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Cosmetic changes --- fonts, typoes, and some minor errors are corrected.

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So Hirata 2002-02-06 19:38:53 +00:00
parent 7e0e66f8d9
commit efaf5fdb30
21 changed files with 192 additions and 196 deletions
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8
doc/user/basis.tex
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@ -12,7 +12,7 @@ functions\footnote{An $sp$ shell is two-component general contraction.
$p$ shell. Again, reuse of the radial functions increases the efficiency
of integral generation.} . The {\tt BASIS} directive is used to
define these, and also to specify use of an effective core potential
(ECP) that is associated with a basis set; see Section \ref{sec:ecp}.)
(ECP) that is associated with a basis set; see Section \ref{sec:ecp}.
The basis functions to be used for a given calculation can be drawn
from a standard set in the EMSL basis set library that is included in
@ -53,7 +53,7 @@ Examining the keywords on the first line of the \verb+BASIS+ directive:
\verb+"ao basis"+. Another name may be specified in the \verb+BASIS+
directive, thus, multiple basis sets may be stored simultaneously in the
database. Also, the DFT (Section \ref{sec:dft}), RI-SCF (Section
\ref{sec:riscf}) and RIMP2 (Section \ref{sec:rimp2}) modules and the
\ref{sec:riscf}) and RI-MP2 (Section \ref{sec:rimp2}) modules and the
Dyall-modified-Dirac relativistic method (Section \ref{sec:dyall-mod-dir})
require multiple basis sets with specific names.
@ -232,7 +232,7 @@ and a finite nucleus of Gaussian shape. These are usually distinguished by
the suffixex {\tt \_pt} and {\tt \_fi}. It is the user's responsibility to
ensure that the contraction matches the nuclear type specified in the
geometry object. The specification of a finite nucleus basis set does NOT
automagically set the nuclear type for that atom to be finite. See
automatically set the nuclear type for that atom to be finite. See
Section \ref{sec:geom} for information.
\section{Explicit basis set definition}
@ -249,7 +249,7 @@ center using an input line of the following form:
\end{verbatim}
The variable \verb+<shell_type>+ identifies the angular momentum of the
shell, $s$, $p$, $d$, \ldots. NWChem is configured to handle up to $i$
shell, $s$, $p$, $d$, \ldots. NWChem is configured to handle up to $h$
shells. The keyword \verb+rel+ marks the shell as relativistic --- see
Section \ref{sec:dyall-mod-dir} for more details. Subsequent lines define
the primitive function exponents and contraction coefficients. General

8
doc/user/ccsd.tex
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@ -21,8 +21,8 @@ block
\begin{verbatim}
CCSD
[MAXITER <integer maxiter default 20>]
[THRESH <real thresh default 10^-6>]
[TOL2E <real tol2e default min(10^-12 , 0.01*$thresh$)>]
[THRESH <real thresh default 10e-6>]
[TOL2E <real tol2e default min(10e-12 , 0.01*$thresh$)>]
[DIISBAS <integer diisbas default 5>]
[FREEZE [[core] (atomic || <integer nfzc default 0>)] \
[virtual <integer nfzv default 0>]]
@ -53,13 +53,13 @@ calculation. Both the RMS error in the amplitudes {\em and} the
change in energy must be less than {\tt thresh}.
\begin{verbatim}
THRESH <real thresh default 10^-6>
THRESH <real thresh default 10e-6>
\end{verbatim}
\section{{\tt TOL2E} --- integral screening threshold}
\begin{verbatim}
TOL2E <real tol2e default min(10^-12 , 0.01*$thresh$)>
TOL2E <real tol2e default min(10e-12 , 0.01*$thresh$)>
\end{verbatim}
The variable \verb+tol2e+ is used in determining the integral

