# (brief and detailed) documentation of class members so that constructors and
+# destructors are listed first. If set to NO the constructors will appear in the
+# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
+# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
+# member documentation.
+# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
+# detailed member documentation.
+# The default value is: NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
+# of group names into alphabetical order. If set to NO the group names will
+# appear in their defined order.
+# The default value is: NO.
+
+SORT_GROUP_NAMES       = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
+# fully-qualified names, including namespaces. If set to NO, the class list will
+# be sorted only by class name, not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the alphabetical
+# list.
+# The default value is: NO.
+
+SORT_BY_SCOPE_NAME     = NO
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
+# type resolution of all parameters of a function it will reject a match between
+# the prototype and the implementation of a member function even if there is
+# only one candidate or it is obvious which candidate to choose by doing a
+# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
+# accept a match between prototype and implementation in such cases.
+# The default value is: NO.
+
+STRICT_PROTO_MATCHING  = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
+# list. This list is created by putting \todo commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TODOLIST      = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
+# list. This list is created by putting \test commands in the documentation.
+# The default value is: YES.
+
+GENERATE_TESTLIST      = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
+# list. This list is created by putting \bug commands in the documentation.
+# The default value is: YES.
+
+GENERATE_BUGLIST       = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
+# the deprecated list. This list is created by putting \deprecated commands in
+# the documentation.
+# The default value is: YES.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional documentation
+# sections, marked by \if <section_label> ... \endif and \cond <section_label>
+# ... \endcond blocks.
+
+ENABLED_SECTIONS       =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
+# initial value of a variable or macro / define can have for it to appear in the
+# documentation. If the initializer consists of more lines than specified here
+# it will be hidden. Use a value of 0 to hide initializers completely. The
+# appearance of the value of individual variables and macros / defines can be
+# controlled using \showinitializer or \hideinitializer command in the
+# documentation regardless of this setting.
+# Minimum value: 0, maximum value: 10000, default value: 30.
+
+MAX_INITIALIZER_LINES  = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
+# the bottom of the documentation of classes and structs. If set to YES, the
+# list will mention the files that were used to generate the documentation.
+# The default value is: YES.
+
+SHOW_USED_FILES        = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
+# will remove the Files entry from the Quick Index and from the Folder Tree View
+# (if specified).
+# The default value is: YES.
+
+SHOW_FILES             = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
+# page. This will remove the Namespaces entry from the Quick Index and from the
+# Folder Tree View (if specified).
+# The default value is: YES.
+
+SHOW_NAMESPACES        = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command command input-file, where command is the value of the
+# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
+# by doxygen. Whatever the program writes to standard output is used as the file
+# version. For an example see the documentation.
+
+FILE_VERSION_FILTER    =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option. You can
+# optionally specify a file name after the option, if omitted DoxygenLayout.xml
+# will be used as the name of the layout file.
+#
+# Note that if you run doxygen from a directory containing a file called
+# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
+# tag is left empty.
+
+LAYOUT_FILE            =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
+# the reference definitions. This must be a list of .bib files. The .bib
+# extension is automatically appended if omitted. This requires the bibtex tool
+# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info.
+# For LaTeX the style of the bibliography can be controlled using
+# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
+# search path. See also \cite for info how to create references.
+
+CITE_BIB_FILES         =
+
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated to
+# standard output by doxygen. If QUIET is set to YES this implies that the
+# messages are off.
+# The default value is: NO.
+
+QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
+# this implies that the warnings are on.
+#
+# Tip: Turn warnings on while writing the documentation.
+# The default value is: YES.
+
+WARNINGS               = YES
+
+# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
+# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
+# will automatically be disabled.
+# The default value is: YES.
+
+WARN_IF_UNDOCUMENTED   = YES
+
+# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some parameters
+# in a documented function, or documenting parameters that don't exist or using
+# markup commands wrongly.
+# The default value is: YES.
+
+WARN_IF_DOC_ERROR      = YES
+
+# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
+# are documented, but have no documentation for their parameters or return
+# value. If set to NO, doxygen will only warn about wrong or incomplete
+# parameter documentation, but not about the absence of documentation.
+# The default value is: NO.
+
+WARN_NO_PARAMDOC       = NO
+
+# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
+# a warning is encountered.
+# The default value is: NO.
+
+WARN_AS_ERROR          = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that doxygen
+# can produce. The string should contain the $file, $line, and $text tags, which
+# will be replaced by the file and line number from which the warning originated
+# and the warning text. Optionally the format may contain $version, which will
+# be replaced by the version of the file (if it could be obtained via
+# FILE_VERSION_FILTER)
+# The default value is: $file:$line: $text.
+
+WARN_FORMAT            = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning and error
+# messages should be written. If left blank the output is written to standard
+# error (stderr).
+
+WARN_LOGFILE           =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag is used to specify the files and/or directories that contain
+# documented source files. You may enter file names like myfile.cpp or
+# directories like /usr/src/myproject. Separate the files or directories with
+# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
+# Note: If this tag is empty the current directory is searched.
+
+INPUT                  = ../../Src \
+		       ford-pages
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
+# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
+# documentation (see: http://www.gnu.org/software/libiconv) for the list of
+# possible encodings.
+# The default value is: UTF-8.
+
+INPUT_ENCODING         = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
+# *.h) to filter out the source-files in the directories.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# read by doxygen.
+#
+# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
+# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
+# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
+# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf.
+
+FILE_PATTERNS          = *.c \
+                         *.cc \
+                         *.cxx \
+                         *.cpp \
+                         *.c++ \
+                         *.java \
+                         *.ii \
+                         *.ixx \
+                         *.ipp \
+                         *.i++ \
+                         *.inl \
+                         *.idl \
+                         *.ddl \
+                         *.odl \
+                         *.h \
+                         *.hh \
+                         *.hxx \
+                         *.hpp \
+                         *.h++ \
+                         *.cs \
+                         *.d \
+                         *.php \
+                         *.php4 \
+                         *.php5 \
+                         *.phtml \
+                         *.inc \
+                         *.m \
+                         *.markdown \
+                         *.md \
+                         *.mm \
+                         *.dox \
+                         *.py \
+                         *.pyw \
+                         *.F90 \
+                         *.f90 \
+                         *.f95 \
+                         *.f03 \
+                         *.f08 \
+                         *.f \
+                         *.F \
+                         *.for \
+                         *.tcl \
+                         *.vhd \
+                         *.vhdl \
+                         *.ucf \
+                         *.qsf
+
+# The RECURSIVE tag can be used to specify whether or not subdirectories should
+# be searched for input files as well.
+# The default value is: NO.
+
+RECURSIVE              = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+#
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE                = ../../Src/MPI \
+		         ../../Src/fdf \
+			 ../../Src/fdict \
+			 ../../Src/ncdf \
+			 ../../Src/Libs \
+			 ../../Src/Orphans \
+			 ../../Src/SiestaXC \
+			 ../../Src/wxml \
+			 ../../Src/xmlparser
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
+# from the input.
+# The default value is: NO.
+
+EXCLUDE_SYMLINKS       = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories.
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories for example use the pattern */test/*
+
+EXCLUDE_PATTERNS       =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+#
+# Note that the wildcards are matched against the file with absolute path, so to
+# exclude all test directories use the pattern */test/*
+
+EXCLUDE_SYMBOLS        =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or directories
+# that contain example code fragments that are included (see the \include
+# command).
+
+EXAMPLE_PATH           =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
+# *.h) to filter out the source-files in the directories. If left blank all
+# files are included.
+
+EXAMPLE_PATTERNS       = *
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude commands
+# irrespective of the value of the RECURSIVE tag.
+# The default value is: NO.
+
+EXAMPLE_RECURSIVE      = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or directories
+# that contain images that are to be included in the documentation (see the
+# \image command).
+
+IMAGE_PATH             = ford-media
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command:
+#
+# <filter> <input-file>
+#
+# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
+# name of an input file. Doxygen will then use the output that the filter
+# program writes to standard output. If FILTER_PATTERNS is specified, this tag
+# will be ignored.
+#
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+INPUT_FILTER           =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form: pattern=filter
+# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
+# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
+# patterns match the file name, INPUT_FILTER is applied.
+#
+# Note that for custom extensions or not directly supported extensions you also
+# need to set EXTENSION_MAPPING for the extension otherwise the files are not
+# properly processed by doxygen.
+
+FILTER_PATTERNS        =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will also be used to filter the input files that are used for
+# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
+# The default value is: NO.
+
+FILTER_SOURCE_FILES    = NO
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
+# it is also possible to disable source filtering for a specific pattern using
+# *.ext= (so without naming a filter).
+# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
+
+FILTER_SOURCE_PATTERNS =
+
+# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want to reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE = ford-pages/index.md
+
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
+# generated. Documented entities will be cross-referenced with these sources.
+#
+# Note: To get rid of all source code in the generated output, make sure that
+# also VERBATIM_HEADERS is set to NO.
+# The default value is: NO.
+
+SOURCE_BROWSER         = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body of functions,
+# classes and enums directly into the documentation.
+# The default value is: NO.
+
+INLINE_SOURCES         = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
+# special comment blocks from generated source code fragments. Normal C, C++ and
+# Fortran comments will always remain visible.
+# The default value is: YES.
+
+STRIP_CODE_COMMENTS    = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
+# function all documented functions referencing it will be listed.
+# The default value is: NO.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES then for each documented function
+# all documented entities called/used by that function will be listed.
+# The default value is: NO.
+
+REFERENCES_RELATION    = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
+# to YES then the hyperlinks from functions in REFERENCES_RELATION and
+# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
+# link to the documentation.
+# The default value is: YES.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
+# source code will show a tooltip with additional information such as prototype,
+# brief description and links to the definition and documentation. Since this
+# will make the HTML file larger and loading of large files a bit slower, you
+# can opt to disable this feature.
+# The default value is: YES.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+SOURCE_TOOLTIPS        = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code will
+# point to the HTML generated by the htags(1) tool instead of doxygen built-in
+# source browser. The htags tool is part of GNU's global source tagging system
+# (see http://www.gnu.org/software/global/global.html). You will need version
+# 4.8.6 or higher.
+#
+# To use it do the following:
+# - Install the latest version of global
+# - Enable SOURCE_BROWSER and USE_HTAGS in the config file
+# - Make sure the INPUT points to the root of the source tree
+# - Run doxygen as normal
+#
+# Doxygen will invoke htags (and that will in turn invoke gtags), so these
+# tools must be available from the command line (i.e. in the search path).
+#
+# The result: instead of the source browser generated by doxygen, the links to
+# source code will now point to the output of htags.
+# The default value is: NO.
+# This tag requires that the tag SOURCE_BROWSER is set to YES.
+
+USE_HTAGS              = NO
+
+# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
+# verbatim copy of the header file for each class for which an include is
+# specified. Set to NO to disable this.
+# See also: Section \class.
+# The default value is: YES.
+
+VERBATIM_HEADERS       = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
+# compounds will be generated. Enable this if the project contains a lot of
+# classes, structs, unions or interfaces.
+# The default value is: YES.
+
+ALPHABETICAL_INDEX     = YES
+
+# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in
+# which the alphabetical index list will be split.
+# Minimum value: 1, maximum value: 20, default value: 5.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+COLS_IN_ALPHA_INDEX    = 5
+
+# In case all classes in a project start with a common prefix, all classes will
+# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag
+# can be used to specify a prefix (or a list of prefixes) that should be ignored
+# while generating the index headers.
+# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
+
+IGNORE_PREFIX          =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
+# The default value is: YES.
+
+GENERATE_HTML          = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_OUTPUT            = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
+# generated HTML page (for example: .htm, .php, .asp).
+# The default value is: .html.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FILE_EXTENSION    = .html
+
+# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
+# each generated HTML page. If the tag is left blank doxygen will generate a
+# standard header.
+#
+# To get valid HTML the header file that includes any scripts and style sheets
+# that doxygen needs, which is dependent on the configuration options used (e.g.
+# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
+# default header using
+# doxygen -w html new_header.html new_footer.html new_stylesheet.css
+# YourConfigFile
+# and then modify the file new_header.html. See also section "Doxygen usage"
+# for information on how to generate the default header that doxygen normally
+# uses.
+# Note: The header is subject to change so you typically have to regenerate the
+# default header when upgrading to a newer version of doxygen. For a description
+# of the possible markers and block names see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_HEADER            =
+
+# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
+# generated HTML page. If the tag is left blank doxygen will generate a standard
+# footer. See HTML_HEADER for more information on how to generate a default
+# footer and what special commands can be used inside the footer. See also
+# section "Doxygen usage" for information on how to generate the default footer
+# that doxygen normally uses.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FOOTER            =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
+# sheet that is used by each HTML page. It can be used to fine-tune the look of
+# the HTML output. If left blank doxygen will generate a default style sheet.
+# See also section "Doxygen usage" for information on how to generate the style
+# sheet that doxygen normally uses.
+# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
+# it is more robust and this tag (HTML_STYLESHEET) will in the future become
+# obsolete.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_STYLESHEET        =
+
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
+# created by doxygen. Using this option one can overrule certain style aspects.
+# This is preferred over using HTML_STYLESHEET since it does not replace the
+# standard style sheet and is therefore more robust against future updates.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_STYLESHEET  =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
+# files will be copied as-is; there are no commands or markers available.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_EXTRA_FILES       =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
+# will adjust the colors in the style sheet and background images according to
+# this color. Hue is specified as an angle on a colorwheel, see
+# http://en.wikipedia.org/wiki/Hue for more information. For instance the value
+# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
+# purple, and 360 is red again.
+# Minimum value: 0, maximum value: 359, default value: 220.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_HUE    = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
+# in the HTML output. For a value of 0 the output will use grayscales only. A
+# value of 255 will produce the most vivid colors.
+# Minimum value: 0, maximum value: 255, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_SAT    = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
+# luminance component of the colors in the HTML output. Values below 100
+# gradually make the output lighter, whereas values above 100 make the output
+# darker. The value divided by 100 is the actual gamma applied, so 80 represents
+# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
+# change the gamma.
+# Minimum value: 40, maximum value: 240, default value: 80.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE_GAMMA  = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting this
+# to YES can help to show when doxygen was last run and thus if the
+# documentation is up to date.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_TIMESTAMP         = NO
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_DYNAMIC_SECTIONS  = NO
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
+# shown in the various tree structured indices initially; the user can expand
+# and collapse entries dynamically later on. Doxygen will expand the tree to
+# such a level that at most the specified number of entries are visible (unless
+# a fully collapsed tree already exceeds this amount). So setting the number of
+# entries 1 will produce a full collapsed tree by default. 0 is a special value
+# representing an infinite number of entries and will result in a full expanded
+# tree by default.
+# Minimum value: 0, maximum value: 9999, default value: 100.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files will be
+# generated that can be used as input for Apple's Xcode 3 integrated development
+# environment (see: http://developer.apple.com/tools/xcode/), introduced with
+# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a
+# Makefile in the HTML output directory. Running make will produce the docset in
+# that directory and running make install will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
+# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_DOCSET        = NO
+
+# This tag determines the name of the docset feed. A documentation feed provides
+# an umbrella under which multiple documentation sets from a single provider
+# (such as a company or product suite) can be grouped.
+# The default value is: Doxygen generated docs.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+
+# This tag specifies a string that should uniquely identify the documentation
+# set bundle. This should be a reverse domain-name style string, e.g.
+# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+
+# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+# The default value is: org.doxygen.Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+
+# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
+# The default value is: Publisher.
+# This tag requires that the tag GENERATE_DOCSET is set to YES.
+
+DOCSET_PUBLISHER_NAME  = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
+# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
+# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
+# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on
+# Windows.
+#
+# The HTML Help Workshop contains a compiler that can convert all HTML output
+# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
+# files are now used as the Windows 98 help format, and will replace the old
+# Windows help format (.hlp) on all Windows platforms in the future. Compressed
+# HTML files also contain an index, a table of contents, and you can search for
+# words in the documentation. The HTML workshop also contains a viewer for
+# compressed HTML files.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_HTMLHELP      = NO
+
+# The CHM_FILE tag can be used to specify the file name of the resulting .chm
+# file. You can add a path in front of the file if the result should not be
+# written to the html output directory.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_FILE               =
+
+# The HHC_LOCATION tag can be used to specify the location (absolute path
+# including file name) of the HTML help compiler (hhc.exe). If non-empty,
+# doxygen will try to run the HTML help compiler on the generated index.hhp.
+# The file has to be specified with full path.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+HHC_LOCATION           =
+
+# The GENERATE_CHI flag controls if a separate .chi index file is generated
+# (YES) or that it should be included in the master .chm file (NO).
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+GENERATE_CHI           = NO
+
+# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
+# and project file content.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+CHM_INDEX_ENCODING     =
+
+# The BINARY_TOC flag controls whether a binary table of contents is generated
+# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+BINARY_TOC             = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members to
+# the table of contents of the HTML help documentation and to the tree view.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
+
+TOC_EXPAND             = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
+# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
+# (.qch) of the generated HTML documentation.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_QHP           = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
+# the file name of the resulting .qch file. The path specified is relative to
+# the HTML output folder.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QCH_FILE               =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
+# Project output. For more information please see Qt Help Project / Namespace
+# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace).
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_NAMESPACE          = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
+# Help Project output. For more information please see Qt Help Project / Virtual
+# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual-
+# folders).
+# The default value is: doc.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_VIRTUAL_FOLDER     = doc
+
+# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
+# filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_NAME   =
+
+# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see Qt Help Project / Custom
+# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom-
+# filters).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_CUST_FILTER_ATTRS  =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's filter section matches. Qt Help Project / Filter Attributes (see:
+# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes).
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHP_SECT_FILTER_ATTRS  =
+
+# The QHG_LOCATION tag can be used to specify the location of Qt's
+# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
+# generated .qhp file.
+# This tag requires that the tag GENERATE_QHP is set to YES.
+
+QHG_LOCATION           =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
+# generated, together with the HTML files, they form an Eclipse help plugin. To
+# install this plugin and make it available under the help contents menu in
+# Eclipse, the contents of the directory containing the HTML and XML files needs
+# to be copied into the plugins directory of eclipse. The name of the directory
+# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
+# After copying Eclipse needs to be restarted before the help appears.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_ECLIPSEHELP   = NO
+
+# A unique identifier for the Eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have this
+# name. Each documentation set should have its own identifier.
+# The default value is: org.doxygen.Project.
+# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
+
+ECLIPSE_DOC_ID         = org.doxygen.Project
+
+# If you want full control over the layout of the generated HTML pages it might
+# be necessary to disable the index and replace it with your own. The
+# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
+# of each HTML page. A value of NO enables the index and the value YES disables
+# it. Since the tabs in the index contain the same information as the navigation
+# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+DISABLE_INDEX          = NO
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information. If the tag
+# value is set to YES, a side panel will be generated containing a tree-like
+# index structure (just like the one that is generated for HTML Help). For this
+# to work a browser that supports JavaScript, DHTML, CSS and frames is required
+# (i.e. any modern browser). Windows users are probably better off using the
+# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
+# further fine-tune the look of the index. As an example, the default style
+# sheet generated by doxygen has an example that shows how to put an image at
+# the root of the tree instead of the PROJECT_NAME. Since the tree basically has
+# the same information as the tab index, you could consider setting
+# DISABLE_INDEX to YES when enabling this option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+GENERATE_TREEVIEW      = NO
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
+# doxygen will group on one line in the generated HTML documentation.
+#
+# Note that a value of 0 will completely suppress the enum values from appearing
+# in the overview section.
+# Minimum value: 0, maximum value: 20, default value: 4.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+ENUM_VALUES_PER_LINE   = 4
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
+# to set the initial width (in pixels) of the frame in which the tree is shown.
+# Minimum value: 0, maximum value: 1500, default value: 250.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+TREEVIEW_WIDTH         = 250
+
+# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
+# external symbols imported via tag files in a separate window.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+EXT_LINKS_IN_WINDOW    = NO
+
+# Use this tag to change the font size of LaTeX formulas included as images in
+# the HTML documentation. When you change the font size after a successful
+# doxygen run you need to manually remove any form_*.png images from the HTML
+# output directory to force them to be regenerated.
+# Minimum value: 8, maximum value: 50, default value: 10.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_FONTSIZE       = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are not
+# supported properly for IE 6.0, but are supported on all modern browsers.
+#
+# Note that when changing this option you need to delete any form_*.png files in
+# the HTML output directory before the changes have effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+FORMULA_TRANSPARENT    = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
+# http://www.mathjax.org) which uses client side Javascript for the rendering
+# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
+# installed or if you want to formulas look prettier in the HTML output. When
+# enabled you may also need to install MathJax separately and configure the path
+# to it using the MATHJAX_RELPATH option.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+USE_MATHJAX            = NO
+
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. See the MathJax site (see:
+# http://docs.mathjax.org/en/latest/output.html) for more details.
+# Possible values are: HTML-CSS (which is slower, but has the best
+# compatibility), NativeMML (i.e. MathML) and SVG.
+# The default value is: HTML-CSS.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_FORMAT         = HTML-CSS
+
+# When MathJax is enabled you need to specify the location relative to the HTML
+# output directory using the MATHJAX_RELPATH option. The destination directory
+# should contain the MathJax.js script. For instance, if the mathjax directory
+# is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
+# Content Delivery Network so you can quickly see the result without installing
+# MathJax. However, it is strongly recommended to install a local copy of
+# MathJax from http://www.mathjax.org before deployment.
+# The default value is: http://cdn.mathjax.org/mathjax/latest.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
+# extension names that should be enabled during MathJax rendering. For example
+# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_EXTENSIONS     =
+
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
+# of code that will be used on startup of the MathJax code. See the MathJax site
+# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# example see the documentation.
+# This tag requires that the tag USE_MATHJAX is set to YES.
+
+MATHJAX_CODEFILE       =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
+# the HTML output. The underlying search engine uses javascript and DHTML and
+# should work on any modern browser. Note that when using HTML help
+# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
+# there is already a search function so this one should typically be disabled.
+# For large projects the javascript based search engine can be slow, then
+# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
+# search using the keyboard; to jump to the search box use <access key> + S
+# (what the <access key> is depends on the OS and browser, but it is typically
+# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
+# key> to jump into the search results window, the results can be navigated
+# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
+# the search. The filter options can be selected when the cursor is inside the
+# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
+# to select a filter and <Enter> or <escape> to activate or cancel the filter
+# option.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+SEARCHENGINE           = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a web server instead of a web client using Javascript. There
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SERVER_BASED_SEARCH    = NO
+
+# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
+# search results.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/).
+#
+# See the section "External Indexing and Searching" for details.
+# The default value is: NO.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH        = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will return the search results when EXTERNAL_SEARCH is enabled.
+#
+# Doxygen ships with an example indexer (doxyindexer) and search engine
+# (doxysearch.cgi) which are based on the open source search engine library
+# Xapian (see: http://xapian.org/). See the section "External Indexing and
+# Searching" for details.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHENGINE_URL       =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+# The default file is: searchdata.xml.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+SEARCHDATA_FILE        = searchdata.xml
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTERNAL_SEARCH_ID     =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
+# to a relative location where the documentation can be found. The format is:
+# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
+# This tag requires that the tag SEARCHENGINE is set to YES.
+
+EXTRA_SEARCH_MAPPINGS  =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
+# The default value is: YES.
+
+GENERATE_LATEX         = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_OUTPUT           = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked.
+#
+# Note that when enabling USE_PDFLATEX this option is only used for generating
+# bitmaps for formulas in the HTML output, but not in the Makefile that is
+# written to the output directory.
+# The default file is: latex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_CMD_NAME         = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
+# index for LaTeX.
+# The default file is: makeindex.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+MAKEINDEX_CMD_NAME     = makeindex
+
+# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+COMPACT_LATEX          = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used by the
+# printer.
+# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
+# 14 inches) and executive (7.25 x 10.5 inches).
+# The default value is: a4.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PAPER_TYPE             = a4
+
+# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
+# that should be included in the LaTeX output. The package can be specified just
+# by its name or with the correct syntax as to be used with the LaTeX
+# \usepackage command. To get the times font for instance you can specify :
+# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
+# To use the option intlimits with the amsmath package you can specify:
+# EXTRA_PACKAGES=[intlimits]{amsmath}
+# If left blank no extra packages will be included.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+EXTRA_PACKAGES         =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
+# generated LaTeX document. The header should contain everything until the first
+# chapter. If it is left blank doxygen will generate a standard header. See
+# section "Doxygen usage" for information on how to let doxygen write the
+# default header to a separate file.
+#
+# Note: Only use a user-defined header if you know what you are doing! The
+# following commands have a special meaning inside the header: $title,
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empty
+# string, for the replacement values of the other commands the user is referred
+# to HTML_HEADER.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HEADER           =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
+# generated LaTeX document. The footer should contain everything after the last
+# chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer.
+#
+# Note: Only use a user-defined footer if you know what you are doing!
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_FOOTER           =
+
+# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# LaTeX style sheets that are included after the standard style sheets created
+# by doxygen. Using this option one can overrule certain style aspects. Doxygen
+# will copy the style sheet files to the output directory.
+# Note: The order of the extra style sheet files is of importance (e.g. the last
+# style sheet in the list overrules the setting of the previous ones in the
+# list).
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_STYLESHEET =
+
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the LATEX_OUTPUT output
+# directory. Note that the files will be copied as-is; there are no commands or
+# markers available.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_EXTRA_FILES      =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
+# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
+# contain links (just like the HTML output) instead of page references. This
+# makes the output suitable for online browsing using a PDF viewer.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+PDF_HYPERLINKS         = YES
+
+# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# the PDF file directly from the LaTeX files. Set this option to YES, to get a
+# higher quality PDF documentation.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+USE_PDFLATEX           = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
+# command to the generated LaTeX files. This will instruct LaTeX to keep running
+# if errors occur, instead of asking the user for help. This option is also used
+# when generating formulas in HTML.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BATCHMODE        = NO
+
+# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
+# index chapters (such as File Index, Compound Index, etc.) in the output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_HIDE_INDICES     = NO
+
+# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
+# code with syntax highlighting in the LaTeX output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_SOURCE_CODE      = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. See
+# http://en.wikipedia.org/wiki/BibTeX and \cite for more info.
+# The default value is: plain.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_BIB_STYLE        = plain
+
+# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
+# page will contain the date and time when the page was generated. Setting this
+# to NO can help when comparing the output of multiple runs.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_LATEX is set to YES.
+
+LATEX_TIMESTAMP        = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
+# RTF output is optimized for Word 97 and may not look too pretty with other RTF
+# readers/editors.
+# The default value is: NO.
+
+GENERATE_RTF           = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: rtf.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_OUTPUT             = rtf
+
+# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
+# documents. This may be useful for small projects and may help to save some
+# trees in general.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+COMPACT_RTF            = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
+# contain hyperlink fields. The RTF file will contain links (just like the HTML
+# output) instead of page references. This makes the output suitable for online
+# browsing using Word or some other Word compatible readers that support those
+# fields.
+#
+# Note: WordPad (write) and others do not support links.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_HYPERLINKS         = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's config
+# file, i.e. a series of assignments. You only have to provide replacements,
+# missing definitions are set to their default value.
+#
+# See also section "Doxygen usage" for information on how to generate the
+# default style sheet that doxygen normally uses.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_STYLESHEET_FILE    =
+
+# Set optional variables used in the generation of an RTF document. Syntax is
+# similar to doxygen's config file. A template extensions file can be generated
+# using doxygen -e rtf extensionFile.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_EXTENSIONS_FILE    =
+
+# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
+# with syntax highlighting in the RTF output.
+#
+# Note that which sources are shown also depends on other settings such as
+# SOURCE_BROWSER.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_RTF is set to YES.
+
+RTF_SOURCE_CODE        = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
+# classes and files.
+# The default value is: NO.
+
+GENERATE_MAN           = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it. A directory man3 will be created inside the directory specified by
+# MAN_OUTPUT.
+# The default directory is: man.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_OUTPUT             = man
+
+# The MAN_EXTENSION tag determines the extension that is added to the generated
+# man pages. In case the manual section does not start with a number, the number
+# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
+# optional.
+# The default value is: .3.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_EXTENSION          = .3
+
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR             =
+
+# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
+# will generate one additional man file for each entity documented in the real
+# man page(s). These additional files only source the real man page, but without
+# them the man command would be unable to find the correct page.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_LINKS              = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
+# captures the structure of the code including all documentation.
+# The default value is: NO.
+
+GENERATE_XML           = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
+# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
+# it.
+# The default directory is: xml.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_OUTPUT             = xml
+
+# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
+# listings (including syntax highlighting and cross-referencing information) to
+# the XML output. Note that enabling this will significantly increase the size
+# of the XML output.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_XML is set to YES.
+
+XML_PROGRAMLISTING     = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
+# that can be used to generate PDF.
+# The default value is: NO.
+
+GENERATE_DOCBOOK       = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it.
+# The default directory is: docbook.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_OUTPUT         = docbook
+
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
+
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
+# AutoGen Definitions (see http://autogen.sf.net) file that captures the
+# structure of the code including all documentation. Note that this feature is
+# still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_AUTOGEN_DEF   = NO
+
+#---------------------------------------------------------------------------
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
+# file that captures the structure of the code including all documentation.
+#
+# Note that this feature is still experimental and incomplete at the moment.
+# The default value is: NO.
+
+GENERATE_PERLMOD       = NO
+
+# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
+# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
+# output from the Perl module output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_LATEX          = NO
+
+# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
+# formatted so it can be parsed by a human reader. This is useful if you want to
+# understand what is going on. On the other hand, if this tag is set to NO, the
+# size of the Perl module output will be much smaller and Perl will parse it
+# just the same.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_PRETTY         = YES
+
+# The names of the make variables in the generated doxyrules.make file are
+# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
+# so different doxyrules.make files included by the same Makefile don't
+# overwrite each other's variables.
+# This tag requires that the tag GENERATE_PERLMOD is set to YES.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
+# C-preprocessor directives found in the sources and include files.
+# The default value is: YES.
+
+ENABLE_PREPROCESSING   = YES
+
+# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
+# in the source code. If set to NO, only conditional compilation will be
+# performed. Macro expansion can be done in a controlled way by setting
+# EXPAND_ONLY_PREDEF to YES.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+MACRO_EXPANSION        = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
+# the macro expansion is limited to the macros specified with the PREDEFINED and
+# EXPAND_AS_DEFINED tags.
+# The default value is: NO.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_ONLY_PREDEF     = NO
+
+# If the SEARCH_INCLUDES tag is set to YES, the include files in the
+# INCLUDE_PATH will be searched if a #include is found.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SEARCH_INCLUDES        = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by the
+# preprocessor.
+# This tag requires that the tag SEARCH_INCLUDES is set to YES.
+
+INCLUDE_PATH           =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will be
+# used.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+INCLUDE_FILE_PATTERNS  =
+
+# The PREDEFINED tag can be used to specify one or more macro names that are
+# defined before the preprocessor is started (similar to the -D option of e.g.
+# gcc). The argument of the tag is a list of macros of the form: name or
+# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
+# is assumed. To prevent a macro definition from being undefined via #undef or
+# recursively expanded use the := operator instead of the = operator.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+PREDEFINED             =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
+# tag can be used to specify a list of macro names that should be expanded. The
+# macro definition that is found in the sources will be used. Use the PREDEFINED
+# tag if you want to use a different macro definition that overrules the
+# definition found in the source code.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+EXPAND_AS_DEFINED      =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
+# removed.
+# The default value is: YES.
+# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
+
+SKIP_FUNCTION_MACROS   = YES
+
+#---------------------------------------------------------------------------
+# Configuration options related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES tag can be used to specify one or more tag files. For each tag
+# file the location of the external documentation should be added. The format of
+# a tag file without this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where loc1 and loc2 can be relative or absolute paths or URLs. See the
+# section "Linking to external documentation" for more information about the use
+# of tag files.
+# Note: Each tag file must have a unique name (where the name does NOT include
+# the path). If a tag file is not located in the directory in which doxygen is
+# run, you must also specify the path to the tagfile here.
+
+TAGFILES               =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
+# tag file that is based on the input files it reads. See section "Linking to
+# external documentation" for more information about the usage of tag files.
+
+GENERATE_TAGFILE       =
+
+# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
+# the class index. If set to NO, only the inherited external classes will be
+# listed.
+# The default value is: NO.
+
+ALLEXTERNALS           = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will be
+# listed.
+# The default value is: YES.
+
+EXTERNAL_GROUPS        = YES
+
+# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
+# the related pages index. If set to NO, only the current project's pages will
+# be listed.
+# The default value is: YES.
+
+EXTERNAL_PAGES         = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of 'which perl').
+# The default file (with absolute path) is: /usr/bin/perl.
+
+PERL_PATH              = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
+# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
+# NO turns the diagrams off. Note that this option also works with HAVE_DOT
+# disabled, but it is recommended to install and use dot, since it yields more
+# powerful graphs.
+# The default value is: YES.
+
+CLASS_DIAGRAMS         = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see:
+# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH            =
+
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
+
+DIA_PATH               =
+
+# If set to YES the inheritance and collaboration graphs will hide inheritance
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=== added directory 'Docs/developer/ford-media'
=== added file 'Docs/developer/ford-media/Interactions.png'
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=== added file 'Docs/developer/ford-media/RectangularMatrix.png'
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=== added directory 'Docs/developer/ford-pages'
=== added directory 'Docs/developer/ford-pages/datastructures'
=== added file 'Docs/developer/ford-pages/datastructures/1-buds.md'
--- Docs/developer/ford-pages/datastructures/1-buds.md	1970-01-01 00:00:00 +0000
+++ Docs/developer/ford-pages/datastructures/1-buds.md	2018-09-12 13:10:27 +0000
@@ -0,0 +1,59 @@
+title: Reference-counted derived types
+
+(Work in progress)
+
+Derived types are a very useful addition to a programming
+language. They allow to keep together in the same place a number or
+related variables.
+
+Sometimes, the same basic data in a derived-type variable needs to be
+associated to larger data structures. The sparsity pattern of SIESTA
+matrices is an example: every matrix in the program (for a given
+geometry) uses the same sparse indexing arrays. Traditionally, there
+was a set of global arrays (numh, listh, etc) that would take care of
+the indexing throughout. With derived types, those arrays could be put in
+a "sparsity_info" variable for easier handling.
+
+Now consider what would happen if one wants to implement an
+extrapolation scheme for density matrices in molecular-dynamics
+runs. We must keep some past history of "geometry/density matrix"
+pairs. Since different geometries need potentially different indexing
+arrays, the old "array set" scheme would break down very soon (a
+primitive extrapolation was implemented at some point, with only one
+previous geometry: it used numh_old, listh_old, etc arrays...), and
+the bookeeping was already a nightmare.
+
+With the derived-type approach, one could keep an array of
+sparsity_info elements, and associate them somehow to the relevant
+density-matrix and geometry history (maybe implemented also as
+arrays). This is do-able but also complicated.
+
+Now imagine that the density matrix "object" contains within itself a
+pointer to the relevant "sparsity_info" object, and that a
+finite-stack of geometry/density-matrix objects is implemented. The
+extrapolation algorithm can transparently use the stack metaphor
+(which is the appropriate one for a finite-length re-cyclable
+history), and forget about the array bookeeping. When the information
+for a geometry step is no longer needed, the objects can be destroyed,
+taking care that no other object in the program is using references to
+the internal data. This can be easily achieved by implementing
+[reference counting](https://en.wikipedia.org/wiki/Reference_counting).
+
+In SIESTA, reference-counted derived types (and containers) are
+implemented in modules whose name begins with `class` (this is an
+unfortunate, probably temporary, choice), and use
+[templates](https://en.wikipedia.org/wiki/Template_metaprogramming) to
+support containers of various types.
+
+For example, the sparsity pattern "bud" is defined in [[class_sparsity]], and
+the containers involved in density-matrix extrapolation are
+
+* A "sparse-2D matrix" bud, defined in 
+* A pair container, defined in "class_Pair..."
+* A finite-stack container, defined in " ...."
+
+Template files have `.T90` extensions.
+
+The basic implementation of reference counting and the associated
+functionality is in the [[basic_type.inc]] file.
+

