Commit 66a3de1f authored by Nick R. Papior's avatar Nick R. Papior
Browse files

Updated documentation for change of list in fdf

Added documentation of PEXSI

Added documentation of Accuracy control and principal
cell connections.
parent 1d355450
......@@ -553,6 +553,7 @@ libraries and how each of them may be added to the compilation step
where \shell{<>} refers to the MPI version used, (\shell{intelmpi},
\shell{openmpi}, \shell{sgimpt}).
\end{description}
Additionally \siesta\ may be compiled with support for several other
......@@ -657,7 +658,45 @@ libraries
\index{compile!pre-processor!-DSIESTA\_\_MUMPS}
where \shell{<>} are any libraries that MUMPS depend on.
\item[PEXSI]%
\index{PEXSI}%
\index{External library!PEXSI}%
The PEXSI library may be used with \siesta\ for exa-scale
calculations. Currently the interface is implemented (tested) as in
PEXSI version 0.8.0, 0.9.0 and 0.9.2. If newer versions retain the same
interface they may also be used.
To successfully compile \siesta\ with PEXSI support one requires the
PEXSI fortran interface. When installing PEXSI copy the
\shell{f\_interface.f90} file to the include directory of
PEXSI such that the module may be found\footnote{Optionally the file
may be copied to the \shell{Obj} directory where the compilation
takes place.} when compiling \siesta.
Add these flags to your \file{arch.make} file to enable PEXSI
\begin{shellexample}
LIBS += -L/opt/pexsi/0.9.2/lib -lpexsi_linux <>
FPPFLAGS += -DSIESTA__PEXSI
\end{shellexample}
\index{compile!pre-processor!-DSIESTA\_\_PEXSI}
where \shell{<>} are any libraries that PEXSI depend on.
%
If one experiences linker failures, one possible solution may help
is
\begin{shellexample}
LIBS += -lmpi_cxx -lstdc++
\end{shellexample}
which is due to PEXSI being a C++ library, and the Fortran compiler
is the linker. The exact library name for your MPI vendor may
vary.
Additionally the PEXSI linker step may have duplicate objects which
can be circumvented by prefixing the PEXSI libraries with
\begin{shellexample}
LIBS += -Wl,--allow-multiple-definition -lpexsi_linux <>
\end{shellexample}
\end{description}
......@@ -6297,14 +6336,6 @@ $xy$, $yz$, $z^2$, $xz$, and $x^2-y^2$ for $d$ orbitals.
\textit{Default value:} \texttt{0} (see \textbf{LongOutput})
\item[\textbf{MullikenInSCF}] (\textit{logical}):
\index{MullikenInSCF@\textbf{MullikenInSCF}}
If true, the Mulliken populations will be written for every SCF step
at the level of detail specified in \textbf{WriteMullikenPop}. Useful
when dealing with SCF problems, otherwise too verbose.
\textit{Default value:} \texttt{.false.}
\item[\textbf{MullikenInSCF}] (\textit{logical}):
\index{MullikenInSCF@\textbf{MullikenInSCF}}
If true, the Mulliken populations will be written for every SCF step
......@@ -8537,16 +8568,21 @@ involving molecules.
\emph{s}.
% Generic input (compatible with the <= 4.0)
\option[atom {\{\emph{A}, \emph{B} -\mbox{}- \emph{C} [step \emph{s}], \emph{D}\}}]%
\option[atom {[\emph{A}, \emph{B} -\mbox{}- \emph{C} [step \emph{s}], \emph{D}]}]%
Equivalent to \fdf*{from \dots to} specification, however in a
shorter variant. Note that the list may contain arbitrary number
of ranges and/or individual indices.
\begin{fdfexample}
atom {2, 3 -- 10 step 2, 6}
atom [2, 3 -- 10 step 2, 6]
\end{fdfexample}
will constrain atoms 2, 3, 5, 7, 9 and 6.
\begin{fdfexample}
atom [2, 3 -- 6, 8]
\end{fdfexample}
will constrain atoms 2, 3, 4, 5, 6 and 8.
\option[atom all]%
Constrain all atoms.
......@@ -8686,11 +8722,11 @@ involving molecules.
atom from 1 to 12 step 2
%endblock
%block Geometry.Constraints
atom {1 -- 12 step 2}
atom [1 -- 12 step 2]
%endblock
%block Geometry.Constraints
atom all
clear-prev {2 -- 12 step 2}
clear-prev [2 -- 12 step 2]
%endblock
\end{fdfexample}
where the 3 last blocks all create the same result.
......@@ -9199,6 +9235,10 @@ following will be shown in the output file.
It is imperative that you have a \emph{perfect} electrode as otherwise
nonphysical results will occur.
By default \tsiesta\ will die if there are connections beyond the