40
doc/user/cosmo.tex
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@ -1,17 +1,17 @@
% $Id: cosmo.tex,v 1.3 2001-01-22 19:24:17 windus Exp $
% $Id: cosmo.tex,v 1.4 2002-02-06 19:38:51 sohirata Exp $
\label{sec:cosmo}
COSMO is the continuum solvation 'Conductor-Like Screening' Model
of A. Klamt and G. Schuurmann to describe dielectric screening
COSMO is the continuum solvation `COnductor-like Screening MOdel'
of A. Klamt and G. Sch\"{u}\"{u}rmann to describe dielectric screening
effects in solvents.
\begin{enumerate}
\item A. Klamt and G. Schuurmann, J.Chem.Soc. Perkin Trans. 2, 1993,
\item A. Klamt and G. Sch\"{u}\"{u}rmann, J.~Chem.~Soc.~Perkin Trans. 2, 1993,
p799-805.
\end{enumerate}
The NWChem COSMO module implements algorithm for calculation of the
energy for Hartree-Fock (RHF and ROHF) and Kohn-Sham (DFT and UDFT)
energy for Hartree-Fock (RHF and ROHF) and Kohn-Sham (restricted and unrestricted)
wavefunctions. At the present gradients are calculated by finite
difference of the energy and the code does not work with spherical
basis functions or ECPs. In the current implementation the code
@ -62,14 +62,12 @@ The codes uses the following Van der Waals radii by default:
2 0.00,0.00,0.00/
\end{verbatim}
with 0.0 values replaced by 1.80 . Other radii can be used as well.
with 0.0 values replaced by 1.80. Other radii can be used as well.
See for examples:
\begin{enumerate}
\item E. V. Stefanovich and T. N. Truong, Chem. Phys. Lett. 244 (1995)
p65-74.
\item V. Barone, M. Cossi, and J. Tomasi, J. Chem. Phys. 107 (1997)
p3210-3221.
\item E. V. Stefanovich and T. N. Truong, Chem.~Phys.~Lett. 244, 65 (1995).
\item V. Barone, M. Cossi, and J. Tomasi, J.~Chem.~Phys. 107, 3210 (1997).
\end{enumerate}
\verb+Rsolv+ is a parameter used to define the solvent accessible
@ -77,36 +75,36 @@ surface. See the original reference of Klamt and Schuurmann for a
description. The default value is 0.00 (in angstroms).
\verb+Iscren+ is a flag to define the dielectric charge scaling option.
"iscren 1" implies the original scaling from Klamt and Schuurmann,
mainly "(eps-1)/(eps+1/2)", where 'eps' is the dielectric constant.
"iscren 0" implies the modified scaling suggested by Stefanovich and
Truong, mainly "(eps-1)/eps". Default is to use the modified scaling.
``{\tt iscren 1}'' implies the original scaling from Klamt and Sch\"{u}\"{u}rmann,
mainly ``$(\epsilon-1)/(\epsilon+1/2)$'', where $\epsilon$ is the dielectric constant.
``{\tt iscren 0}'' implies the modified scaling suggested by Stefanovich and
Truong, mainly ``$(\epsilon-1)/\epsilon$''. Default is to use the modified scaling.
For high dielectric the difference between the scaling is not
significant.
The next three parameters define the tesselation of the unit sphere.
The approach follows the original proposal by Klamt and Schuurmann.
The approach follows the original proposal by Klamt and Sch\"{u}\"{u}rmann.
A very fine tesselation is generated from \verb+maxbem+ refining
passes starting from either an octahedron or an icosahedron. The
boundary elements created with the fine tesselation are condensed
down to a coarser tesselation based on \verb+minbem+. The induced
point charges from the polarization of the medium are assigned to
the centers of the coarser tesselation. Default values are
"minbem 2" and "maxbem 3". The flag \verb+ificos+ serves to
select the original tesselation, "ificos 0" for an octahedron
(default) and "ificos 1" for an icoshedron. Starting from an icosahedron
``{\tt minbem 2}'' and ``{\tt maxbem 3}''. The flag \verb+ificos+ serves to
select the original tesselation, ``{\tt ificos 0}'' for an octahedron
(default) and ``{\tt ificos 1}'' for an icoshedron. Starting from an icosahedron
yields a somewhat finer tesselation that converges somewhat faster.
Solvation energies are not really sensitive to this choice for
sufficiently fine tesselations.
The \verb+lineq+ parameter serves to select the numerical algorithm to solve
the linear equations yielding the effective charges that represent
the polarization of the medium. "lineq 0" selects an iterative method
(default), "lineq 1" selects a dense matrix linear equation solver.
the polarization of the medium. ``{\tt lineq 0}'' selects an iterative method
(default), ``{\tt lineq 1}'' selects a dense matrix linear equation solver.
For large molecules where the number of effective charges is large,
the codes selects the iterative method.
The following example is for a water molecule in 'water', using
The following example is for a water molecule in `water', using
the HF/6-31G** level of theory:
\begin{verbatim}