=== added file 'Docs/developer/ford-pages/datastructures/2-sparse.md'
--- Docs/developer/ford-pages/datastructures/2-sparse.md	1970-01-01 00:00:00 +0000
+++ Docs/developer/ford-pages/datastructures/2-sparse.md	2018-09-12 13:10:27 +0000
@@ -0,0 +1,74 @@
+title: Sparse Matrices in SIESTA
+
+Sparse matrices are widespread in Siesta due to the use of a basis set
+of finite-range atomic orbitals. Matrix elements between orbitals
+which are "too far" from each other are zero, leading to sparse
+matrices for all but the smallest systems.
+
+The following discussion is focused on the global data found in [[sparse_matrices]].
+
+Take the Hamiltonian. If `no_u` is the number of orbitals, its matrix
+elements \(H_{\mu\nu}\) can be simply arranged in a square matrix with
+`no_u` rows and columns.
+
+In the presence of a sizable number of zeros, it pays to represent
+this matrix in a more compact form.
+
+The sparse matrix is in CSR/CSC matrix format with some slight
+differences from the elsewhere found CSR format. Because Siesta
+(primarily) deals with Hermitian matrices, CSR and CSC are equivalent.
+In Siesta the CSR format is composed of the following (integer) components.
+
+*  `maxnh`: 
+     number of total non-zero elements (sum of numh array)
+*  `numh(no_u)`:
+    number of non-zero elements each orbital connects too
+    @note
+      This is a specific to Siesta, since many
+      sparse implementations of CSR matrices in Fortran use
+      only the `listhptr` array with one more element.
+     @endnote
+*  `listhptr(no_u)`
+     index pointer to listh such that `listh(listhptr(1) + 1)`
+     is the first non-zero element of orbital 1.
+     `listh(listhptr(io) + 1)` is thus the first non-zero element
+     of orbital 'io' while `listh(listhptr(io) + numh(io))` is the
+     last non-zero element of orbital 'io'.
+     @note
+      `listhptr` is 0-based (`listhptr(1) == 0`, ALWAYS)
+      while many implementations in Fortran would have used listhptr(1) == 1
+      this is not so in Siesta. Secondly, in other typical CSR implementations
+	  this array would be of size `no_u + 1` with `listhptr(no_u+1) == maxnh + 1`.
+     @endnote
+*  `listh(maxnh)`:
+     the column indices for the non-zero elements.
+     `listh(listhptr(io)+1)`
+     would correspond to the element `M(io, listh(listhptr(io)+1))`
+
+Note that these matrices are 1D block cyclic distributed and the
+routines found in [[class_OrbitalDistribution]] or module [[parallelsubs]]
+are required to translate local rows to global rows (columns
+are not distributed).
+
+The discussion above assumes that only a single MPI node is used
+such that `no_l == no_u`, where the former is the number of distributed
+rows on the MPI node.
+
+See the discussion of the [auxiliary supercell](|page|/implementation/1-auxiliary-supercell.html) for the modifications
+introduced by the support for periodic systems with k-point sampling.
+
+The sparse pattern information is handled by the program in two forms:
+
+* Through a set of arrays, as mentioned above.
+* Through a [reference-counted](|page|/datastructures/1-buds.html) derived type [[class_Sparsity:sparsity]] and its instantiation in ([[sparse_matrices:sparse_pattern]]).
+  The old arrays are *actually* pointing to the arrays in the variable `sparse_pattern`.
+
+
+@note
+ The suffix 'h' (`numh`, `maxh`, ...) is a legacy name and should be avoided
+ in subsequent usages (i.e. when new routines are being passed the above arrays
+ or the sparse_pattern.
+ Currently Siesta does not distinguish between H/DM/S/EDM/... sparsity patterns
+ and thus the sparse pattern is not specific to any physical array, it is a global
+ definition of all sparse matrices used in Siesta.
+@endnote