principal cell. One may control whether this is allowed or not by
using \fdf{TS.Elecs!Neglect.Principal}.
\subsection{\texorpdfstring{\tsiesta}{TranSIESTA} Options}
The fdf options shown here are only to be used at the input file for
......@@ -9788,6 +9828,16 @@ electrodes in a generic input format.
Control the imaginary part of the surface Green function for this
electrode. See \fdf{TS!Elecs!Eta}.
\option[Accuracy]%
\fdfindex{TS!Elec.<>!Accuracy}%
Control the convergence accuracy required for the self-energy
calculation when using the Lopez-Sanchez, Lopez-Sanchez iterative
scheme.
%
See \fdf{TS.Elecs!Accuracy}.
\note advanced use \emph{only}.
\option[DE]%
\fdfindex{TS!Elec.<>!DE}%
Density and energy density matrix file for the electrode. This may
......@@ -9860,6 +9910,24 @@ for the electrodes (with \fdf{TS!Elec.<>} taking precedence).
\end{fdfentry}
\begin{fdfentry}{TS!Elecs!Accuracy}[energy]<$10^{-13}\,\mathrm{eV}$>
Globally control the accuracy required for convergence of the self-energy.
%
See \fdf{TS!Elec.<>!Accuracy}.
\end{fdfentry}
\begin{fdflogicalF}{TS!Elecs!Neglect.Principal}
If this is \fdffalse\ \tsiesta\ dies if there are connections beyond
the principal cell.
\note set this to \fdftrue\ with care, non-physical results may
arise.
\end{fdflogicalF}
\begin{fdflogicalT}{TS!Elecs!GF.Reuse}
Globally control whether the surface Green function files should
......
......@@ -832,8 +832,8 @@ currents may only be calculated in the selected device region.
%
\begin{fdfexample}
%block TBT.Atoms.Device
atom { 10 -- 20 }
atom { 30 -- 40 }
atom [ 10 -- 20 ]
atom [ 30 -- 40 ]
%endblock
\end{fdfexample}
will limit the device region to atoms [10--20, 30--40].
......@@ -851,7 +851,7 @@ currents may only be calculated in the selected device region.
%
\begin{fdfexample}
%block TBT.Atoms.Buffer
atom { 1 -- 5 }
atom [ 1 -- 5 ]
%endblock
\end{fdfexample}
will remove atoms [1--5] from the calculation.
......@@ -1293,6 +1293,16 @@ work. However, the \fdf*{TBT} has precedence.
Control the imaginary part of the surface Green function for this
electrode. See \fdf{TBT.Elecs!Eta}.
\option[tbt.Accuracy/Accuracy]%
\fdfindex{TBT.Elec.<>!tbt.Accuracy}%
Control the convergence accuracy required for the self-energy
calculation when using the Lopez-Sanchez, Lopez-Sanchez iterative
scheme.
%
See \fdf{TBT.Elecs!Accuracy}.
\note advanced use \emph{only}.
\option[Bloch]%
\fdfindex{TBT.Elec.<>!Bloch}%
$3$ integers are present on this line which each denote the number
......@@ -1358,6 +1368,24 @@ for the electrodes (with \fdf{TBT.Elec.<>} taking precedence).
\end{fdfentry}
\begin{fdfentry}{TBT.Elecs!Accuracy}[energy]<$10^{-13}\,\mathrm{eV}$>
Globally control the accuracy required for convergence of the self-energy.
%
See \fdf{TBT!Elec.<>!tbt.Accuracy}.
\end{fdfentry}
\begin{fdflogicalF}{TBT.Elecs!Neglect.Principal}
If this is \fdffalse\ \tsiesta\ dies if there are connections beyond
the principal cell.
\note set this to \fdftrue\ with care, non-physical results may
arise.
\end{fdflogicalF}
\begin{fdflogicalT}{TBT.Elecs!GF.Reuse}
Globally control whether the surface Green function files should
......@@ -1632,14 +1660,14 @@ region. \tbtrans\ will die if this is not enforced.
\emph{s}.
% Generic input (compatible with the <= 4.0)
\option[atom {\{<A>, \emph{B} -\mbox{}- \emph{C} [step
\emph{s}], \emph{D}\}}]%
\option[atom {[<A>, \emph{B} -\mbox{}- \emph{C} [step
\emph{s}], \emph{D}]}]%
Equivalent to \fdf*{from \dots to} specification, however in a
shorter variant. Note that the list may contain arbitrary number
of ranges and/or individual indices.
\begin{fdfexample}
atom {2, 3 -- 10 step 2, 6}
atom [2, 3 -- 10 step 2, 6]
\end{fdfexample}
will add atoms 2, 3, 5, 7, 9 and 6.
......@@ -1704,7 +1732,7 @@ region. \tbtrans\ will die if this is not enforced.
All eigenstates specified will be part of the molecular orbitals
that constitute this projection
\option[level \{ <list> \}] %
\option[level {[ <list> ]}] %
A comma-separated list specification.
\option[end] %
......
trunk-536-doc-24
trunk-536-doc-25
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