49
doc/user/dft.tex
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@ -1,5 +1,5 @@
%
% $Id: dft.tex,v 1.55 2001-12-31 18:58:29 edo Exp $
% $Id: dft.tex,v 1.56 2002-02-06 19:38:51 sohirata Exp $
%
\label{sec:dft}
@ -97,7 +97,7 @@ the DFT module are:
TOLERANCES [[tight] [tol_rho <real tol_rho default 1e-10>] \
[accCoul <integer accCoul default 10>] \
[accCoul <integer accCoul default 8>] \
[radius <real radius default 25.0>]]
@ -136,7 +136,7 @@ The charge density fitting basis set must have the name {\tt "cd basis"}.
This can be the actual name of a basis set, or a basis set can be
assigned this name using the \verb+SET+ directive, as described in
Section \ref{sec:set}. If this basis set is not defined by input,
the $O(N^4)$y exact Coulomb contribution is computed.
the $O(N^4)$ exact Coulomb contribution is computed.
The user also has the option of specifying a third basis set for the
evaluation of the exchange-correlation potential. This basis set must
@ -157,7 +157,7 @@ optional, and usually not recommended
\end{itemize}
\section{VECTORS and MAX\_OVL --- KS-MO Vectors}
\section{{\tt VECTORS} and {\tt MAX\_OVL} --- KS-MO Vectors}
The \verb+VECTORS+ directive is the same as that in the SCF module
(Section \ref{sec:vectors}). Currently, the \verb+LOCK+ keyword
@ -167,7 +167,7 @@ is not supported by the DFT module, however the directive
\end{verbatim}
has the same effect.
\section{XC and DECOMP --- Exchange-Correlation Potentials}
\section{{\tt XC} and {\tt DECOMP} --- Exchange-Correlation Potentials}
\label{sec:xc}
\begin{verbatim}
XC [[acm] [b3lyp] [beckehandh] [pbe0]\
@ -407,10 +407,10 @@ appears in table \ref{tablexc}.
The available hybrid functionals
(where a Hartree-Fock Exchange component is present) consist of the Becke
``{\sl half and half}'' (see A.D.~Becke, J.~Chem.~Phys.~98, 1372 (1992)), the
``{\it half and half}'' (see A.D.~Becke, J.~Chem.~Phys.~98, 1372 (1992)), the
adiabatic connection method (see A.D.~Becke, J.~Chem.~Phys.~98, 5648
(1993)), b3lyp (popularized by Gaussian9X), Becke 1997
(``Becke V'' paper: A.D.Becke, J. Chem. Phys., {\bf 107}, 8554 (1997)
(1993)), B3LYP (popularized by Gaussian9X), Becke 1997
(``Becke V'' paper: A.D.Becke, J. Chem. Phys., {\bf 107}, 8554 (1997)).
%These options can be invoked by specifying any of the following input lines,
%\begin{verbatim}
@ -457,7 +457,7 @@ The keyword \verb+b3lyp+ specifies that the exchange-correlation energy
is computed as
\begin{eqnarray*}
E_{XC} \ &=& \ a_0 E^{\rm HF}_X + (1-a_0) E^{\rm Slater}_{X} +
a_X \Delta E^{\rm Becke88}_{X} + (1-a_C)E^{\rm \verb+VWN_1_RPA+}_C + a_C E^{LYP}_C \\
a_X \Delta E^{\rm Becke88}_{X} + (1-a_C)E^{\rm VWN\_1\_RPA}_C + a_C E^{LYP}_C \\
& &{\rm where } \\
a_0 &=& 0.20, \ a_X = 0.72, \ a_C = 0.81
\end{eqnarray*}
@ -480,7 +480,7 @@ a_0 &=& 0.20, \ a_X = 0.72, \ a_C = 0.81
\begin{tabular}{|l|cccc|r|}
\hline
& & & & & \\
Keyword & X & C & GCA & Hybrid & Ref.\\
Keyword & X & C & GGA & Hybrid & Ref.\\
& & & & & \\
\hline
slater & $\star$ & & & &[1]\\
@ -570,7 +570,7 @@ M.Sprik. J. Chem. Phys. {\bf 112}, 1670 (2000). \\
%\end{table}
\onecolumn
\section{ITERATIONS --- Number of SCF iterations}
\section{{\tt ITERATIONS} --- Number of SCF iterations}
\begin{verbatim}
ITERATIONS <integer iterations default 30>
@ -588,7 +588,7 @@ is \verb+ITERATIONS+, and has the following general form,
The optimization procedure will stop when the specified number of
iterations is reached or convergence is met.
\section{CONVERGENCE --- SCF Convergence Control}
\section{{\tt CONVERGENCE} --- SCF Convergence Control}
\begin{verbatim}
CONVERGENCE [energy <real energy default 1e-6>] \
@ -698,7 +698,7 @@ keyword \verb+lshift+. For example the directive,
CONVERGENCE lshift 0.5
\end{verbatim}
causes the diagonal elements of the Fock matrix
corresponding to the virtual orbitals to be shifted by 0.5 au.
corresponding to the virtual orbitals to be shifted by 0.5 a.u.
By default, this level-shifting procedure is switched on whenever the
HOMO-LUMO gap is small. Small is defined by default to be 0.05 au but
can be modified by the directive \verb+hl_tol+. An example of
@ -747,7 +747,7 @@ active, you need to use the following line
\section{SMEAR --- Fractional Occupation of the Molecular Orbitals}
\section{{\tt SMEAR} --- Fractional Occupation of the Molecular Orbitals}
\label{smear}
The {\tt \bf SMEAR} keyword is useful in cases with many degenerate states
@ -766,7 +766,7 @@ energy in order to have
energies and gradients consistent.
\section{GRID --- Numerical Integration of the XC Potential}
\section{{\tt GRID} --- Numerical Integration of the XC Potential}
\label{grgrid}
\begin{verbatim}
GRID [(xcoarse||coarse||medium||fine||xfine) default medium] \
@ -1081,7 +1081,7 @@ in this paper).\\
GRID [[old||new] default new]
\end{verbatim}
In Nwchem 4.0 the XC integration code has been re-written using a
In NWChem 4.0 the XC integration code has been re-written using a
space decomposiition scheme similar to the one proposed in R.E.Stratmann, G.Scuseria and M.J.Frisch,
Chem. Phys. Lett. {\bf 257}, 213 (1996) (keyword
{\bf \tt new}).
@ -1090,11 +1090,11 @@ To use the XC integration routines available in
older version of NWChem, use the keyword {\bf \tt old}.
\section{TOLERANCES --- Screening tolerances}
\section{{\tt TOLERANCES} --- Screening tolerances}
\begin{verbatim}
TOLERANCES [[tight] [tol_rho <real tol_rho default 1e-10>] \
[accCoul <integer accCoul default 10>] \
[accCoul <integer accCoul default 8>] \
[radius <real radius default 25.0>]]
\end{verbatim}
% [accQrad <integer accQrad default 12>] \
@ -1198,7 +1198,7 @@ This option sets all tolerances to their
default/user specified values at the very first iteration.
\section{DIRECT and NOIO --- Hardware Resource Control}
\section{{\tt DIRECT} and {\tt NOIO} --- Hardware Resource Control}
\begin{verbatim}
DIRECT||INCORE
NOIO
@ -1224,7 +1224,7 @@ are computed ``on-the-fly''.
\fussy
\section{ODFT and MULT --- Open shell systems}
\section{{\tt ODFT} and {\tt MULT} --- Open shell systems}
\begin{verbatim}
ODFT
MULT <integer mult default 1>
@ -1244,7 +1244,8 @@ electrons minus beta electrons, plus 1.
The keyword \verb+ODFT+ is unnecessary except in the context
of forcing a singlet system to be computed as an open shell
system (i.e., using a spin-unrestricted wavefunction).
\section{SIC --- Self-Interaction Correction}
\section{{\tt SIC} --- Self-Interaction Correction}
\begin{verbatim}
sic [perturbative || oep || oep-loc <default perturbative>]
@ -1284,11 +1285,7 @@ print "SIC information"
\end{verbatim}
\section{MULLIKEN --- Mulliken analysis}
\begin{verbatim}
MULLIKEN
\end{verbatim}
\section{{\tt MULLIKEN} --- Mulliken analysis}
Mulliken analysis of the charge distribution is invoked by the keyword:
\begin{verbatim}
MULLIKEN