=== added file 'Docs/developer/ford-pages/datastructures/index.md'
--- Docs/developer/ford-pages/datastructures/index.md	1970-01-01 00:00:00 +0000
+++ Docs/developer/ford-pages/datastructures/index.md	2018-09-12 13:10:27 +0000
@@ -0,0 +1,8 @@
+title: Data structures
+
+In this section we describe the data structures used throughout Siesta.
+
+All data-structures are considered generic, in the sense that they may be
+exported to other projects if so desired.
+There will, however, be links to specific files where the datastructures are used.
+

=== added directory 'Docs/developer/ford-pages/implementation'
=== added file 'Docs/developer/ford-pages/implementation/1-auxiliary-supercell.md'
--- Docs/developer/ford-pages/implementation/1-auxiliary-supercell.md	1970-01-01 00:00:00 +0000
+++ Docs/developer/ford-pages/implementation/1-auxiliary-supercell.md	2018-09-12 13:10:27 +0000
@@ -0,0 +1,133 @@
+title: Auxiliary Supercell
+
+For periodic systems SIESTA uses an auxiliary supercell as an indexing
+tool to represent all the orbital interactions present in the
+Hamiltonian (and other matrices). These interactions can extend to
+orbitals beyond the unit cell, so extra bookeeping is needed
+beyond the simple \(H_{\mu\nu}\) notation used previously.
+
+Consider the simplified system depicted in the figure below. The unit
+cell contains two atoms (open and black circles) with a single orbital
+each (orbitals are not marked to avoid clutter). The orbitals of the
+atoms in the unit cell at the center of the figure overlap with those
+of other atoms in the crystal whenever the distance between atoms is
+less than the sum of the orbital ranges. In the figure these
+interactions extend to the first-neighboring cells only. In this
+two-dimensional example, the atoms in the unit cell interact with
+those in nine cells, and this geometrical construct is fit to
+represent the complete set of non-zero Hamiltonian matrix elements
+\(H_{\mu\nu}({\mathbf R}) \), where \(\mu\) and \(\nu\) are orbital
+indexes (ranging over the unit cell only) and \({\mathbf R}\) is a
+relative vector from the unit cell. This vector could just be a cell
+lattice vector, but in practice SIESTA uses the relative vector
+between the atoms involved.
+
+![Orbital Interactions](|media|/Interactions.png "Orbital interactions")
+{: style="text-align: center" ; width="50%" }
+
+There are multiple image interactions for the same pair, each
+associated with a different \({\mathbf R}\).  The set of nine cells is the
+auxiliary supercell. In this case it is a 3x3 repetition of the unit
+cell, and the "3" can be seen as "2x1+1": the central cell plus one
+neighboring cell in either side.  We can also represent the
+interactions with a rectangular matrix:
+
+![RectangularMatrix](|media|/RectangularMatrix.png "Interaction
+Matrix")
+
+
+which has a row for each unit-cell orbital, and as many columns as
+orbitals in the nine cells involved in the interactions. Any matrix
+element $$H_{\mu\nu}({\mathbf R}) = \langle\phi_\mu({\mathbf R=0})|H|\phi_\nu({\mathbf
+R})\rangle$$ can be stored by itself in the appropriate slot.
+
+When it it time to build the Hamiltonian matrix for a given k-point \({\mathbf k}\):
+
+$$ H_{\mu\nu}({\mathbf k}) =
+\sum_{\mathbf R} { H_{\mu\nu}({\mathbf R}) e^{i{\mathbf k}\cdot{\mathbf R}}} $$
+
+every slot's contribution, with the appropriate phase, is folded back
+and reduced into the left-most square matrix, as the arrows in the
+figure indicate.
+
+For periodic systems with large unit cells, k-point sampling is not
+really necessary, and the phases involved are all 1 (formally only the
+\(\Gamma\) point \({\mathbf k=0}\) is used). In this case the auxiliary supercell
+is not strictly necessary: the matrix elements can be reduced on the
+fly to the unit-cell square interaction matrix, and other operations
+can be similarly folded automatically throughout. It is possible,
+however, to request that an auxiliary supercell be used, since the
+extra level of bookeeping can be useful for other purposes (e.g. for
+COHP analysis of the orbital-pairs contributions to the energy).
+
+In the program, the auxiliary supercell is handled in several key routines:
+
+* The need for a supercell is assessed in [[siesta_init]], by checking whether k-points are
+  going to be used anywhere in the program.
+* The size of the supercell needed is stored in the [[siesta_geom:nsc(variable)]] array
+* The supercell offsets for each supercell index are stored in the [[siesta_geom:isc_off(variable)]]
+  array.
+* Indexing arrays live in [[sparse_matrices]] and are initialized in [[state_init]]
+
+When an auxiliary supercell is used, the "column" stored in the
+`listh` array defined in the [sparsity](|page|/datastructures/2-sparse.html) page ranges
+over the long dimension of the rectangular interaction matrix. The
+"unit-cell" column to which the folding is done is recorded in the
+array `indxuo`. Its contents, however, can be really computed on the
+fly, since the column indexes in the rectangular matrix are just
+juxtapositions of blocks of size `no_u`.
+
+The following idiom can be used to go through the arrays:
+```fortran
+do io = 1, no_u
+  do ind = listhptr(io) + 1, lishptr(io) + numh(io)
+    is = (listh(ind) - 1) / no_u + 1
+    col = mod(listh(ind) - 1, no_u) + 1
+	! or equivalently (found in some parts of the code):
+    !   col = indxuo(listh(ind))
+    H(io, col) = H(io, col) + H_sparse(ind) * exp(-1j * sum(xijo(:, ind) * k(:)))
+  end do
+end do
+```
+
+## MD or geometry optimizations
+
+The auxiliary supercell is a fixed size for any given atomic configuration due to the
+constant distances between atoms and neighbouring cell atoms.
+In MD or geometry optimization simulations where atoms are being displaced the auxiliary cell
+may change. In the following MD refers to _any_ kind of geometry movement, be it actual MD or
+geometry relaxations.
+
+<!---
+Consider two atoms currently at a distance \(R>R_\mathrm{max}\)
+with \(R_\mathrm{max}\) being the sum of orbital range belonging to the atoms. In a following geometry
+iteration the atoms are brought closer to each other such that \(R<R_\mathrm{max}\). This will lead
+to an increase in the number of non-zero elements in the sparse matrix.
+Concintly for the reverse action where the atoms are moved farther apart one finds a reduction in the
+number of non-zero elements.
+ --->
+
+In the following we will use `nsc` to refer to the variable [[siesta_geom:nsc(variable)]].
+
+Generically one may find that the following list of actions are carried out:
+
+1. [[siesta_init]]: figure out initial number of supercells and call [[atomlist:superc]]
+2. Begin MD iterations
+
+	1. [[state_init]]: figure out number of supercells for this geometry configuration
+	2. If any of the supercells has changed we need to copy the old information to the
+       new supercell information
+	3. Perform SCF, move atoms and go to 2.1.
+  
+3. End Siesta and analyse
+
+The step 2.1 and 2.2 requries some further explanation. Siesta keeps a history of SCF converged
+density matrices from previous MD steps. When 2.1 is initiated the new initial density matrix is
+an extrapolation of these previous density matrices. Since all density matrices are stored using
+the [sparsity matrix](|page|/datastructures/2-sparse.html) definitions we need to make a conversion
+between different auxiliary supercells. The conversion (in-place) between two different auxiliary
+supercells may be found in [[m_handle_sparse:correct_supercell_SpD]].
+Additionally, since the number of non-zero elements may also change during the MD cycle one also
+needs to remove/add new non-zero elements in the sparse matrix. This is done
+in [[m_restruct_SpData2D:restruct_dSpData2D]].
+

=== added file 'Docs/developer/ford-pages/implementation/index.md'
--- Docs/developer/ford-pages/implementation/index.md	1970-01-01 00:00:00 +0000
+++ Docs/developer/ford-pages/implementation/index.md	2018-09-12 13:10:27 +0000
@@ -0,0 +1,6 @@
+title: Specific implementation details
+
+The details of the implementation that are specific to Siesta may be found here.
+
+Contrary to the [data structures](|page|/datastructures/index.html), the documentation found
+here is not easily transferable to other codes.

