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manual.lyx
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#LyX 1.6.4 created this file. For more info see http://www.lyx.org/
\lyxformat 345
\begin_document
\begin_header
\textclass article
\use_default_options false
\language english
\inputencoding auto
\font_roman default
\font_sans default
\font_typewriter default
\font_default_family default
\font_sc false
\font_osf false
\font_sf_scale 100
\font_tt_scale 100
\graphics default
\paperfontsize default
\use_hyperref false
\papersize default
\use_geometry false
\use_amsmath 1
\use_esint 0
\cite_engine basic
\use_bibtopic false
\paperorientation portrait
\secnumdepth 3
\tocdepth 3
\paragraph_separation indent
\defskip medskip
\quotes_language english
\papercolumns 1
\papersides 1
\paperpagestyle default
\tracking_changes false
\output_changes false
\author ""
\author ""
\end_header
\begin_body
\begin_layout Title
Input Prepartion Guide for the Program ppp.x
\end_layout
\begin_layout Standard
All the input data is written in the free format to minimize errors.
Therefore, before each important input card, there is a compulsory comment
line to make the input self explanatory.
It is irrelevant as to what is written in the comment lines, but, by writing
something meaningful, one can keep the input process transparent.
We do require that all the ASCII input cards (not the ones in the comment
lines) should be in uppercase letters.
To distinguish comment lines from the input, in this guide we precede each
comment line with the character '#', although in actual input files, that
is not necessary to use.
We encourage the user to compare the explanation provided here with the
actual input files available in the 'examples' subdirectory.
Next, we explain the preparation of input files card by card.
\end_layout
\begin_layout Enumerate
The input file starts with a title.
Thus, the first line is for a title of the calculations.
A user can give a relevant title so as to provide an idea about the calculation
or system at the first glance.
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# Title
\end_layout
\begin_layout Enumerate
As the purpose of our code is to perform calculations using various semi-empiric
al model Hamiltonians, the first input card is an ASCII card describing
the model Hamiltonian to be used for the calculations.
Options are: P-P-P, Hubbard, extended Hubbard, and Hückel.
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
(a) For a system using P-P-P model, the input card may read:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# The Hamiltonian to be used
\begin_inset Newline newline
\end_inset
PPP
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
(b) For a system using Hubbard model, the input card may read:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# The Hamiltonian to be used
\begin_inset Newline newline
\end_inset
HUBBARD
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
(c) For a system using extended Hubbard model, the input card may read:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# The Hamiltonian to be used
\begin_inset Newline newline
\end_inset
EXTHUB
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
(d) For a system using Hückel model, the input card may read:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# The Hamiltonian to be used
\begin_inset Newline newline
\end_inset
HUECKEL
\end_layout
\begin_layout Enumerate
If P-P-P model Hamiltonian is to be used, one can use various parametrization.
Thus, our second card is also an ASCII card, stating which parametrization
is to use.
Options are: Ohno, Mataga-Nishimoto, and exponential parametrization.
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
(a) For Ohno parametrization, the input card may read:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# Parameterization for the P-P-P Hamiltonian
\begin_inset Newline newline
\end_inset
OHNO
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
(b) For Mataga-Nishimoto parametrization, the input card may read:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# Parametrization for the P-P-P Hamiltonian
\begin_inset Newline newline
\end_inset
MATNIS
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
(c) For exponential parametrization, the input card may read:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# Parametrization for the P-P-P Hamiltonian
\begin_inset Newline newline
\end_inset
EXP
\begin_inset Newline newline
\end_inset
\end_layout
\begin_layout Enumerate
The long-range Coulomb potentials in case of Ohno parametrization can be
parametrized using different sets of parameters, such as standard parameters
or screened parameters.
If STANDARD is given as input card, the program automatically takes
\begin_inset Formula $U$
\end_inset
=11.13d0,
\begin_inset Formula $r_{0}$
\end_inset
\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
=1.2785884d0
\family default
\series default
\shape default
\size default
\emph default
\bar default
\noun default
\color inherit
, and
\begin_inset Formula $\kappa_{i,j}$
\end_inset
\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
=1.d0
\family default
\series default
\shape default
\size default
\emph default
\bar default
\noun default
\color inherit
, while in case of input card SCREENED, it takes
\begin_inset Formula $U$
\end_inset
,
\begin_inset Formula $r_{0}$
\end_inset
, and
\begin_inset Formula $\kappa_{i,j}$
\end_inset
as
\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
8.d0,
\family default
\series default
\shape default
\size default
\emph default
\bar default
\noun default
\color inherit
\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
1.2785884d0
\family default
\series default
\shape default
\size default
\emph default
\bar default
\noun default
\color inherit
, and
\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
2.d0
\family default
\series default
\shape default
\size default
\emph default
\bar default
\noun default
\color inherit
, respectively.
However, one can also directly give the parameters.
If the user opts for Hubbard or extended Hubbard model, then parameters
should be provided explicitly.
\begin_inset Newline newline
\end_inset
\begin_inset Newline newline
\end_inset
If Ohno parametrization is set as an option then the next card will be an
ASCII, mentioning the parameters to use.
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
(a) For standard parameters, the input card may read:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# Parameters for the Ohno parametrization in the P-P-P Hamiltonian
\begin_inset Newline newline
\end_inset
STANDARD
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
(b) For screened parameters, the input card may read:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# Parameters for the Ohno parametrization in the P-P-P Hamiltonian
\begin_inset Newline newline
\end_inset
SCREENED
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
(c) For other parameters, the input card may read:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# Parameters for the Ohno parametrization in the P-P-P Hamiltonian
\begin_inset Newline newline
\end_inset
PARA
\begin_inset Newline newline
\end_inset
11.d0,1.28d0,1.d0
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
If the user wants to use other than Ohno parametrization such as Mataga-Nishimot
o or exponential then one needs to just provide the values of
\begin_inset Formula $U$
\end_inset
and
\begin_inset Formula $r_{0}$
\end_inset
.