20
doc/user/dplot.tex
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@ -1,5 +1,5 @@
%
% $Id: dplot.tex,v 1.11 2001-04-09 22:42:56 edo Exp $
% $Id: dplot.tex,v 1.12 2002-02-06 19:38:52 sohirata Exp $
%
\label{sec:dplot}
\begin{verbatim}
@ -17,10 +17,10 @@ from SCF or DFT calculation. The output file is either in
(default)
or in the
\htmladdnormallink{Gaussian Cube}{http://www.gaussian.com/00000430.htm}
format. DPLOT is not executed until the "task dplot" directive is given.
format. DPLOT is not executed until the ``\verb+task dplot+'' directive is given.
Different sub-directives are described below.
\section{GAUSSIAN --- Gaussian Cube format}
\section{{\tt GAUSSIAN} --- Gaussian Cube format}
\begin{verbatim}
GAUSSIAN
@ -38,7 +38,7 @@ You can visualize this file using \htmladdnormallink{gOpenMol}
\htmladdnormallink{Molekel}
{http://www.cscs.ch/molekel/}.
\section{TITLE --- Title directive}
\section{{\tt TITLE} --- Title directive}
\begin{verbatim}
TITLE <string Title default Unknown Title>
@ -48,7 +48,7 @@ This sub-directive specifies a title line for the generated
input to the {\em Insight} program or for the Gaussian cube
file. Only one line is allowed.
\section{LIMITXYZ --- Plot limits}
\section{{\tt LIMITXYZ} --- Plot limits}
\begin{verbatim}
LIMITXYZ [units <string Units default angstroms>]
@ -64,7 +64,7 @@ along each direction. The known names for \verb+Units+ are
\section{SPIN --- Density to be plotted}
\section{{\tt SPIN} --- Density to be plotted}
\begin{verbatim}
SPIN <string Spin default total>
@ -77,7 +77,7 @@ $\alpha$ and $\beta$ electron densities.
\section{OUTPUT --- Filename}
\section{{\tt OUTPUT} --- Filename}
\begin{verbatim}
OUTPUT <string File_Name default dplot>
@ -90,7 +90,7 @@ standard NWChem output.
\section{VECTORS --- MO vector file name}
\section{{\tt VECTORS} --- MO vector file name}
\begin{verbatim}
VECTORS <string File_Name default movecs> [<string File_Name2>]
@ -103,7 +103,7 @@ files have to match.
\section{WHERE --- Density evaluation}
\section{{\tt WHERE} --- Density evaluation}
\begin{verbatim}
WHERE <string Where default grid>
@ -118,7 +118,7 @@ the position of the nuclei and written to the NWChem output) and
\verb+g++\verb+n+ (both).
\section{ORBITAL --- Orbital sub-space}
\section{{\tt ORBITAL} --- Orbital sub-space}
\begin{verbatim}
ORBITALS [<string Option default density>]