=== added file 'Docs/developer/ford-pages/index.md'
--- Docs/developer/ford-pages/index.md	1970-01-01 00:00:00 +0000
+++ Docs/developer/ford-pages/index.md	2018-09-12 13:10:27 +0000
@@ -0,0 +1,11 @@
+title: Program Overview
+
+These pages provide some documentation on the internals of the SIESTA program. At present just a few
+pages are present, and their integration with the in-code documentation is not yet very complete.
+
+You can get more information from:
+
+* [Project webpage](http://www.icmab.es/siesta)
+* [Development platform](http://launchpad.net/siesta)
+
+

=== added file 'Docs/developer/ford-siesta.md'
--- Docs/developer/ford-siesta.md	1970-01-01 00:00:00 +0000
+++ Docs/developer/ford-siesta.md	2018-09-12 13:10:27 +0000
@@ -0,0 +1,66 @@
+project: SIESTA
+version: {!../../version.info!} 
+author: SIESTA Group
+src_dir: ../../Src
+output_dir: ./doc-ford-build
+page_dir: ./ford-pages
+media_dir: ./ford-media
+display: public
+         private
+source: true
+search: false
+graph: false
+exclude_dir: ../../Src/MPI
+             ../../Src/fdf
+             ../../Src/fdict
+             ../../Src/ncdf
+             ../../Src/Libs
+             ../../Src/Orphans
+             ../../Src/SiestaXC
+             ../../Src/wxml
+             ../../Src/xmlparser
+exclude:   m_gauss_fermi_17.f90
+		   m_gauss_fermi_18.f90
+		   m_gauss_fermi_19.f90
+		   m_gauss_fermi_20.f90
+		   m_gauss_fermi_22.f90
+		   m_gauss_fermi_24.f90
+		   m_gauss_fermi_26.f90
+		   m_gauss_fermi_28.f90
+		   m_gauss_fermi_30.f90
+		   m_gauss_fermi_inf.f90
+		   spinorbit.f
+project_website: https://www.icmab.es/siesta
+summary: ![SIESTA](logo) <br/>
+         A first-principles materials simulation code 
+         using Density Functional Theory.
+         {: style="text-align: center" }
+preprocess: true
+preprocessor: gfortran -E -P
+docmark_alt: *
+predocmark: >
+fpp_extensions: F90
+                F
+license: gfdl
+extra_filetypes: sh #
+                 inc ! 
+md_extensions: markdown.extensions.toc
+
+@note
+This is an early stage work-in-progress build of developers documentation for SIESTA.
+@endnote
+
+## Project Dashboard
+
+@todo
+Add more topics
+@endtodo
+
+
+<!-- useful options -->
+<!-------------------->
+<!-- graph_maxdepth: 100 -->
+<!-- graph_maxnodes: 100 -->
+
+
+<!-- predocmark: >  -->

=== modified file 'Docs/siesta.tex'
--- Docs/siesta.tex	2018-09-04 13:37:24 +0000
+++ Docs/siesta.tex	2018-09-12 13:10:27 +0000
@@ -4984,6 +4984,27 @@
 
 \end{fdflogicalF}
 
+\begin{fdflogicalT}{DM!Init.Unfold}
+  \fdfdepend{DM!UseSaveDM}
+  \index{reading saved data!density matrix}
+
+  When reading the DM from a previous calculation there may be
+  inconsistencies in the auxiliary supercell. E.g. if the previous
+  calculation did not use an auxiliary supercell and the current
+  calculation does (adding $k$-point sampling). \siesta\ will
+  automatically \emph{unfold} the $\Gamma$-only DM to the auxiliary
+  supercell elements (if \fdftrue).
+
+  For \fdffalse\ the DM elements are assumed to originate from an
+  auxiliary supercell calculation and the sparse elements are not
+  unfolded but directly copied.
+
+  \note Generally this shouldn't not be touched, however, if the
+  initial DM is generated using \sisl\cite{sisl} and only on-site DM
+  elements are set, this should be set to \fdffalse.
+
+\end{fdflogicalT}
+
 \begin{fdflogicalF}{DM!FormattedFiles}
   \index{reading saved data!density matrix}
 
@@ -5784,35 +5805,6 @@
 
 \end{fdflogicalF}
 
-\begin{fdfentry}{NaiveAuxiliaryCell}[logical]<\fdfvalue{MD.TypeOfRun}>
-
-  The auxiliary supercell needed can be determined using the atomic positions,
-  the orbital extent and the lattice parameters. For a fixed geometry
-  configuration the tightest auxiliary supercell is uniquely defined. However,
-  when performing MD simulations (or relaxations) the displacement of
-  certain atoms may result in changes to the required auxiliary
-  supercell, thus inhibiting re-use of DM information across geometry steps.
-  When this is option is \fdftrue\ the auxiliary supercell will be computed
-  with a simpler algorithm using only the orbital extent (fixed for \emph{any}
-  calculation) and the lattice vectors. The resulting supercell might
-  be larger than strictly needed, but it will remain mostly constant
-  during the run (even when the \fdf{MD.VariableCell} option is used,
-  if the lattice changes are moderate).
-
-  By default this will be \fdffalse\ when performing single-point calculations
-  (\fdf{MD.TypeOfRun:CG} with \fdf{MD.Steps:1} or below). Otherwise
-  this will default to \fdftrue.
-
-  \note one may try to set this to \fdffalse\ for better performance,
-  at the risk of inhibiting the re-use of DM information.
-
-  \note this option may made obsolete in later versions when a
-  supercell conversion routine is in place.
-
-  \note the name of the option reflects historical usage.
-
-\end{fdfentry}
-
 
 
 \subsection{Calculation of the electronic structure}

=== modified file 'Src/Fstack.T90'
--- Src/Fstack.T90	2018-02-01 11:04:12 +0000
+++ Src/Fstack.T90	2018-09-12 13:10:27 +0000
@@ -22,6 +22,7 @@
     character(len=36)  :: id = "null_id"
     !-------------------------------------
     character(len=256) :: name = "(null Fstack_)"
+    !> See [[_T_(type)]]
     type(_T_), pointer :: val(:) => null()
     integer            :: size = 0
     integer            :: nvals = 0

=== modified file 'Src/Makefile'
--- Src/Makefile	2018-09-04 11:56:15 +0000
+++ Src/Makefile	2018-09-12 13:10:27 +0000
@@ -831,7 +831,7 @@
 m_geom_plane.o: intrinsic_missing.o m_geom_aux.o
 m_geom_square.o: intrinsic_missing.o m_geom_aux.o m_geom_plane.o
 m_getopts.o: f2kcli.o
-m_handle_sparse.o: class_OrbitalDistribution.o class_SpData1D.o
+m_handle_sparse.o: class_Data2D.o class_OrbitalDistribution.o class_SpData1D.o
 m_handle_sparse.o: class_SpData2D.o class_Sparsity.o geom_helper.o m_iodm.o
 m_handle_sparse.o: m_os.o m_region.o m_ts_io.o parallel.o precision.o units.o
 m_hartree_add.o: intrinsic_missing.o m_cite.o m_geom_objects.o m_mesh_node.o
@@ -921,7 +921,7 @@
 m_spin.o: alloc.o parallel.o precision.o sys.o units.o
 m_stress.o: precision.o
 m_supercell.o: atom_graph.o class_OrbitalDistribution.o class_SpData2D.o
-m_supercell.o: intrinsic_missing.o parallel.o parallelsubs.o precision.o
+m_supercell.o: parallel.o parallelsubs.o precision.o
 m_svd.o: precision.o
 m_target_stress.o: parallel.o precision.o sys.o units.o
 m_test_io.o: class_SpData2D.o class_Sparsity.o m_iodm.o m_matio.o parallel.o
@@ -1091,7 +1091,6 @@
 madelung.o: parallel.o precision.o sys.o
 matel_registry.o: m_trialorbitalclass.o precision.o radial.o spher_harm.o sys.o
 md_out.o: files.o m_energies.o precision.o sys.o units.o
-md_utils.o: precision.o
 memory.o: alloc.o memoryinfo.o parallel.o precision.o
 memory_all.o: rusage.o
 memory_snapshot.o: rusage.o
@@ -1201,7 +1200,8 @@
 save_density_matrix.o: atomlist.o files.o iodm_netcdf.o m_energies.o m_iodm.o
 save_density_matrix.o: m_matio.o m_ncdf_siesta.o m_spin.o m_steps.o
 save_density_matrix.o: m_ts_global_vars.o m_ts_iodm.o m_ts_options.o
-save_density_matrix.o: precision.o siesta_options.o sparse_matrices.o
+save_density_matrix.o: precision.o siesta_geom.o siesta_options.o
+save_density_matrix.o: sparse_matrices.o
 savepsi.o: alloc.o parallel.o parallelsubs.o precision.o
 scfconvergence_test.o: atomlist.o ldau.o ldau_specs.o m_convergence.o
 scfconvergence_test.o: m_energies.o m_spin.o m_wallclock.o parallel.o
@@ -1292,18 +1292,20 @@
 state_analysis.o: m_wallclock.o parallel.o remove_intramol_pressure.o
 state_analysis.o: siesta_cml.o siesta_geom.o siesta_options.o sparse_matrices.o
 state_analysis.o: units.o write_subs.o zmatrix.o
-state_init.o: alloc.o atomlist.o class_Data2D.o class_SpData1D.o
-state_init.o: class_SpData2D.o class_Sparsity.o create_Sparsity_SC.o
-state_init.o: domain_decom.o files.o hsparse.o iodm_netcdf.o iodmhs_netcdf.o
-state_init.o: ioxv.o kpoint_grid.o ldau_specs.o m_energies.o m_eo.o m_mixing.o
+state_init.o: alloc.o atomlist.o class_Data2D.o
+state_init.o: class_Fstack_Pair_Geometry_SpData2D.o
+state_init.o: class_Pair_Geometry_SpData2D.o class_SpData1D.o class_SpData2D.o
+state_init.o: class_Sparsity.o create_Sparsity_SC.o domain_decom.o files.o
+state_init.o: hsparse.o iodm_netcdf.o iodmhs_netcdf.o ioxv.o kpoint_grid.o
+state_init.o: ldau_specs.o m_energies.o m_eo.o m_handle_sparse.o m_mixing.o
 state_init.o: m_mixing_scf.o m_mpi_utils.o m_ncdf_siesta.o m_new_dm.o m_os.o
 state_init.o: m_pivot_methods.o m_rmaxh.o m_sparse.o m_sparsity_handling.o
 state_init.o: m_spin.o m_steps.o m_supercell.o m_test_io.o m_ts_charge.o
 state_init.o: m_ts_electype.o m_ts_global_vars.o m_ts_io.o m_ts_kpoints.o
 state_init.o: m_ts_options.o m_ts_sparse.o m_ts_tri_init.o normalize_dm.o
-state_init.o: overlap.o parallel.o proximity_check.o siesta_cml.o
-state_init.o: siesta_dicts.o siesta_geom.o siesta_options.o sparse_matrices.o
-state_init.o: sys.o units.o write_subs.o zmatrix.o
+state_init.o: overlap.o parallel.o proximity_check.o restructSpData2D.o
+state_init.o: siesta_cml.o siesta_dicts.o siesta_geom.o siesta_options.o
+state_init.o: sparse_matrices.o sys.o units.o write_subs.o zmatrix.o
 struct_init.o: alloc.o atmfuncs.o atomlist.o files.o ioxv.o m_exp_coord.o
 struct_init.o: m_iostruct.o m_mpi_utils.o m_steps.o parallel.o periodic_table.o
 struct_init.o: siesta_cml.o siesta_geom.o siesta_master.o siesta_options.o

=== modified file 'Src/Pair.T90'
--- Src/Pair.T90	2016-03-01 14:55:57 +0000
+++ Src/Pair.T90	2018-09-12 13:10:27 +0000
@@ -22,7 +22,9 @@
     character(len=36)  :: id = "null_id"
     !-------------------------------------
     character(len=256) :: name = "(null Pair_)"
+    !> First component: [[_T1_(type)]]
     type(_T1_)         :: first
+    !> Second component: [[_T2_(type)]]
     type(_T2_)         :: second
 end type Pair_
 

=== modified file 'Src/basic_type.inc'
--- Src/basic_type.inc	2015-01-27 14:25:15 +0000
+++ Src/basic_type.inc	2018-09-12 13:10:27 +0000
@@ -1,6 +1,7 @@
 !--------------------------------------------------------------
 !
-! Basic functionality for reference-counted data structures
+!! Basic functionality for reference-counted data structures
+!! For some background, see [here](|url|/page/buds.html)
 !
 !   This file has to be included after the global declarations
 !   for extra functionality, just where a "contains" statement

=== modified file 'Src/class_SpData1D.T90'
--- Src/class_SpData1D.T90	2016-03-01 14:24:48 +0000
+++ Src/class_SpData1D.T90	2018-09-12 13:10:27 +0000
@@ -26,8 +26,11 @@
     character(len=36)  :: id = "null_id"
     !----------------------
     character(len=256)   :: name = "null "//STR_TYPE_NAME
+    !> See [[Sparsity(type)]]
     type(Sparsity)            :: sp
+    !> See [[VAR_TYPE(type)]]
     type(VAR_TYPE)            :: a
+    !> See [[OrbitalDistribution(type)]]
     type(OrbitalDistribution) :: dist
   end type TYPE_NAME_
 

=== modified file 'Src/class_SpData2D.T90'
--- Src/class_SpData2D.T90	2017-01-24 18:43:31 +0000
+++ Src/class_SpData2D.T90	2018-09-12 13:10:27 +0000
@@ -26,8 +26,11 @@
     character(len=36)  :: id = "null_id"
     !----------------------
     character(len=256)   :: name = "null "//STR_TYPE_NAME
+    !> See [[Sparsity(type)]]
     type(Sparsity)            :: sp
+    !> See [[VAR_TYPE(type)]]
     type(VAR_TYPE)            :: a
+    !> See [[OrbitalDistribution(type)]]
     type(OrbitalDistribution) :: dist
   end type TYPE_NAME_
 

=== modified file 'Src/class_Sparsity.F90'
--- Src/class_Sparsity.F90	2016-03-01 14:24:48 +0000
+++ Src/class_Sparsity.F90	2018-09-12 13:10:27 +0000
@@ -7,7 +7,12 @@
 ! ---
 
 module class_Sparsity
-  
+  !! Implements a reference-counted derived type ([bud](|url|/page/buds.html))
+  !! to hold the [sparsity pattern](|url|/page/sparse.html)  of the program's matrices
+  !! Objects of this type (notably [[sparse_matrices:sparse_pattern]] can be passed around
+  !! and put in container types.
+  !! The legacy indexing arrays can be linked to this bud's data [[class_Sparsity:attach]]
+  !! when necessary.
   use alloc, only: re_alloc, de_alloc
   
   implicit none

=== modified file 'Src/extrae_eventllist.F90'
--- Src/extrae_eventllist.F90	2014-02-06 12:14:44 +0000
+++ Src/extrae_eventllist.F90	2018-09-12 13:10:27 +0000
@@ -124,4 +124,4 @@
   end subroutine deleteList
 
 end module extrae_eventllist
-#endif TRACING
+#endif /* TRACING */

=== modified file 'Src/extrapolateSpData2D.F90'
--- Src/extrapolateSpData2D.F90	2016-12-27 11:08:17 +0000
+++ Src/extrapolateSpData2D.F90	2018-09-12 13:10:27 +0000
@@ -5,7 +5,7 @@
    use class_Sparsity
    use class_OrbitalDistribution
 
-   use m_restruct_SpData2D, only: restructdSpData2D
+   use m_restruct_SpData2D, only: restruct_dSpData2D
 
    type(dSpData2D), intent(in)    :: SpM1, SpM2
    type(Sparsity), intent(in)    :: sp_out
@@ -20,8 +20,8 @@
    integer                              :: dim2
    real(dp), dimension(:,:), pointer    :: a_1, a_2, a_out
 
-   call restructdSpData2D(SpM1,sp_out,SpM1_out)
-   call restructdSpData2D(SpM2,sp_out,SpM2_out)
+   call restruct_dSpData2D(SpM1,sp_out,SpM1_out)
+   call restruct_dSpData2D(SpM2,sp_out,SpM2_out)
 
    a_1  => val(SpM1_out)
    a_2  => val(SpM2_out)

=== modified file 'Src/m_handle_sparse.F90'
--- Src/m_handle_sparse.F90	2018-07-09 18:29:17 +0000
+++ Src/m_handle_sparse.F90	2018-09-12 13:10:27 +0000
@@ -7,11 +7,7 @@
 
   use precision, only : dp
   use parallel, only : Node, Nodes
-
   use geom_helper, only : ucorb, iaorb
-  use class_OrbitalDistribution
-  use class_Sparsity
-  use class_dSpData2D
 
   implicit none
 
@@ -19,13 +15,32 @@
 
   public :: bulk_expand
   public :: expand_spd2spd_2D
+  public :: fold_auxiliary_supercell_SpD
+  public :: unfold_noauxiliary_supercell_SpD
+  public :: correct_supercell_SpD
   public :: reduce_spin_size
 