For example,
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# Parameters for the Mataga-Nishimoto or exponential parametrization in
the P-P-P Hamiltonian
\begin_inset Newline newline
\end_inset
11.d0, 1.28d0
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
If one is using Hubbard model, the value for
\begin_inset Formula $U$
\end_inset
should be given directly.
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
11.d0
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
In case of extended Hubbard model calculations, the value for
\begin_inset Formula $U$
\end_inset
and
\begin_inset Formula $V$
\end_inset
(nearest neighbours potential) should also be given directly.
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
11.d0,3.d0
\begin_inset Newline newline
\end_inset
\family default
\series default
\shape default
\size default
\emph default
\bar default
\noun default
\color inherit
\begin_inset VSpace defskip
\end_inset
\end_layout
\begin_layout Enumerate
Next card will read the electric charge (ionicity) on the system.
The magnitude of the nuclear charges have been defined as unity (
\begin_inset Formula $=1$
\end_inset
).
For the neutral system the ionicity will be zero, and so on.
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
For example, in case of
\begin_inset Formula $trans$
\end_inset
-polyacetylene, the card will read as follows
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
#Charge on the system
\begin_inset Newline newline
\end_inset
0
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
In order to handle a singly ionized cation the input is:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
#Charge on the system
\begin_inset Newline newline
\end_inset
1
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
while for a singly ionized anion, the input will be:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
#Charge on the system
\begin_inset Newline newline
\end_inset
-1
\end_layout
\begin_layout Enumerate
As our code has been framed to handle mainly molecules and polymers, the
next input card will read the total number of atoms in the unit cell, after
the comment line.
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
For example, if we are handling a system having two number of atoms in
the unit cell, then the card will read
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# Total number of atoms in the unit cell
\begin_inset Newline newline
\end_inset
2
\end_layout
\begin_layout Enumerate
Next card deals with the Cartesian coordinates of the different atoms in
the unit cell, to be provided in the units of
\begin_inset Formula $\textrm{Å}$
\end_inset
.
We have two options to facilitate this: (a) Automatic generation through
various keywords, (b) by explicitly providing coordinates of each atom.
First we will describe the keywords involved in the automatic generation
of coordinates followed by one example illustrating their use.
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
# Give the coordinates of the atoms involved in the system
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
(a) For example, for the benzene ring oriented in parallel direction to
the conventional orientation, in the
\begin_inset Formula $xy$
\end_inset
-plane, the input card may read:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
BEN-XY
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
In case of ring lying in
\begin_inset Formula $yz$
\end_inset
- or
\begin_inset Formula $zx$
\end_inset
-plane, one should give card as 'BEN-YZ' or 'BEN-ZX', respectively.
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
The next card will specify the center of the benzene ring.
For example input,
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
-3.2725,0.575907,0.0
\family default
\series default
\shape default
\size default
\emph default
\bar default
\noun default
\color inherit
\begin_inset Newline newline
\end_inset
implies that the phenyl ring is centered at the point
\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
(-3.2725,0.575907,0.0), in Cartesian coordinates
\family default
\series default
\shape default
\size default
\emph default
\bar default
\noun default
\color inherit
.
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
The next card must specify the bond length of the hexagon constituting the
phenyl ring and whether we need to rotate this ring with respect to some
axis.
For example input,
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
1.4,0
\begin_inset Newline newline
\end_inset
implies that the bond length is 1.4
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
AA
\end_layout
\end_inset
\begin_inset space ~
\end_inset
and no rotations need to be performed on the ring.
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
If instead this input is like:
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
1.4,2
\begin_inset Newline newline
\end_inset
3,-90.d0
\begin_inset Newline newline
\end_inset
2,30.d0
\begin_inset Newline newline
\end_inset
which implies that the C--C bond length in the ring is 1.4
\begin_inset ERT
status open
\begin_layout Plain Layout
\backslash
AA
\end_layout
\end_inset
, which will undergo two subsequent rotations.
First rotation is a clockwise one by
\begin_inset Formula $90^{\circ}$
\end_inset
about the
\begin_inset Formula $z$
\end_inset
-axis, followed by second counter clockwise rotation by
\begin_inset Formula $30^{\circ}$
\end_inset
about the
\begin_inset Formula $y$
\end_inset
-axis.
For example, in an entry of the type 3, -90.d0, first number denotes the
axis of the rotation, while the second number denotes the angle of the
rotation.
\begin_inset Newline newline
\end_inset
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
(b) For a benzene ring oriented in perpendicular direction to the conventional
orientation, in the
\begin_inset Formula $xy$
\end_inset
-plane, the keyword will be:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
BENP-XY
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
and rest of the input will be identical to the case of BEN-XY, discussed
above.
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
(c) For generating a bond (a unit consisting of two atoms separated by a
distance) whose location is specified by the coordinates of the bond center,
the input card is:
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
BOND
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
Next to this card, the user should specify origin, bond length and number
of rotations to be performed on the bond because by default the bond is
assumed to be along the
\begin_inset Formula $x$
\end_inset
-axis.
Rotations, if desired, are performed keeping the center fixed.
Positive angles imply counter-clockwise rotations, while the negative angles
denote clockwise rotations.
For example input,
\begin_inset VSpace defskip
\end_inset
\begin_inset Newline newline
\end_inset
\family roman
\series medium
\shape up
\size normal
\emph off
\bar no
\noun off
\color none
1.0,0.0,0.0
\family default
\series default
\shape default
\size default
\emph default
\bar default
\noun default
\color inherit