14
doc/user/driver.tex
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@ -267,13 +267,13 @@ recognized
\end{itemize}
and these specific print options
\begin{itemize}
\item finish (low) - print geometry data at end of calculation
\item bonds (default) - print bonds at end of calculation
\item angles (default) - print angles at end of calculation
\item hvecs (never) - print eigen-values/vectors of the Hessian
\item searchdir (high) - print the search direction in internals
\item 'internal gradient' (default) - print the gradient in internals
\item sadmode (default) - print the mode being followed to the saddle point
\item {\tt finish} (low) - print geometry data at end of calculation
\item {\tt bonds} (default) - print bonds at end of calculation
\item {\tt angles} (default) - print angles at end of calculation
\item {\tt hvecs} (never) - print eigen-values/vectors of the Hessian
\item {\tt searchdir} (high) - print the search direction in internals
\item `{\tt internal gradient}' (default) - print the gradient in internals
\item {\tt sadmode} (default) - print the mode being followed to the saddle point
\end{itemize}
\fussy

5
doc/user/esp.tex
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@ -11,8 +11,9 @@ task esp
The input for the module is taken from the ESP input block
\begin{verbatim}
esp
end
ESP
...
END
\end{verbatim}
\section{Grid specification}

20
doc/user/functionality.tex
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@ -25,11 +25,13 @@ the first derivatives.
\begin{itemize}
\item Self Consistent Field (SCF) or Hartree Fock (RHF, UHF, high-spin
ROHF).
\item Gaussian Density Functional Theory (DFT), using many local and
non-local exchange-correlation potentials (RHF or UHF)
\item Gaussian Density Functional Theory (DFT), using many local,
non-local (gradient-corrected), and hybrid (local, non-local, and HF)
exchange-correlation potentials
(spin-restricted or unrestricted)
with formal $N^3$ and $N^4$ scaling.
\item Spin-orbit DFT (SODFT), using many local and non-local
exchange-correlation potentials (UHF).
\item Spin-orbit DFT (SODFT), using many local and non-local (gradient-corrected)
exchange-correlation potentials (spin-unrestricted).
\item MP2 including semi-direct using frozen core and RHF and UHF reference.
\item Complete active space SCF (CASSCF).
@ -64,8 +66,8 @@ For all methods, the following operations may be performed:
For closed and open shell SCF and DFT:
\begin{itemize}
\item COSMO energies - the continuum solvation 'Conductor-Like Screening' Model
of A. Klamt and G. Schuurmann to describe dielectric screening effects in
\item COSMO energies - the continuum solvation `COnductor-like Screening MOdel'
of A. Klamt and G. Sch\"{u}\"{u}rmann to describe dielectric screening effects in
solvents.
\end{itemize}
@ -92,20 +94,20 @@ calculations are available:
\section{Pseudopotential plane-wave electronic structure}
The following modules are available to compute the energy, minimize the
The following modules are available to compute the energy, optimize the
geometry and perform ab initio molecular dynamics using pseudopotential
plane-wave DFT.
\begin{itemize}
\item Fixed step length steepest descent
\item Conuugate Gradient
\item Conuugate gradient
\item Car-Parrinello (extended Lagrangian dynamics)
\end{itemize}
With
\begin{itemize}
\item Vosko and PBE96 exchange-correlation potentials (restricted
\item Vosko and PBE96 exchange-correlation potentials (spin-restricted
and unrestricted)
\item (Gamma point) Periodic orthorhombic simulation cells for calculating
molecules, liquids, crystals, and surfaces