+  interface fold_auxiliary_supercell_SpD
+    module procedure fold_auxiliary_supercell_Sp2D
+  end interface fold_auxiliary_supercell_SpD
+
+  interface unfold_noauxiliary_supercell_SpD
+    module procedure unfold_noauxiliary_supercell_Sp2D
+  end interface unfold_noauxiliary_supercell_SpD
+
+  interface correct_supercell_SpD
+    module procedure correct_supercell_Sp1D
+    module procedure correct_supercell_Sp2D
+  end interface correct_supercell_SpD
+
 contains
 
   subroutine bulk_expand(na_u,xa,lasto,cell,nsc,isc_off,DM_2D)
 
     use fdf
+    use class_OrbitalDistribution
+    use class_Sparsity
+    use class_dSpData2D
     use class_dSpData1D
     use m_os, only: file_exist
     use units, only: Ang
@@ -47,14 +62,14 @@
     type(dSpData2D) :: fDM_2D
     real(dp) :: fcell(3,3), fkdispl(3), fEf, fQtot, fTemp
     real(dp), pointer :: fxa(:,:) => null()
-    integer :: fnsc(3), fna_u, fno_u, fnspin, fkscell(3,3), at, fn_s
-    integer :: Tile(3), Reps(3)
+    integer :: fnsc(3), fna_u, fno_u, fnspin, fkcell(3,3), at, fn_s
+    integer :: Tile(3), Reps(3), fnsc_DM(3)
     real(dp) :: def_xa_EPS, xa_EPS
 
     integer, pointer :: flasto(:) => null(), fisc_off(:,:) => null()
 
     integer :: allowed(na_u), itmp, s_na, c_na
-    character(len=400) :: HSfile, DMfile, ln
+    character(len=256) :: HSfile, DMfile, ln
     logical :: d_log1, d_log2, d_log3
     type(block_fdf) :: bfdf
     type(parsed_line), pointer :: pline => null()
@@ -146,7 +161,7 @@
       call ts_read_TSHS(HSfile, &
           d_log1, d_log2, d_log3, &
           fcell, fnsc, fna_u, fno_u, fnspin,  &
-          fkscell, fkdispl, &
+          fkcell, fkdispl, &
           fxa, flasto, &
           fsp, fDM_2D, tmp_1D, fisc_off, &
           fEf, fQtot, fTemp, &
@@ -174,7 +189,8 @@
       ! exactly the same, except that TSDE has an extra EDM and Ef
       ! at the end, we do not care about that! :)
       ! read in DM file
-      call read_DM( DMfile, fake_dit, fDM_2D, d_log1, Bcast=.true.)
+      call read_DM( DMfile, fake_dit, fnsc_DM, fDM_2D, d_log1, Bcast=.true.)
+      if ( fnsc_DM(1) == 0 ) fnsc_DM = fnsc
       if ( size(fDM_2D, 2) /= fnspin ) then
         call die('bulk_expand: DM and TSHS does not have the same spin')
       end if
@@ -221,6 +237,9 @@
       print, allowed_a)
 
     use units, only: Ang
+    use class_OrbitalDistribution
+    use class_Sparsity
+    use class_dSpData2D
 #ifdef MPI
     use mpi_siesta
 #endif
@@ -466,8 +485,795 @@
 
   end subroutine expand_spd2spd_2D
 
+#ifdef SIESTA__NOT_USED
+  
+  ! Copy one super-cell sparse pattern to another super-cell sparse
+  ! pattern. This will copy [in] to [out].
+  ! The data D2_in contains one sparsity pattern with nsc_in supercells.
+  ! See sparse_matrices.F90 for details regarding the sparsity pattern layout.
+  ! The data D2_out contains the "new" sparsity pattern we want to retain.
+  ! I.e. if the number of supercells change, we only retain the equivalent supercell
+  ! elements. And if the number of non-zero elements change we retain only the
+  ! new ones (discarding the older ones).
+  subroutine copy_supercell_Sp2D(d2_out, nsc_out, d2_in, nsc_in)
+    
+    use class_Sparsity
+    use class_dSpData2D
+#ifdef MPI
+    use mpi_siesta
+#endif
+
+    ! output D2 sparse pattern
+    type(dSpData2D), intent(inout) :: d2_out
+    ! output D2 number of supercells
+    integer, intent(in) :: nsc_out(3)
+    ! input D2 sparse pattern
+    type(dSpData2D), intent(inout) :: d2_in
+    ! input D2 number of supercells
+    integer, intent(in) :: nsc_in(3)
+
+    ! We are ready to check and copy the sparsity pattern...
+    type(Sparsity), pointer :: sp_i, sp_o
+
+    ! Local variables
+    integer :: no_u, no_l
+    integer :: io, i, i_ind, o_ind, isc(3)
+    integer :: i_is, o_is, o_hsc(3)
+    integer :: discarded(2), dim_min
+
+    ! arrays for the sparsity patterns
+    integer, pointer :: o_ptr(:), o_ncol(:), o_col(:)
+    integer, pointer :: i_ptr(:), i_ncol(:), i_col(:)
+    real(dp), pointer :: a_o(:,:), a_i(:,:)
+    integer, allocatable :: o_isc(:,:,:), i_isc(:,:)
+    integer, allocatable :: out_index(:)
+
+    if ( all(nsc_out == nsc_in) ) return
+
+    sp_i => spar(d2_in)
+    a_i => val(d2_in)
+    sp_o => spar(d2_out)
+    a_o => val(d2_out)
+
+    call attach(sp_i,n_col=i_ncol, list_ptr=i_ptr, list_col=i_col, &
+        nrows=no_l, nrows_g=no_u)
+    call attach(sp_o,n_col=o_ncol, list_ptr=o_ptr, list_col=o_col, &
+        nrows=io, nrows_g=i)
+
+    dim_min = min(size(a_i,2), size(a_o,2))
+    if ( no_u /= i ) &
+        call die('copy_supercell_sp_d2: error in number of global orbitals.')
+    if ( no_l /= io ) &
+        call die('copy_supercell_sp_d2: error in number of local orbitals.')
+
+    ! Now create the conversion tables
+    call generate_isc(nsc_out, o_isc)
+    call generate_linear_isc(nsc_in, i_isc)
+
+    ! Allocate look-up table
+    allocate(out_index(product(nsc_out)*no_u))
+    ! Set all elements to zero
+    out_index(:) = 0
+
+    ! Count the number of discarded non-zero elements
+    !   (1) is the supercell discarded (for missing supercells)
+    !   (2) is because the orbital interaction does not exist
+    discarded = 0
+
+    ! We need to check whether in-put SC is too large
+    o_hsc = nsc_out / 2
+
+    ! Since we are going to copy, then we have to set it to zero...
+    a_o(:,:) = 0._dp
+
+    do io = 1, no_l
+      
+      ! copy output lookup table to not search every element
+      do i = 1, o_ncol(io)
+        out_index(o_col(o_ptr(io)+i)) = o_ptr(io) + i
+      end do
+
+      ! Now we can do the copy...
+      inner_columns: do i = 1, i_ncol(io)
+        i_ind = i_ptr(io) + i
+        i_is = (i_col(i_ind)-1) / no_u
+
+        ! Get isc
+        isc = i_isc(:, i_is)
+
+        ! Check that the out supercell exists
+        if ( any(abs(isc) > o_hsc) ) then
+          discarded(1) = discarded(1) + 1
+          cycle inner_columns
+        end if
+
+        ! We know the supercell exists, lets see if the orbital connection
+        ! exists.
+        o_is = o_isc(isc(1),isc(2),isc(3))
+
+        ! Transfer the orbital index to the correct supercell
+        o_ind = out_index(o_is * no_u + ucorb(i_col(i_ind), no_u))
+
+        if ( o_ind == 0 ) then
+          ! The orbital interaction does not exist
+          discarded(2) = discarded(2) + 1
+        else
+          a_o(o_ind,1:dim_min) = a_i(i_ind,1:dim_min)
+        end if
+
+      end do inner_columns
+
+      ! restore lookup table
+      do i = 1, o_ncol(io)
+        out_index(o_col(o_ptr(io)+i)) = 0
+      end do
+      
+    end do
+
+    deallocate(o_isc, i_isc, out_index)
+
+  end subroutine copy_supercell_Sp2D
+
+  subroutine copy_supercell_Sp1D(d1_out, nsc_out, d1_in, nsc_in)
+    
+    use class_Sparsity
+    use class_dSpData1D
+#ifdef MPI
+    use mpi_siesta
+#endif
+
+    ! output D1 sparse pattern
+    type(dSpData1D), intent(inout) :: d1_out
+    ! output D1 number of supercells
+    integer, intent(in) :: nsc_out(3)
+    ! input D1 sparse pattern
+    type(dSpData1D), intent(inout) :: d1_in
+    ! input D1 number of supercells
+    integer, intent(in) :: nsc_in(3)
+
+    ! We are ready to check and copy the sparsity pattern...
+    type(Sparsity), pointer :: sp_i, sp_o
+
+    ! Local variables
+    integer :: no_u, no_l
+    integer :: io, i, i_ind, o_ind, isc(3)
+    integer :: i_is, o_is, o_hsc(3)
+    integer :: discarded(2)
+
+    ! arrays for the sparsity patterns
+    integer, pointer :: o_ptr(:), o_ncol(:), o_col(:)
+    integer, pointer :: i_ptr(:), i_ncol(:), i_col(:)
+    real(dp), pointer :: a_o(:), a_i(:)
+    integer, allocatable :: o_isc(:,:,:), i_isc(:,:)
+    integer, allocatable :: out_index(:)
+
+    if ( all(nsc_out == nsc_in) ) return
+
+    sp_i => spar(d1_in)
+    a_i => val(d1_in)
+    sp_o => spar(d1_out)
+    a_o => val(d1_out)
+    
+    call attach(sp_i,n_col=i_ncol, list_ptr=i_ptr, list_col=i_col, &
+        nrows=no_l, nrows_g=no_u)
+    call attach(sp_o,n_col=o_ncol, list_ptr=o_ptr, list_col=o_col, &
+        nrows=io, nrows_g=i)
+
+    if ( no_u /= i ) &
+        call die('copy_supercell_sp_d2: error in number of global orbitals.')
+    if ( no_l /= io ) &
+        call die('copy_supercell_sp_d2: error in number of local orbitals.')
+
+    ! Now create the conversion tables
+    call generate_isc(nsc_out, o_isc)
+    call generate_linear_isc(nsc_in, i_isc)
+
+    ! Allocate look-up table
+    allocate(out_index(product(nsc_out)*no_u))
+    ! Set all elements to zero
+    out_index(:) = 0
+
+    ! Count the number of discarded non-zero elements
+    !   (1) is the supercell discarded (for missing supercells)
+    !   (2) is because the orbital interaction does not exist
+    discarded = 0
+
+    ! We need to check whether in-put SC is too large
+    o_hsc = nsc_out / 2
+
+    ! Since we are going to copy, then we have to set it to zero...
+    a_o(:) = 0._dp
+
+    do io = 1, no_l
+      
+      ! copy output lookup table to not search every element
+      do i = 1, o_ncol(io)
+        out_index(o_col(o_ptr(io)+i)) = o_ptr(io) + i
+      end do
+
+      ! Now we can do the copy...
+      inner_columns: do i = 1, i_ncol(io)
+        i_ind = i_ptr(io) + i
+        i_is = (i_col(i_ind)-1) / no_u
+
+        ! Get isc
+        isc = i_isc(:, i_is)
+
+        ! Check that the out supercell exists
+        if ( any(abs(isc) > o_hsc) ) then
+          discarded(1) = discarded(1) + 1
+          cycle inner_columns
+        end if
+
+        ! We know the supercell exists, lets see if the orbital connection
+        ! exists.
+        o_is = o_isc(isc(1),isc(2),isc(3))
+        
+        ! Transfer the orbital index to the correct supercell
+        o_ind = out_index(o_is * no_u + ucorb(i_col(i_ind), no_u))
+        
+        if ( o_ind == 0 ) then
+          ! The orbital interaction does not exist
+          discarded(2) = discarded(2) + 1
+        else
+          a_o(o_ind) = a_i(i_ind)
+        end if
+        
+      end do inner_columns
+
+      ! restore lookup table
+      do i = 1, o_ncol(io)
+        out_index(o_col(o_ptr(io)+i)) = 0
+      end do
+      
+    end do
+
+    deallocate(o_isc, i_isc, out_index)
+
+  end subroutine copy_supercell_Sp1D
+
+#endif
+  
+  
+  !> Expand an nsc == 1 DM to an nsc_ == * supercell.
+  !>
+  !> In cases where the DM is constructed from all(nsc == 1) we know that
+  !> all elements in the supercell have the same value as in the folded DM.
+  !>
+  !> @note
+  !> This will actually work even in the presence of degenerate folding
+  !> (S(io,io)>1). This can only appear if a
+  !> supercell is not used, so k-points are not used, so no phases are
+  !> needed. The DM elements in the base cell are just the products of
+  !> appropriate wavefunction coefficients, and they can be replicated
+  !> to the rest of the supercell. Note that it is S (or H) that is folded,
+  !> not the DM.
+  !> @endnote
+  !>
+
+  subroutine unfold_noauxiliary_supercell_Sp2D(sp_sc, D2)
+
+    use class_Sparsity
+    use class_OrbitalDistribution
+    use class_dSpData2D
+    use class_dData2D
+#ifdef MPI
+    use mpi_siesta
+#endif
+
+    !> Input supercell sparsity pattern (this will contain periodic connections)
+    type(Sparsity), intent(inout) :: sp_sc
+    !> Input/Output 2D data with associated non-supercell sparse pattern. Upon exit
+    !> this contains as many non-zero elements as in sp_sc with expanded elements.
+    type(dSpData2D), intent(inout) :: D2
+
+    ! Local variables
+    type(OrbitalDistribution) :: dit
+    type(Sparsity), pointer :: sp
+    type(dData2D) :: A2D
+
+    real(dp), pointer :: A2(:,:), A2_sc(:,:)
+    integer :: no_u, no_l
+    integer :: io, jo, ind, scind
+
+    ! arrays for the sparsity patterns
+    integer, pointer :: ptr(:), ncol(:), col(:)
+    integer, pointer :: scptr(:), scncol(:), sccol(:)
+
+    ! This will silently assume same sizes in the sparse patterns
+
+    sp => spar(D2)
+    A2 => val(D2)
+    call attach(sp,n_col=ncol, list_ptr=ptr, list_col=col, &
+        nrows=no_l, nrows_g=no_u)
+
+    ! Supercell sparsity pattern
+    call attach(sp_sc, n_col=scncol, list_ptr=scptr, list_col=sccol, &
+        nnzs=io)
+
+    ! Create array that hosts the new data
+    ind = size(A2, dim=2)
+    call newdData2D(A2D, io, ind,"(unfolded DM vals)")
+    A2_sc => val(A2D)
+    A2_sc(:,:) = 0._dp
+
+    do io = 1, no_l
+
+      ! Loop supercell sparse pattern
+      do scind = scptr(io) + 1, scptr(io) + scncol(io)
+
+        jo = ucorb(sccol(scind), no_u)
+        
+        do ind = ptr(io) + 1, ptr(io) + ncol(io)
+          if ( col(ind) == jo ) then
+            A2_sc(scind, :) = A2(ind, :)
+            exit
+          end if
+        end do
+        
+      end do
+    end do
+
+    dit = dist(D2)
+    call newdSpData2D(sp_sc, A2D, dit, D2, name="Unfolded DM")
+
+    call delete(dit)
+    call delete(A2D)
+
+  end subroutine unfold_noauxiliary_supercell_Sp2D
+
+  !> Fold an nsc > 1 DM to an nsc_ == 1 supercell.
+  !>
+  !> In cases where the DM is constructed from any(nsc > 1), some orbital
+  !> connections are kept in image cells, and not in the unit cell that
+  !> is going to be retained, so we need to copy them. This is a special
+  !> sub-case of the "new supercell is smaller than the old one" case
+  !> treated more coarsely in routine [[correct_supercell_SpD]]
+  !> The name `fold` is not completely appropriate.
+
+  !> In more detail: the elements which in A2 are already in the
+  !> leftmost square of the rectangular interaction matrix should be
+  !> retained, even if for some reason they are not the first in the
+  !> series of elements of A2 with that ucorb jo. 
+
+  !> In the absence of other information, the criterion 'closer is
+  !> more important' is likely the right one, rather than averages or
+  !> tests for size of the DM element. If the old calculation was
+  !> simply a Gamma-point-with-auxcell one, all this is irrelevant, as
+  !> *all* the DM entries in A2 for a given jo are identical, but if
+  !> it came from a real k-point calculation, phases might be at work
+  !> and we do not know how. So the copying code below gives preference to
+  !> col(ind) == jo elements, and, if not present, to other images.
+  
+  subroutine fold_auxiliary_supercell_Sp2D(sp_uc, D2)
+
+    use class_Sparsity
+    use class_OrbitalDistribution
+    use class_dSpData2D
+    use class_dData2D
+#ifdef MPI
+    use mpi_siesta
+#endif
+
+    !> Input sparsity pattern (no auxiliary supercell)
+    type(Sparsity), intent(inout) :: sp_uc
+    !> Input/Output 2D data with associated supercell sparse pattern, upon exit
+    !> this contains as many non-zero elements as in sp_uc with expanded elements.
+    type(dSpData2D), intent(inout) :: D2
+
+    ! Local variables
+    type(OrbitalDistribution) :: dit
+    type(Sparsity), pointer :: sp
+    type(dData2D) :: A2D
+
+    real(dp), pointer :: A2(:,:), A2_uc(:,:)
+    integer :: no_u, no_l
+    integer :: io, jo, ind, ucind
+
+    ! arrays for the sparsity patterns
+    integer, pointer :: ptr(:), ncol(:), col(:)
+    integer, pointer :: ucptr(:), ucncol(:), uccol(:)
+
+    ! This will silently assume same sizes in the sparse patterns
+
+    sp => spar(D2)
+    A2 => val(D2)
+    call attach(sp,n_col=ncol, list_ptr=ptr, list_col=col, &
+        nrows=no_l, nrows_g=no_u)
+
+    ! Primary unit-cell sparsity pattern
+    call attach(sp_uc, n_col=ucncol, list_ptr=ucptr, list_col=uccol, &
+        nnzs=io)
+
+    ! Create array that hosts the new data
+    ind = size(A2, dim=2)
+    call newdData2D(A2D, io, ind,"(fold 2D)")
+    A2_uc => val(A2D)
+    A2_uc(:,:) = 0._dp
+
+    ! Copy relevant elements. Do not add. Remember that the DM
+    ! is not folded, only H and S are.
+
+    do io = 1, no_l
+
+      ! Loop unitcell sparse pattern
+      do ucind = ucptr(io) + 1, ucptr(io) + ucncol(io)
+
+        ! Strictly not needed, but retained for consistency!
+        jo = ucorb(uccol(ucind), no_u)
+        
+        do ind = ptr(io) + 1, ptr(io) + ncol(io)
+          
+          ! We look for A2 elements with ucorb(col) == jo, giving
+          ! preference to those coming from 000 interactions
+          
+          if ( col(ind) == jo ) then
+
+            A2_uc(ucind, :) = A2(ind, :)
+            ! and we are done for this io,jo combination,
+            ! as this 000 element has preference
+            exit
+
+          else if ( ucorb(col(ind), no_u) == jo ) then
+
+            ! tentatively copy
+            A2_uc(ucind, :) = A2(ind, :)
+            ! but we keep looking for more elements for this io,jo combination, in
+            ! case one satisfying the first test appears.
+
+            cycle
+
+            ! Other possibilities such as storing averages of all
+            ! elements with the same ucorb jo, or the element with
+            ! maximum magnitude, are probably not worth it, lacking
+            ! more information. Perhaps some statistical analysis
+            ! might help, but it would be overkill.
+
+          end if
+        end do
+        
+      end do
+    end do
+
+    dit = dist(D2)
+    call newdSpData2D(sp_uc, A2D, dit, D2, name="Folded Sp2D")
+
+    call delete(dit)
+    call delete(A2D)
+
+  end subroutine fold_auxiliary_supercell_Sp2D
+
+  !> Correct a sparse pattern (in-place) from an old NSC to a new NSC.
+  !>
+  !> Here we take a sparse data pattern and change all column indices
+  !> so that they are appropriate for the new supercell.  
+  !> The supercell sparse matrix layout is described in sparse_matrices.F90
+  !> Recall that each column value also holds implicitly the image cell index,
+  !> using an offset `image_index*no_u`.
+  !>  
+  !> If the original supercell is larger than the new one, the elements
+  !> associated to image cells that no longer exist will be set to zero,
+  !> and their column indexes set to something beyond the acceptable values.  
+  !> The elements in the retained image cells have their column indexes recomputed,
+  !> as the image cell indexes depend on the size of the supercell.
+  !>
+  !> If nsc_old == nsc_new, nothing is done.
+  !>
+  !> @note
+  !> The sparse pattern and the nsc multipliers live independently. This could
+  !> lead to errors. A possible improvement is to have nsc as part of the sparse-pattern
+  !> information.
+  !> @endnote
+  !>
+  !> @note
+  !> After a call to this routine, we still need to purge from the sparse index arrays
+  !> those elements of D2 which are no longer needed.
+  !> @endnote
+  subroutine correct_supercell_Sp2D(nsc_old, D2, nsc_new)
+
+    use class_Sparsity
+    use class_dSpData2D
+#ifdef MPI
+    use mpi_siesta
+#endif
+
+    !> A sparse-matrix object, containing a sparse pattern
+    type(dSpData2D), intent(inout) :: D2
+    !> Auxiliary supercell multipliers for D2, typically read
+    !> from file at the same time as other D2 information
+    !> (see, for example, the new DM file format)
+    integer, intent(in) :: nsc_old(3)
+    !> New auxiliary supercell multipliers for D2
+    integer, intent(in) :: nsc_new(3)
+
+    ! Local variables
+    type(Sparsity), pointer :: sp
+    integer :: no_u, no_l
+    integer :: io, ind, isc(3)
+    integer :: old_n_s, new_outside
+    integer :: old_is, new_is, new_hsc(3)
+
+    ! arrays for the sparsity patterns
+    integer, pointer :: ptr(:), ncol(:), col(:)
+    integer, allocatable :: old_isc(:,:), new_isc(:,:,:)
+    real(dp), pointer :: a2(:,:)
+
+    if ( all(nsc_old == nsc_new) ) return
+
+    sp => spar(D2)
+    call attach(sp,n_col=ncol, list_ptr=ptr, list_col=col, &
+        nrows=no_l, nrows_g=no_u)
+
+    ! Required to set removed elements to 0
+    A2 => val(D2)
+
+    !> Calls [[generate_linear_isc]] to create a table (naming confusing!).  
+    !> The linear isc is a list of index offsets (equivalent to isc_off)  
+    !> The order of indices may be found in [[atomlist:superx]] (or in the ORB_INDX output file)
+    !>
+    call generate_linear_isc(nsc_old, old_isc)
+    !> Create the isc_off in supercell format such that:
+    !>   new_isc(1, 1, 1) yields the index for the [1, 1, 1] supercell.
+    !>
+    !> Calls [[generate_isc]] to create
+    !> *another* table with the same naming convention  
+    call generate_isc(nsc_new, new_isc)
+
+    ! Calculate total number of image cells in old supercell
+    old_n_s = product(nsc_old)
+    ! Offset to mark un-needed elements
+    new_outside = product(nsc_new) * no_u
+
+    ! Maximum cell image extents on either side. 
+    ! This assumes that nsc(:) are all odd. For example
+    ! (5,3,5) ==> (2,1,2) 
+    new_hsc = nsc_new / 2
+
+    !> Calls [[intrinsic_missing:modp]] (renamed to `ucorb`)
+    !> to map the column index to the unit cell
+    do io = 1, no_l
+
+      inner_columns: do ind = ptr(io) + 1, ptr(io) + ncol(io)
+        ! Calculate the old image cell index
+        old_is = (col(ind)-1) / no_u
+
+        ! This is just sanity checking, in case the column indexes are obviously wrong
+        if ( old_is >= old_n_s ) then ! it should be removed
+
+          ! It is better to stop the program
+          call die("Mismatch in sparsity pattern and nsc values")
+
+          ! Set it to zero
+          A2(ind, :) = 0._dp
+          ! Also set the column index to a position outside the new sparse pattern
+          col(ind) = ucorb(col(ind), no_u) + new_outside
+          cycle inner_columns
+        end if
+
+        ! The image cell coordinates
+        isc(:) = old_isc(:, old_is)
+
+        ! Check that the new supercell has room for this cell image
+        if ( any(abs(isc) > new_hsc) ) then
+          ! Set it to zero
+          A2(ind, :) = 0._dp
+          ! Also set the column index to a position outside the new sparse pattern
+          ! since it isn't defined in the old sparse pattern, it can't be defined in
+          ! the new one.
+          col(ind) = ucorb(col(ind), no_u) + new_outside
+
+       else
+
+          ! We know the image cell exists, so convert the column
+          ! orbital index to the correct image cell using the new offset.
+          new_is = new_isc(isc(1),isc(2),isc(3))
+          col(ind) = ucorb(col(ind), no_u) + new_is * no_u
+       endif
+       
+      end do inner_columns
+      
+    end do
+
+    deallocate(old_isc, new_isc)
+
+  end subroutine correct_supercell_Sp2D
+
+  subroutine correct_supercell_Sp1D(nsc_old, D1, nsc_new)
+
+    use class_Sparsity
+    use class_dSpData1D
+#ifdef MPI
+    use mpi_siesta
+#endif
+
+    type(dSpData1D), intent(inout) :: D1
+    integer, intent(in) :: nsc_old(3)
+    integer, intent(in) :: nsc_new(3)
+
+    ! Local variables
+    type(Sparsity), pointer :: sp
+    integer :: no_u, no_l
+    integer :: io, ind, isc(3)
+    integer :: old_n_s, new_outside
+    integer :: old_is, new_is, new_hsc(3)
+
+    ! arrays for the sparsity patterns
+    integer, pointer :: ptr(:), ncol(:), col(:)
+    integer, allocatable :: old_isc(:,:), new_isc(:,:,:)
+    real(dp), pointer :: A1(:)
+
+    if ( all(nsc_old == nsc_new) ) return
+
+    sp => spar(D1)
+    call attach(sp,n_col=ncol, list_ptr=ptr, list_col=col, &
+        nrows=no_l, nrows_g=no_u)
+
+    ! Required to set removed elements to 0
+    A1 => val(D1)
+
+    ! Now create the conversion tables
+    !> The linear isc is a list of index offsets (equivalent to isc_off)
+    !> The order of indices may be found in [[atomlist:superx]] (or in the ORB_INDX output file)
+    call generate_linear_isc(nsc_old, old_isc)
+    !> Create the isc_off in supercell format such that:
+    !>   new_isc(1, 1, 1) yields the index for the [1, 1, 1] supercell.
+    call generate_isc(nsc_new, new_isc)
+
+    ! Calculate total number of supercells
+    old_n_s = product(nsc_old)
+    new_outside = product(nsc_new) * no_u
+
+    ! We need to check whether in-put SC is too large
+    new_hsc = nsc_new / 2
+    do io = 1, no_l
+
+      ! Now we can do the copy...
+      inner_columns: do ind = ptr(io) + 1, ptr(io) + ncol(io)
+        !> Calculate the old supercell index (supercell offset is old_isc(:, old_is))
+        old_is = (col(ind)-1) / no_u
+        isc = old_isc(:, old_is)
+
+        ! Simple error handling in case a user has supplied a too large column index
+        if ( old_is >= old_n_s ) then ! it should be removed
+          ! Set it to zero
+          A1(ind) = 0._dp
+          ! Also set the column index to a position outside the new sparse pattern
+          ! since it isn't defined in the old sparse pattern, it can't be defined in
+          ! the new one.
+          col(ind) = ucorb(col(ind), no_u) + new_outside
+          cycle inner_columns
+        end if
+
+        ! Check that the out supercell exists
+        if ( any(abs(isc) > new_hsc) ) then
+          ! Set it to zero
+          A1(ind) = 0._dp
+          ! Also set the column index to a position higher
+          col(ind) = ucorb(col(ind), no_u) + new_outside
+          cycle inner_columns
+        end if
+
+        ! We know the supercell exists, so convert column
+        new_is = new_isc(isc(1),isc(2),isc(3))
+        
+        ! Transfer the orbital index to the correct supercell
+        col(ind) = ucorb(col(ind), no_u) + new_is * no_u
+        
+      end do inner_columns
+      
+    end do
+
+    deallocate(old_isc, new_isc)
+    
+  end subroutine correct_supercell_Sp1D
+
+  !> Generate image cell offsets in a supercell
+  !>
+  !> The given supercell offsets for a given supercell is:
+  !>
+  !>```fortran
+  !>   isc(:, is)
+  !>```
+  !>
+  !> where `is` is the supercell index `(list_col(ind) - 1)/no_u`.
+  !> and the first dimension is the cell direction (x,y,z)
+  !> The order is equivalent to those generated in [[atomlist::superx]].
+  !
+  subroutine generate_linear_isc(nsc, isc)
+    integer, intent(in) :: nsc(3)
+    integer, allocatable :: isc(:,:)
+
+    integer :: x, y, z, i
+    integer :: nx, ny, nz
+
+    allocate(isc(3,0:product(nsc)-1))
+
+    !> Calls [[linear2pm]] to set the correct ordering
+    i = 0
+    do z = 0, nsc(3) - 1
+      nz = linear2pm(z, nsc(3))
+      do y = 0, nsc(2) - 1
+        ny = linear2pm(y, nsc(2))
+        do x = 0, nsc(1) - 1
+          nx = linear2pm(x, nsc(1))
+          isc(1,i) = nx
+          isc(2,i) = ny
+          isc(3,i) = nz
+          i = i + 1
+        end do
+      end do
+    end do
+
+  end subroutine generate_linear_isc
+
+  !> Generate a supercell index array comprising of 3 dimensions of size `nx`, `ny` and `nz`
+  !>
+  !> To obtain the index of a given supercell simply do:
+  !>
+  !>```fortran
+  !>   isc(ix, iy, iz)
+  !>```
+  !>
+  !> where `ix`, `iy` and `iz` are the supercells for the individiual
+  !> lattice vector directions. The order of supercells is equivalent to
+  !> those generated in [[atomlist:superx]].
+  !
+  subroutine generate_isc(nsc, isc)
+    integer, intent(in) :: nsc(3)
+    integer, allocatable :: isc(:,:,:)
+
+    integer :: x, y, z, i
+    integer :: nx, ny, nz
+    integer :: hsc(3)
+
+    ! nsc % 2 == 1, nsc / 2 % 2 == 0
+    hsc = nsc / 2
+
+    allocate(isc(-hsc(1):hsc(1),-hsc(2):hsc(2),-hsc(3):hsc(3)))
+
+    !> Calls [[linear2pm]] to get the correct ordering
+    i = 0
+    do z = 0, nsc(3) - 1
+      nz = linear2pm(z, nsc(3))
+      do y = 0, nsc(2) - 1
+        ny = linear2pm(y, nsc(2))
+        do x = 0, nsc(1) - 1
+          nx = linear2pm(x, nsc(1))
+          isc(nx,ny,nz) = i
+          i = i + 1
+        end do
+      end do
+    end do
+
+  end subroutine generate_isc
+
+  !> Routine to reorder the [0,nsc-1] range of cell images
+  !> so that it follows the [[atomlist:superx]] convention  
+  !> Example: nsc=5  (2*4+1)  
+  !> in:   0  1  2  3  4  
+  !> out:  0  1  2 -2 -1  \
+  !> This corresponds to starting at the center cell, going to the right,
+  !> and then moving to the far left and get back towards the center:
+  !>
+  !>        3  4  0  1  2
+  !>
+  pure function linear2pm(i,n) result(j)
+    integer, intent(in) :: i, n
+    integer :: j
+    !> Note that n needs to be odd for left-right symmetry to
+    !> be preserved
+    if ( i > n / 2 ) then
+      j = -n + i
+    else
+      j = i
+    end if
+  end function linear2pm
+
   subroutine reduce_spin_size(ispin,H_2D,S_1D,Ef)
+    use class_OrbitalDistribution
+    use class_Sparsity
     use class_dSpData1D
+    use class_dSpData2D
     integer, intent(in) :: ispin
     type(dSpData2D), intent(inout) :: H_2D
     type(dSpData1D), intent(inout), optional :: S_1D

=== modified file 'Src/m_iodm.F90'
--- Src/m_iodm.F90	2016-12-09 10:26:17 +0000
+++ Src/m_iodm.F90	2018-09-12 13:10:27 +0000
@@ -26,7 +26,7 @@
 
 contains
         
-  subroutine read_dm( file, dit, DM, found, Bcast )
+  subroutine read_dm( file, dit, nsc, DM, found, Bcast )
 
 #ifdef MPI
     use mpi_siesta
@@ -39,6 +39,8 @@
     ! The orbital distribution that should be attached to
     ! DM
     type(OrbitalDistribution), intent(in) :: dit
+    ! The supercell information (if present, otherwise return 0s)
+    integer, intent(inout) :: nsc(3)
     ! The density matrix
     type(dSpData2D), intent(inout) :: DM
     logical, intent(out) :: found
@@ -48,9 +50,9 @@
 ! * LOCAL variables      *
 ! ************************
     type(Sparsity) :: sp
-    character(len=500) :: fn
+    character(len=256) :: fn
     logical :: lBcast
-    integer :: iu, two(2), no_u, nspin
+    integer :: iu, five(5), no_u, nspin, ierr
     integer, allocatable, target :: gncol(:)
 #ifdef MPI
     integer :: MPIerror
@@ -80,15 +82,28 @@
        call io_assign(iu)
        open( iu, file=file, form='unformatted', status='old' )
        rewind(iu)
-       read(iu) two
+       read(iu,iostat=ierr) five
+       if ( ierr /= 0 ) then
+         rewind(iu)
+         read(iu) five(1), five(2)
+         five(3:5) = 0
+       end if
     end if
 
 #ifdef MPI
-    call MPI_Bcast(two,2,MPI_integer,0,MPI_Comm_World,MPIerror)
+    if ( lBcast ) then
+      call MPI_Bcast(five,5,MPI_integer,0,MPI_Comm_World,MPIerror)
+    else
+      ierr = dist_comm(dit)
+      call MPI_Bcast(five,5,MPI_integer,0,ierr,MPIerror)
+    end if
 #endif
 
-    no_u = two(1)
-    nspin = two(2)
+    no_u = five(1)
+    nspin = five(2)
+    nsc(1) = five(3)
+    nsc(2) = five(4)
+    nsc(3) = five(5)
 
     allocate(gncol(no_u))
     gncol(1) = 1
@@ -123,12 +138,13 @@
 
   end subroutine read_dm
   
-  subroutine write_dm( file, DM )
+  subroutine write_dm( file, nsc, DM )
     
 ! **********************
 ! * INPUT variables    *
 ! **********************
     character(len=*), intent(in) :: file
+    integer, intent(in) :: nsc(3)
     type(dSpData2D), intent(inout) :: DM
     
 ! ************************
@@ -153,11 +169,10 @@
 
        ! Open file
        call io_assign( iu )
-       open( iu, file=file, &
-            form='unformatted', status='unknown' )
+       open( iu, file=file, form='unformatted', status='unknown' )
        rewind(iu)
        