24
doc/user/geometry.tex
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@ -82,7 +82,7 @@ detail, describing the options available and the usages of the various
keywords in each of the three main parts.
\section{Keywords on the GEOMETRY directive}
\section{Keywords on the {\tt GEOMETRY} directive}
\label{sec:geomkeys}
This section presents the options that can be specified using the keywords
@ -109,7 +109,7 @@ list describes all options and their defaults.
geometry with this name. However, multiple geometries may
be specified by using a different name for each. Subsequently,
the user can direct a module to a named geometry by
by using the the \verb+SET+ directive (see
using the \verb+SET+ directive (see
the example in Section \ref{sec:set}) to associate the default
name of \verb+geometry+ with the alternate name.
@ -124,8 +124,8 @@ list describes all options and their defaults.
recognizes the following possible values for the string variable
\verb+<units>+:
\begin{itemize}
\item \verb+angstroms+ or \verb+an+ --- Angstroms ($\AA$), the default
(converts to A.U. using the $\AA$ to A.U. conversion factor)
\item \verb+angstroms+ or \verb+an+ --- Angstroms (\AA), the default
(converts to A.U. using the \AA to A.U. conversion factor)
\item \verb+au+ or \verb+atomic+ or \verb+bohr+ --- Atomic units (A.U.)
\item \verb+nm+ or \verb+nanometers+ --- nanometers (converts to
A.U. using a conversion factor computed as $10.0$ times the
@ -160,7 +160,7 @@ list describes all options and their defaults.
of nuclear charge to the origin.
\item \verb+autosym+ -- keyword to specify that the symmetry of the
geometric system should be automatically determined. This option is off
geometric system should be automatically determined. This option is on
by default. Only groups up to and including $O_{h}$ are recognized.
Occasionally NWChem will be unable to determine the full symmetry
of a molecular system, but will find a proper subgroup of the full
@ -220,7 +220,7 @@ bond length of 0.732556\ \AA):
end end
\end{verbatim}
\section{Symmetry Group Input}
\section{{\tt SYMMETRY} --- Symmetry Group Input}
\label{sec:symgrp}
The \verb+SYMMETRY+ directive is used (optionally) within the compound
@ -383,7 +383,7 @@ coordinates, and then specifies the remainder of the system using the
optional \verb+ZMATRIX+ directive described below in Section
\ref{sec:Z-matrix}.
\section{Z-matrix input}
\section{{\tt ZMATRIX} --- Z-matrix input}
\label{sec:Z-matrix}
The \verb+ZMATRIX+ directive is an optional directive that can be used
@ -439,7 +439,7 @@ subsequently defined using the \verb+VARIABLES+ or \verb+CONSTANTS+
directives. The numerical values of the symbolic strings labeled
\verb+VARIABLES+ may be subject to changes during a geometry
optimization say, while the numerical values of the symbolic strings
labeled |verb+CONSTANTS+ will stay frozen to the value given in the
labeled \verb+CONSTANTS+ will stay frozen to the value given in the
input. The same symbolic string can be used more than once, and
any mixture of numeric data and symbols is acceptable. Bond angles
($\alpha$) must be in the range $0 < \alpha < 180$.
@ -673,7 +673,7 @@ internal coordinates. These are arranged as follows:
\item The third center is placed in the z-x plane.
\end{itemize}
\section{ZCOORD --- Forcing internal coordinates}
\section{{\tt ZCOORD} --- Forcing internal coordinates}
\label{sec:zcoord}
By default redundant internal coordinates are generated for use in
@ -742,7 +742,7 @@ an optional sign for torsions) then they are forced to have
the same value. This may be used to force bonds or angles to
be equal even if they are not related by symmetry.
When atoms have been specified by their cartesian coordinates, {\em
When atoms have been specified by their Cartesian coordinates, {\em
and} internal coordinates are not being used, it is possible to freeze
the cartesian position of selected atoms. This is useful for such
purposes as optimizing a molecule absorbed on the surface of a cluster
@ -784,7 +784,7 @@ of the \verb+UNSET+ directive is as follows:
unset geometry:actlist
\end{verbatim}
\section{SYSTEM --- Lattice parameters for periodic systems}
\section{{\tt SYSTEM} --- Lattice parameters for periodic systems}
\label{sec:latticeparam}
This keyword is needed only for for 1-, 2-, and 3-dimensional
@ -805,7 +805,7 @@ This means that for crystals $x$, $y$ and $z$ are fractional, for
surfaces $x$ and $y$ are fractional, whereas for polymers only $z$ is
fractional.
For example, in the following H$_2$O layer input (a 2-d periodic
system), $x$ and $y$ coordinates are fractionay, whereas $z$
system), $x$ and $y$ coordinates are fractional, whereas $z$
is expressed in \AA .
\begin{verbatim}
geometry units angstrom