-       write(iu) no_u, nspin
+       write(iu) no_u, nspin, nsc
 
     end if
 

=== modified file 'Src/m_new_dm.F90'
--- Src/m_new_dm.F90	2018-06-28 13:53:17 +0000
+++ Src/m_new_dm.F90	2018-09-12 13:10:27 +0000
@@ -60,7 +60,9 @@
   subroutine new_DM(SC_changed, DM_history, DM_2D, EDM_2D)
 
     use siesta_options
-    use siesta_geom,      only: ucell, xa, na_u, isc_off, nsc
+    use siesta_geom,      only: ucell, xa, na_u, isc_off
+    use siesta_geom,      only: nsc, nsc_old
+
     use sparse_matrices,  only: sparse_pattern, block_dist
     use atomlist,         only: Datm, iaorb, lasto, no_u
     use m_steps,          only: istp
@@ -82,7 +84,7 @@
     use m_energies, only: Ef
 
     logical, intent(in) :: SC_changed ! Has auxiliary supercell changed?
-    type(Fstack_Pair_Geometry_dSpData2D), intent(inout)      :: DM_history
+    type(Fstack_Pair_Geometry_dSpData2D), intent(inout) :: DM_history
     type(dSpData2D), intent(inout) :: DM_2D, EDM_2D
 
     ! Local variables
@@ -100,7 +102,7 @@
 
     if ( IONode ) then
        write(*,"(a,i5)") "new_DM -- step: ", istp
-    endif
+    end if
 
     ! In principle we allow the re-use of the DM (i.e, we do not initialize it)
     ! Initialization is either:
@@ -147,8 +149,9 @@
             DM_init = .true.
     end if
 
+#ifdef TO_BE_REMOVED
     ! ... or if the auxiliary cell has changed
-    ! (in this case we have to  avoid reading back saved copy from file)
+    ! (in this case we have to avoid reading back saved copy from file)
     if ( SC_changed ) then
        
        if ( initDMaux ) then
@@ -167,7 +170,8 @@
              write(*,"(a)") "** Warning: since 'ReinitialiseDM' is set to .false."
           end if
        end if
-    end if
+     end if
+#endif
 
     if ( DM_init ) then
        
@@ -175,7 +179,7 @@
           write(*,"(a)") "Initializing Density Matrix..."
        end if
 
-       call init_DM(spin, na_u, no_u, lasto, iaorb, &
+       call init_DM(spin, na_u, no_u, nsc, lasto, iaorb, &
             Datm, &
             block_dist, sparse_pattern, &
             DM_2D, EDM_2D, &
@@ -193,7 +197,7 @@
        if ( IONode ) then
           write(*,'(a,i0)') "Number of DMs in history: ", DM_in_history
        end if
-       call extrapolate_dm_with_coords(DM_history, na_u, xa(:,1:na_u), &
+       call extrapolate_DM_with_coords(DM_history, na_u, xa(:,1:na_u), &
             sparse_pattern, DM_2D)
        if ( IONode ) then
           write(*,'(a)') "New DM after history re-use:"
@@ -356,7 +360,7 @@
   !  1) reading a DM/TSDE(transiesta) file
   !  2) fall-back to atomic initialization using
   !     a possibly user-defined spin-configuration.
-  subroutine init_DM(spin, na_u, no_u, lasto, iaorb, &
+  subroutine init_DM(spin, na_u, no_u, nsc, lasto, iaorb, &
        DM_atom, &
        dit, sp, DM_2D, EDM_2D, &
        read_DM, &
@@ -381,6 +385,7 @@
     ! type(tSpin) spin              : spin configuration for this system
     ! integer na_u                  : number of atoms in unit-cell
     ! integer no_u                  : number of orbitals in unit-cell
+    ! integer nsc(3)                : number of supercells along each direction
     ! integer lasto(0:na_u)         : last orbital of each atom
     ! integer iaorb(no_u)           : the atomic index of the corresponding orbital
     ! real(dp) DM_atom(no_u)        : atomic density based on atomic configuration
@@ -401,6 +406,8 @@
     integer, intent(in) :: na_u
     ! Number of orbitals in the unit-cell
     integer, intent(in) :: no_u
+    ! Number of supercells along each direction
+    integer, intent(in) :: nsc(3)
     ! The last orbital on each atom
     integer, intent(in) :: lasto(0:na_u)
     ! The atom containing orbital "io"
@@ -434,7 +441,7 @@
     if ( read_DM ) then
        
        ! Try and read the DM from the files
-       call init_DM_file(spin, no_u, &
+       call init_DM_file(spin, no_u, nsc, &
             dit, sp, DM_2D, EDM_2D, &
             init_method)
 
@@ -488,15 +495,14 @@
 
   end subroutine init_DM
 
-
-  subroutine init_DM_file(spin, no_u, &
+  !> Routine for reading the DM from a file.  
+  !> This is a simple read-inset routine which reads
+  !> a DM/TSDE file, and inserts the quantities
+  !> into the the resulting DM (and/or EDM).
+  subroutine init_DM_file(spin, no_u, nsc, &
        dit, sp, DM_2D, EDM_2D, &
        init_method)
 
-    ! Routine for reading the DM from a file.
-    ! This is a simple read-inset routine which reads
-    ! a DM/TSDE file, and inserts the quantities
-    ! into the the resulting DM (and/or EDM).
 
     ! If the readed DM file has a different number of spin-components,
     ! this routine will easily extrapolate the quantities:
@@ -549,11 +555,14 @@
     ! stored in the TSDE file.
     use m_ts_global_vars,only: TSmode
 
-    use m_restruct_SpData2D, only: restructdSpData2D
+    use m_handle_sparse, only: correct_supercell_SpD
+    use m_handle_sparse, only: unfold_noauxiliary_supercell_SpD
+    use m_handle_sparse, only: fold_auxiliary_supercell_SpD
     
     ! ********* INPUT ***************************************************
     ! type(tSpin) spin              : spin configuration for this system
     ! integer no_u                  : number of orbitals in unit-cell
+    ! integer nsc(3)                : number of supercells along each direction
     ! type(OrbitalDistribution) dit : the distribution used for the orbitals
     ! type(Sparsity) sp             : sparsity pattern of DM
     ! type(dSpData2D) DM_2D         : the density matrix 
@@ -565,29 +574,33 @@
     !                                   2 == .TSDE read
     ! *******************************************************************
 
-    ! The spin-configuration that is used to determine the spin-order.
+    !> The spin-configuration that is used to determine the spin-order.
     type(tSpin), intent(in) :: spin
-    ! Number of orbitals in the unit-cell
+    !> Number of orbitals in the unit-cell
     integer, intent(in) :: no_u
-    ! Parallel distribution of DM/EDM
+    !> Number of supercells along each direction
+    integer, intent(in) :: nsc(3)
+    !> Parallel distribution of DM/EDM
     type(OrbitalDistribution), intent(in) :: dit
-    ! Sparse pattern for DM/EDM
+    !> Sparse pattern for DM/EDM
     type(Sparsity), intent(inout) :: sp
-    ! The DM and EDM, these will be initialiazed upon return
-    ! if the routine could read the files
+    !> The DM and EDM, these will be initialiazed upon return
+    !> if the routine could read the files
     type(dSpData2D), intent(inout) :: DM_2D, EDM_2D
 
-    ! To signal the method by which we have read DM/EDM
+    !> To signal the method by which we have read DM/EDM
     integer, intent(out) :: init_method
 
     
     ! *** Local variables:
+    logical :: corrected_nsc
     logical :: DM_found
     logical :: TSDE_found
     ! The file we should read
     character(len=256) :: fname
     ! Number of spin-components read from the DM/TSDE file
     integer :: nspin_read
+    integer :: nsc_read(3)
 
     ! The currently read stuff
     type(dSpData2D) :: DM_read
@@ -609,13 +622,14 @@
        fname = fdf_get('File.TSDE.Init',trim(slabel)//'.TSDE')
 
        ! Try and read the file
-       call read_ts_dm(trim(fname), dit, DM_read, EDM_read, Ef, TSDE_found)
+       call read_ts_dm(trim(fname), dit, nsc_read, DM_read, EDM_read, Ef, TSDE_found)
 
        if ( TSDE_found ) then
           ! Signal we have read TSDE
           init_method = 2
 
           DM_found = .true.
+
        else if ( IONode ) then
           write(*,'(a)') 'Failed...'
        end if
@@ -629,11 +643,12 @@
        ! Retrieve the name of the initialization file.
        fname = fdf_get('File.DM.Init',trim(slabel)//'.DM')
 
-       call read_DM(trim(fname), dit, DM_read, DM_found)
+       call read_DM(trim(fname), dit, nsc_read, DM_read, DM_found)
 
        if ( DM_found ) then
-          ! Signal that the DM file has been found
-          init_method = 1
+         ! Signal that the DM file has been found
+         init_method = 1
+         
        end if
        
     end if
@@ -652,6 +667,7 @@
           end if
           
           DM_found = .false.
+          TSDE_found = .false.
           
        end if
 
@@ -662,35 +678,81 @@
        
     end if
 
-    ! In case the sparsity pattern does not conform we update 
-    ! the TSDE_found, note that DM_found is a logic containing
-    ! information regarding the sparsity pattern
-    if ( TSDE_found ) TSDE_found = DM_found
 
     ! Density matrix size checks
     if ( DM_found ) then
 
-       nspin_read = size(DM_read, 2)
-
-       if ( spin%DM == nspin_read .and. IONode ) then
+      corrected_nsc = .false.
+      if ( nsc_read(1) /= 0 .and. any(nsc /= nsc_read) ) then
+
+        ! There are three cases:
+        if ( all(nsc_read == 1) .and. fdf_get('DM.Init.Unfold', .true.) ) then
+
+          ! 1. The read DM was created from a Gamma-only calculation and thus nsc == 1, always.
+          !    In this case we know that the DM elements in the Gamma calculation (io,jo)
+          !    are replicated in all image cells (io, jo + i_s * no_u) where i_s is the image cell
+          !    offfset, since there are no k-points and thus no phases to worry about.
+          !
+          !    In very special circumstances the user may avoid this behavior by
+          !    by setting 'DM.Init.Unfold false' 
+          
+          call unfold_noauxiliary_supercell_SpD(sp, DM_read)
+          if ( TSDE_found ) then
+            call unfold_noauxiliary_supercell_SpD(sp, EDM_read)
+          end if
+
+        else if ( all(nsc == 1) ) then
+
+          ! 2. The read DM was created from a calculation with a non-trivial auxiliary cell, 
+          !    and the current calculation is Gamma-only. In this case it is necessary to fold back
+          !    all supercell DM entries.
+
+          call fold_auxiliary_supercell_SpD(sp, DM_read)
+          if ( TSDE_found ) then
+            call fold_auxiliary_supercell_SpD(sp, EDM_read)
+          end if
+            
+        else
+
+          ! 3. The read DM has a different supercell size. In this case we only copy those
+          !    elements that we know exists in the call below.
+         
+          ! Correct the supercell information
+          ! Even for EDM this will work because correct_supercell_SpD
+          ! changes the sparse pattern in-place and EDM and DM have
+          ! a shared sp
+          call correct_supercell_SpD(nsc_read, DM_read, nsc)
+          corrected_nsc = .true.
+          
+        end if
+
+      end if
+
+      nspin_read = size(DM_read, 2)
+
+      if ( IONode ) then
+        if ( spin%DM == nspin_read ) then
           write(*,'(a)') 'Succeeded...'
-       else if ( spin%DM /= nspin_read .and. IONode ) then
-          if ( spin%DM < nspin_read ) then
-             write(*,'(a)') 'Succeeded by reducing spin-components...'
-          else
-             write(*,'(a)') 'Succeeded by increasing spin-components...'
-          end if
-       end if
-
-       if ( IONode ) then
-          write(*,'(a)') "DM from file:"
-          call print_type(DM_read)
-       end if
-
-       call restruct_Data(spin%DM, DM_read, DM_2D)
-       if ( TSDE_found ) then
-          call restruct_Data(spin%EDM, EDM_read, EDM_2D)
-       end if
+        else if ( spin%DM < nspin_read ) then
+          write(*,'(a)') 'Succeeded by reducing the number of spin-components...'
+        else
+          write(*,'(a)') 'Succeeded by increasing the number of spin-components...'
+        end if
+      end if
+      
+      if ( IONode ) then
+        write(*,'(a)') "DM from file:"
+        call print_type(DM_read)
+      end if
+
+      call restruct_Data(spin%DM, DM_read, DM_2D, .not. corrected_nsc)
+      if ( IONode ) then
+        write(*,'(a)') "DM to be used:"
+        call print_type(DM_2D)
+      end if
+      if ( TSDE_found ) then
+        call restruct_Data(spin%EDM, EDM_read, EDM_2D, .false.)
+      end if
 
     end if
 
@@ -702,43 +764,64 @@
 
   contains
 
-    subroutine restruct_Data(nspin, in_2D, out_2D)
+    !> Driver to fix both the spin dimension and the sparsity pattern
+    !> of a DM object, which typically has been read from file.
+    !>
+    !> Note that only the cases in which one of the spin dimensions is 1
+    !> are treated.
+    
+    subroutine restruct_Data(nspin, in_2D, out_2D, show_warning)
+      
+      use m_restruct_SpData2D, only: restruct_dSpData2D
+      
+      !> Current spin dimension in the program
       integer, intent(in) :: nspin
-      type(dSpData2D), intent(inout) :: in_2D, out_2D
+      !> Input (DM) bud, to be mined for info
+      type(dSpData2D), intent(inout) :: in_2D
+      !> Output (DM) bud, created
+      type(dSpData2D), intent(inout) :: out_2D
+      !> Whether to show sanity-check warnings 
+      logical, intent(in) :: show_warning
       
       integer :: nspin_read, i
-      real(dp), pointer :: ar2(:,:)
+      real(dp), pointer :: A2(:,:)
 
       nspin_read = size(in_2D, 2)
       
       if ( nspin == 1 .and. nspin /= nspin_read ) then
          ! This SCF has 1 spin-component.
          
-         ! The readed DM has, at least 2!
-         ! Thus we sum the spinors to form the non-polarized
-         ar2 => val(in_2D)
+         ! The read DM has at least 2!
+         ! Thus we sum the spinors to form the non-polarized version
+         A2 => val(in_2D)
 !$OMP parallel do default(shared), private(i)
-         do i = 1 , size(ar2, 1)
-            ar2(i,1) = ar2(i,1) + ar2(i,2)
+         do i = 1 , size(A2, 1)
+            A2(i,1) = A2(i,1) + A2(i,2)
          end do
 !$OMP end parallel do
 
       end if
 
-      ! Restructure the sparsity data to the output DM
-      ! with maximum spin%DM number of spin-components
-      call restructdSpData2D(in_2D, sp, out_2D, nspin)
+      !> Calls [[restruct_dSpData2D]] to re-structure the sparsity
+      !> data to match the output DM, with maximum spin%DM number of
+      !> spin-components. It returns a new out_2D bud.
+      !> @note
+      !> The current sparsity pattern `sp` is known here by host association from
+      !> the parent routine, which is a bit confusing. 
+      !> `out_2D` in the called routine. Here it is the `out` sparsity, corresponding
+      !> to the current target sparsity in the program.
+      !> @endnote
+      call restruct_dSpData2D(in_2D, sp, out_2D, nspin, show_warning=show_warning)
 
       if ( nspin_read == 1 .and. nspin /= nspin_read ) then
          ! This SCF has more than 2 spin-components.
-         ! The readed DM has 1.
-         ! Thus we divide the spinors to form the polarized
-         ! case.
-         ar2 => val(out_2D)
+         ! The read DM has 1.
+         ! Thus we divide the spinors to form the polarized case.
+         A2 => val(out_2D)
 !$OMP parallel do default(shared), private(i)
-         do i = 1 , size(ar2, 1)
-            ar2(i,1) = ar2(i,1) * 0.5_dp
-            ar2(i,2) = ar2(i,1)
+         do i = 1 , size(A2, 1)
+            A2(i,1) = A2(i,1) * 0.5_dp
+            A2(i,2) = A2(i,1)
          end do
 !$OMP end parallel do
          
@@ -1244,7 +1327,7 @@
     use class_Pair_Geometry_dSpData2D
     use class_Fstack_Pair_Geometry_dSpData2D
 
-    use m_restruct_SpData2D, only: restructdSpData2D
+    use m_restruct_SpData2D, only: restruct_dSpData2D
     use fdf, only: fdf_get
 
     type(Fstack_Pair_Geometry_dSpData2D), intent(in) :: DM_history
@@ -1327,7 +1410,7 @@
        !           if (.not. associated(orb_dist,dist(dm))) then
        !              call die("Different orbital distributions in DM history stack")
        !           endif
-       call restructdSpData2D(dm,sparse_pattern,DMtmp)
+       call restruct_dSpData2D(dm,sparse_pattern,DMtmp)
        ai => val(DMtmp)
 !$OMP parallel workshare default(shared)
        a = a + c(i) * ai