2
doc/user/getstart.tex
View file

@ -294,7 +294,7 @@ For example, the basis set with the descriptive name
\subsection{Input Format}
A (physical) line in the input file is terminated with a newline
character (also known as a 'return' or 'enter' character). A
character (also known as a `return' or `enter' character). A
semicolon (\verb+;+) can be also used to indicate the end of an input
line, allowing a single physical line of input to contain multiple
logical lines of input. For example, five lines of input for the

6
doc/user/interface.tex
View file

@ -1,4 +1,4 @@
% $Id: interface.tex,v 1.9 2001-04-25 20:25:28 windus Exp $
% $Id: interface.tex,v 1.10 2002-02-06 19:38:52 sohirata Exp $
\label{sec:interface}
NWChem has interfaces to several different packages which are listed below.
@ -7,7 +7,7 @@ to make sure that the interface works. However, any problems with the
interface should be reported to the
{\tt nwchem-support@emsl.pnl.gov} e-mail list.
\section{NBO --- Natural Bond Orbital Analysis}
\section{{\tt NBO} --- Natural Bond Orbital Analysis}
\label{sec:nbo}
\begin{verbatim}
NBO
@ -63,7 +63,7 @@ task nbo
\end{verbatim}
\section{DIRDYVTST --- DIRect Dynamics for Variational Transition State Theory}
\section{{\tt DIRDYVTST} --- DIRect Dynamics for Variational Transition State Theory}
\label{sec:dirdyvtst}
by Bruce C. Garrett,\\