=== modified file 'Src/m_sparse.F90'
--- Src/m_sparse.F90	2016-03-01 14:24:48 +0000
+++ Src/m_sparse.F90	2018-09-12 13:10:27 +0000
@@ -294,6 +294,17 @@
 
   end subroutine list_col_correct_sp
 
+  ! Routine used for calculation the supercell offsets using
+  ! the xij_2D array.
+  ! Basically this routine runs through all xijo elements
+  ! and calculates the cell distance:
+  !    R(col(ind) % no_u) = xij(ind) - (xa(j) - xa(i))
+  ! This should result in vectors R(...) which are integer
+  ! multiples of the lattice vectors:
+  !   cell X = R
+  ! returns X as integers.
+  ! This routine will quit/exit if two supercell indices
+  !   col(ind) % no_u does not yield the same R vector.
   subroutine xij_offset_sp(cell,nsc,na_u,xa,lasto, &
        xij_2D,isc_off,Bcast)
     

=== modified file 'Src/m_supercell.F90'
--- Src/m_supercell.F90	2018-05-15 09:48:18 +0000
+++ Src/m_supercell.F90	2018-09-12 13:10:27 +0000
@@ -1,182 +1,16 @@
 module m_supercell
 
 ! Calculates the supercell factors by examining all atoms.
-! 1. We find the smallest vector that connects any atom ia1 to
-!    the neighbouring cell atom ia2 [in direction xyz]
-! 2. Loop on supercell factors until it is not overlapping
-! 3. Save supercell factor
-
-! This will correctly capture no supercell factors in
-! slaps with only UC connections. This supercell size will typically
-! be one less than the usual 1+2*ceiling(rmaxh/vnorm(ucell(:,xyz)))
-
-  ! TODO : create a fully parallel version (each node can take na_u/Nodes
-  ! atoms)
   
   use precision, only : dp
   
   implicit none
   
-  !! public :: exact_sc_size   ! not used anymore
   public :: exact_sc_ag
   private
   
 contains
 
-  subroutine exact_sc_size(rmaxh,ucell,na_u,xa,nsc)
-    use intrinsic_missing, only : VNORM
-    ! Calculates the exact size required to encompass all super-cells
-    ! This is a brute force calculation which is over the top, yet
-    ! it is effictive in reducing the super-cell to the minimum basis
-    real(dp), intent(in) :: rmaxh
-    real(dp), intent(in) :: ucell(3,3)
-    integer,  intent(in) :: na_u
-    real(dp), intent(in) :: xa(3,na_u)
-    integer,  intent(inout) :: nsc(3)
-
-    ! Local variables
-    integer :: xyz, ia, ja, tnsc(3), idiag
-    real(dp) :: recell(3,3), v1(3), v2(3), ucdiag(3)
-    logical :: on_boundary
-
-    call reclat(ucell,recell,0) ! do not add 2 Pi
-
-    ! Initialize new nsc 
-    tnsc(:) = 1
-
-    ! We loop over all atoms and find the two atoms
-    ! that will be connected by the least 
-    ! length across the first cell boundary
-    do ia = 1 , na_u
-       do ja = ia , na_u
-          on_boundary = (ia == ja)
-
-          ! Vector between atoms
-          v1(:) = xa(:,ja) - xa(:,ia)
-
-          do xyz = 1 , 3
-
-             ! from i -> J
-             v2(:) = v1(:) + ucell(:,xyz)
-             ! update the nsc quantity based on this vector
-             call update_nsc(rmaxh,ucell(:,xyz),v2,on_boundary,tnsc(xyz))
-
-             ! from j -> I
-             v2(:) = -v1(:) + ucell(:,xyz)
-             ! update the nsc quantity based on this vector
-             call update_nsc(rmaxh,ucell(:,xyz),v2,on_boundary,tnsc(xyz))
-
-             ! Possibly track the diagonal path when
-             ! having skewed unit-cells. Specifically if 
-             ! |ucell(:,1)|,|ucell(:,2)| > |ucell(:,1) + ucell(:,2)|
-             ! Thus we should track the diagonal of each direction
-
-             if ( xyz == 3 ) cycle
-             do idiag = xyz + 1 , 3
-                
-                ! get the diagonal unit-cell direction
-                ucdiag(:) = ucell(:,xyz) + ucell(:,idiag)
-
-                ! from i -> J
-                v2(:) = v1(:) + ucdiag(:)
-                ! update the nsc quantity based on this vector (note that
-                ! the diagonal now takes two into account
-                call update_nsc(rmaxh,ucdiag,v2,on_boundary,tnsc(xyz))
-                call update_nsc(rmaxh,ucdiag,v2,on_boundary,tnsc(idiag))
-
-                ! from j -> I
-                v2(:) = -v1(:) + ucdiag(:)
-                ! update the nsc quantity based on this vector (note that
-                ! the diagonal now takes two into account
-                call update_nsc(rmaxh,ucdiag,v2,on_boundary,tnsc(xyz))
-                call update_nsc(rmaxh,ucdiag,v2,on_boundary,tnsc(idiag))
-
-             end do
-                
-          end do
-
-          ! Do the last diagonal unit-cell direction (a+b+c)
-          ucdiag(:) = ucell(:,1) + ucell(:,2) + ucell(:,3)
-          
-          ! from i -> J
-          v2(:) = v1(:) + ucdiag(:)
-          ! update the nsc quantity based on this vector (note that
-          ! the diagonal now takes two into account
-          call update_nsc(rmaxh,ucdiag,v2,on_boundary,tnsc(1))
-          call update_nsc(rmaxh,ucdiag,v2,on_boundary,tnsc(2))
-          call update_nsc(rmaxh,ucdiag,v2,on_boundary,tnsc(3))
-
-          ! from j -> I
-          v2(:) = -v1(:) + ucdiag(:)
-          ! update the nsc quantity based on this vector (note that
-          ! the diagonal now takes two into account
-          call update_nsc(rmaxh,ucdiag,v2,on_boundary,tnsc(1))
-          call update_nsc(rmaxh,ucdiag,v2,on_boundary,tnsc(2))
-          call update_nsc(rmaxh,ucdiag,v2,on_boundary,tnsc(3))
-
-       end do
-    end do
-
-    ! Copy over calculated super-cell factors
-    nsc(:) = tnsc(:)
-
-  contains
-
-    subroutine update_nsc(rmaxh,vcell,v,on_boundary,nsc)
-      real(dp), intent(in) :: rmaxh
-      real(dp), intent(in) :: vcell(3)
-      real(dp), intent(inout) :: v(3)
-      logical, intent(in) :: on_boundary
-      integer, intent(inout) :: nsc
-      real(dp), parameter :: EPS = 1.e-8_dp
-      real(dp) :: vl
-      integer :: n
-
-      vl = VNORM(v)
-
-      ! we do not have any connections in the xyz direction
-      ! Hence we can entirely skip that direction
-      ! This will be the case for slap calculations
-      if ( vl > rmaxh + EPS ) return
-
-      n = 1
-      ! Loop and find the minimum supercell factor
-      do while ( vl <= rmaxh + EPS )
-         ! increment supercell atom
-         n = n + 1
-         v(:) = v(:) + vcell(:)
-         vl = vnorm(v)
-      end do
-
-      ! As vl now is larger than rmaxh we can subtract
-      ! one from the number of supercells, truncate
-      ! at 1 as we do have connects across the unit-cell
-      ! This will typically reduce nsc by one from the
-      ! naive auxillary cell as the naive calculation
-      ! must take into account the two atoms lying on the
-      ! boundary. But this is direct interaction! :)
-      if ( .not. on_boundary ) then
-         ! TODO, I think this should ALWAYS be n-1
-         ! Yet a case example of unit cell:
-         ! Unit cell vectors (Ang):
-         !        1.414210   -2.449490    0.000000
-         !        1.414210    2.449490    0.000000
-         !        0.000000    0.000000    6.928200
-         ! yields the wrong supercell indices if using n-1
-         ! I think maybe the hsparse takes too many non-zero elements?
-         ! Or are there some additional corrections for the
-         ! orbital range I do not know of?
-         n = max(1,n - 1)
-      end if
-
-      ! UC + n cells on both sides
-      n = 1 + 2 * n
-      if ( n > nsc ) nsc = n
-
-    end subroutine update_nsc
-    
-  end subroutine exact_sc_size
-
   ! Calculate the exact super-cell size based on the
   ! atomic connection graph.
   ! This routine calculates the exact overlap of the atoms,

=== modified file 'Src/m_test_io.F90'
--- Src/m_test_io.F90	2016-12-08 11:45:49 +0000
+++ Src/m_test_io.F90	2018-09-12 13:10:27 +0000
@@ -6,7 +6,7 @@
 
   ! Module to test various IO-routines
 
-  subroutine time_io(nspin,D_2D)
+  subroutine time_io(nspin,nsc,D_2D)
 
     use precision, only : dp
     use parallel, only : Node
@@ -16,6 +16,7 @@
     use m_iodm
 
     integer, intent(in) :: nspin
+    integer, intent(in) :: nsc(3)
     type(dSpData2D), intent(inout) :: D_2D
 
     type(Sparsity), pointer :: sp
@@ -58,7 +59,7 @@
 
     call timer('NICK-io',1)
     do i = 1 , N_WRITES
-       call write_dm('TESTIO.DM',D_2D)
+       call write_dm('TESTIO.DM',nsc,D_2D)
     end do
     call timer('NICK-io',2)
 

=== modified file 'Src/m_ts_electype.F90'
--- Src/m_ts_electype.F90	2018-08-31 08:16:05 +0000
+++ Src/m_ts_electype.F90	2018-09-12 13:10:27 +0000
@@ -1944,7 +1944,7 @@
     type(dSpData2D) :: f_DM_2D, f_EDM_2D
     real(dp), pointer :: DM(:,:), EDM(:,:)
     real(dp) :: tmp, Ef
-    integer :: Tile(3), Reps(3)
+    integer :: Tile(3), Reps(3), fnsc(3)
     integer :: i
     logical :: found, alloc(3), is_TSDE
 
@@ -1960,10 +1960,10 @@
     is_TSDE = ( this%DEfile(i-3:i) == 'TSDE' )
     if ( is_TSDE ) then
        call read_ts_dm( this%DEfile, fake_dit, &
-            f_DM_2D, f_EDM_2D, Ef, found, &
+            fnsc, f_DM_2D, f_EDM_2D, Ef, found, &
             Bcast = .true. )
     else
-       call read_dm( this%DEfile, fake_dit, f_DM_2D, found, &
+       call read_dm( this%DEfile, fake_dit, fnsc, f_DM_2D, found, &
             Bcast = .true. )
     end if
     if ( .not. found ) call die('Could not read file: '//trim(this%DEfile))
@@ -1972,6 +1972,8 @@
        call die('Bulk electrode expansion, read in sparsity pattern, &
             &does not match the TSHS sparsity pattern.')
     end if
+    ! Correct the number of supercells (currently not used)
+    if ( fnsc(1) == 0 ) fnsc = this%nsc
 
     ! We must delete the additional arrays read in
     call delete(this%H)

=== modified file 'Src/m_ts_iodm.F90'
--- Src/m_ts_iodm.F90	2016-12-09 10:26:17 +0000
+++ Src/m_ts_iodm.F90	2018-09-12 13:10:27 +0000
@@ -27,7 +27,7 @@
 
 contains
   
-  subroutine read_ts_dm( file, dit, DM, EDM, Ef, found, Bcast)
+  subroutine read_ts_dm( file, dit, nsc, DM, EDM, Ef, found, Bcast)
 
 #ifdef MPI
   use mpi_siesta
@@ -38,6 +38,7 @@
 ! **********************
     character(len=*), intent(in) :: file
     type(OrbitalDistribution), intent(in) :: dit
+    integer, intent(inout) :: nsc(3)
     type(dSpData2D), intent(inout) :: DM, EDM
     real(dp), intent(inout) :: Ef
     logical, intent(out) :: found
@@ -47,9 +48,9 @@
 ! * LOCAL variables      *
 ! ************************
     type(Sparsity) :: sp
-    character(len=500) :: fn
+    character(len=256) :: fn
     logical :: lBcast
-    integer :: iu, two(2), no_u, nspin
+    integer :: iu, five(5), no_u, nspin, ierr
     integer, allocatable, target :: gncol(:)
 #ifdef MPI
     integer :: MPIerror
@@ -79,15 +80,28 @@
        call io_assign(iu)
        open( iu, file=file, form='unformatted', status='old' )
        rewind(iu)
-       read(iu) two
+       read(iu,iostat=ierr) five
+       if ( ierr /= 0 ) then
+         rewind(iu)
+         read(iu) five(1), five(2)
+         five(3:5) = 0
+       end if
     end if
     
 #ifdef MPI
-    call MPI_Bcast(two,2,MPI_integer,0,MPI_Comm_World,MPIerror)
+    if ( lBcast ) then
+      call MPI_Bcast(five,5,MPI_integer,0,MPI_Comm_World,MPIerror)
+    else
+      ierr = dist_comm(dit)
+      call MPI_Bcast(five,5,MPI_integer,0,ierr,MPIerror)
+    end if
 #endif
 
-    no_u = two(1)
-    nspin = two(2)
+    no_u = five(1)
+    nspin = five(2)
+    nsc(1) = five(3)
+    nsc(2) = five(4)
+    nsc(3) = five(5)
 
     allocate(gncol(no_u))
     gncol(1) = 1
@@ -128,18 +142,25 @@
     end if
 
 #ifdef MPI
-    call MPI_BCast(Ef,1,MPI_Double_Precision, &
-         0,MPI_Comm_World, MPIerror)
+    if ( lBcast ) then
+      call MPI_BCast(Ef,1,MPI_Double_Precision, &
+          0,MPI_Comm_World, MPIerror)
+    else
+      ierr = dist_comm(dit)
+      call MPI_Bcast(Ef,1,MPI_Double_Precision, &
+          0,ierr,MPIerror)
+    end if
 #endif
 
   end subroutine read_ts_dm
 
-  subroutine write_ts_dm(file, DM, EDM, Ef )
+  subroutine write_ts_dm(file, nsc, DM, EDM, Ef )
     
 ! **********************
 ! * INPUT variables    *
 ! **********************
     character(len=*), intent(in) :: file
+    integer, intent(in) :: nsc(3)
     type(dSpData2D), intent(inout) :: DM, EDM
     real(dp), intent(in) :: Ef
     
@@ -168,7 +189,7 @@
        open( iu, file=file, form='unformatted', status='unknown' )
        rewind(iu)
        
-       write(iu) no_u, nspin
+       write(iu) no_u, nspin, nsc
 
     end if
 

=== removed file 'Src/md_utils.f90'
--- Src/md_utils.f90	2016-01-25 16:00:16 +0000
+++ Src/md_utils.f90	1970-01-01 00:00:00 +0000
@@ -1,40 +0,0 @@
-! 
-! Copyright (C) 1996-2016	The SIESTA group
-!  This file is distributed under the terms of the
-!  GNU General Public License: see COPYING in the top directory
-!  or http://www.gnu.org/copyleft/gpl.txt.
-! See Docs/Contributors.txt for a list of contributors.
-!
-module md_utils
-
-  use precision, only:  dp
-
-  integer, save, public  :: md_io_unit = 99
-  logical, save, public  :: restart_with_mdinfo  = .false.
-  logical, save,  :: file_opened  = .false.
-
-  CONTAINS
-
-    subroutine add_to_md_file(natoms,xa,va,cell,vcell,nose,nosedot)
-
-      integer, intent(in)                                  :: natoms
-      real(dp), dimension(3,natoms), intent(in)            :: xa, va
-      real(dp), dimension(3,3), intent(in), optional       :: cell, vcell
-      real(dp), intent(in), optional                       :: nose, nosedot
-
-!     Here we can save x, xa, va for MD  (experimental)
-!
-        write(99,*) natoms
-        do ia = 1,natoms
-          write(99,'(i4,3f14.8,3x,3f14.8)')
-     .      iza(ia),(xa(i,ia),i=1,3),(va(i,ia),i=1,3)
-        enddo
-
-        have_nose = present(nose)
-        have_nosedot = present(nosedot)
-
-        if (have_nose) then
-           write(99,*) nose
-        endif
-
-        end subroutine add_to_md_file

=== modified file 'Src/post_scf_work.F'
--- Src/post_scf_work.F	2018-06-26 07:41:31 +0000
+++ Src/post_scf_work.F	2018-09-12 13:10:27 +0000
@@ -161,8 +161,8 @@
          ! Save (geom,DM) pair to history stack
          write(msg,"(a,i0)") "step: ",istep
          call newGeometry(geom,na_u,ucell,xa,isa,
-     $                    name="Geometry for " // msg)