38
doc/user/mp2.tex
View file

@ -14,30 +14,28 @@ the size of system that can be treated and use of other approximations
analytic derivatives. This is selected by specifying \verb+mp2+ on
the task directive, e.g.
\begin{verbatim}
task mp2
TASK MP2
\end{verbatim}
\item Fully-direct --- this is of utility if only limited I/O
resources are available (up to about 2800 functions). Only RHF
references and energies are available. This is selected by
specifying \verb+direct_mp2+ on the task directive, e.g.
\begin{verbatim}
task direct_mp2
TASK DIRECT_MP2
\end{verbatim}
\item Resolution of the identity (RI) approximation MP2 (RIMP2) ---
\item Resolution of the identity (RI) approximation MP2 (RI-MP2) ---
this uses the RI approximation and is therefore only exact in the
limit of a complete fitting basis. However, with some care, high
accuracy may be obtained with relatively modest fitting basis sets.
An RIMP2 calculation can cost over 40 times less than the
An RI-MP2 calculation can cost over 40 times less than the
corresponding exact MP2 calculation. RHF and UHF references with
only energies are available. This is selected by specifying
\verb+rimp2+ on the task directive, e.g.,
\begin{verbatim}
task rimp2
TASK RIMP2
\end{verbatim}
\end{itemize}
\section{Input directives}
All three MP2 tasks share the same input block.
\begin{verbatim}
@ -54,7 +52,7 @@ All three MP2 tasks share the same input block.
END
\end{verbatim}
\subsection{{\tt FREEZE} --- Freezing orbitals}
\section{{\tt FREEZE} --- Freezing orbitals}
\label{mp2:core}
All MP2 modules support frozen core orbitals, however, only the direct
@ -128,7 +126,7 @@ keyword. For instance, to freeze the top 5 virtuals
Again, note that this only works for the direct-MP2 and RI-MP2 energy
codes.
\subsection{{\tt TIGHT} --- Increased precision}
\section{{\tt TIGHT} --- Increased precision}
The \verb+TIGHT+ directive can be used to increase the precision
in the MP2 energy and gradients.
@ -145,7 +143,7 @@ $10^{-6}$ to $10^{-8}$) and CPHF (from $10^{-4}$ to $10^{-6}$) are
solved, and also tightens thresholds for computation of the AO and MO
integrals (from $10^{-9}$ to $10^{-11}$) within the MP2 code.
\subsection{{\tt PRINT} and {\tt NOPRINT}}
\section{{\tt PRINT} and {\tt NOPRINT}}
The standard print control options are recognized. The list of
recognized names are given in Table \ref{tbl:mp2-printable}.
@ -182,7 +180,7 @@ Item & Print Level & Description \\
\end{tabular}
\end{table}
\subsection{{\tt VECTORS} --- MO vectors}
\section{{\tt VECTORS} --- MO vectors}
\label{sec:mp2vectors}
All of the (supported) MP2 modules require use of converged canonical
@ -208,7 +206,7 @@ The swap capability is examined in more detail in Section
\ref{sec:vectors}.
\subsection{RI-MP2 fitting basis}
\section{RI-MP2 fitting basis}
\sloppy
@ -244,7 +242,7 @@ the \verb+"ri-mp2 basis"+.
\fussy
\subsection{{\tt FILE3C} --- RI-MP2 3-center integral filename}
\section{{\tt FILE3C} --- RI-MP2 3-center integral filename}
\sloppy
@ -259,7 +257,7 @@ specify the file \verb+/scratch/h2o.3c+, use this directive
\fussy
\subsection{{\tt RIAPPROX} --- RI-MP2 Approximation}
\section{{\tt RIAPPROX} --- RI-MP2 Approximation}
The type of RI approximation used in the RI-MP2 calculation is controlled
by means of the RIAPPROX directive. The two possible values are
@ -270,12 +268,12 @@ and M.~W.~Feyereisen, {\em Chem. Phys. Lett.} {\bf 213}, 514--518
% The \verb+"S"+ approximation will also be supported eventually.
\subsection{Advanced options for RI-MP2}
\section{Advanced options for RI-MP2}
These options, which functioned at the time of writing, are not
currently supported.
\subsubsection{Control of linear dependence}
\subsection{Control of linear dependence}
Construction of the RI fit requires the inversion of a matrix of
fitting basis integrals which is carried out via diagonalization. If
@ -291,7 +289,7 @@ For instance, to set it to $10^{-10}$
set "mp2:fit min eval" 1e-10
\end{verbatim}
\subsubsection{Reference Spin Mapping for RI-MP2 Calculations}
\subsection{Reference Spin Mapping for RI-MP2 Calculations}
The user has the option of specifying that the RI-MP2 calculations are
to be done with variations of the SCF reference wavefunction. This is
@ -339,7 +337,7 @@ follows,
\end{verbatim}
\subsubsection{Batch Sizes for the RI-MP2 Calculation}
\subsection{Batch Sizes for the RI-MP2 Calculation}
The user can control the size of each batch in the transformation and
energy evaluation in the MP2 calculation, and consequently the memory
@ -378,7 +376,7 @@ read in from disk and multiplied together to produce $<batch isize>
performance of the distributed matrix multiplication (which requires
large matrices) versus memory space.
\subsubsection{Energy Memory Allocation Mode: RI-MP2 Calculation}
\subsection{Energy Memory Allocation Mode: RI-MP2 Calculation}
The user must choose a strategy for the memory allocation in the energy
evaluation phase of the RI-MP2 calculation, either by minimizing the amount
@ -401,7 +399,7 @@ possible so that permutational symmetry in the energy evaluation can
be used most effectively.
\subsubsection{Local Memory Usage in Three-Center Transformation}
\subsection{Local Memory Usage in Three-Center Transformation}
For most applications, the code will be able to size the blocks
without help from the user. Therefore, it is unlikely that users will

10
doc/user/oniom.tex
View file

@ -9,12 +9,12 @@ remainder at lower levels of theory, with the end result being of
similar accuracy to a high-level calculation on the full system.
\begin{enumerate}
\item M. Svensson, S. Humbel, R.D.J. Froese, T. Mastubara, S. Sieber and
K. Morokuma, J. Phys. Chem, 100, 1996, p19357.
\item S. Dapprich, I. Komaromi, K.S. Byun, K. Morokuma and M.J. Frisch,
J. Mol. Struct (Theochem), 461-462, 1999, p1-21.
\item M. Svensson, S. Humbel, R.D.J. Froese, T. Mastubara, S. Sieber, and
K. Morokuma, J.~Phys.~Chem., 100, 19357 (1996).
\item S. Dapprich, I. Komaromi, K.S. Byun, K. Morokuma, and M.J. Frisch,
J.~Mol.~Struct.~(Theochem), 461-462, 1 (1999).
\item R.D.J. Froese and K. Morokuma in ``Encylopedia of Computational Chemistry,''
volume 2, p1244-1257, (ed. P. von Rague Schleyer, John Wiley and Sons,
volume 2, pp.1244-1257, (ed. P. von Rague Schleyer, John Wiley and Sons,
Chichester, Sussex, 1998).
\end{enumerate}

42
doc/user/property.tex
View file

@ -45,22 +45,22 @@ Each property can be requested by means of a subdirective among the
subdirectives provided :
\begin{itemize}
\item nbofile
\item dipole
\item quadrupole
\item octupole
\item mulliken
\item esp
\item efield
\item efieldgrad
\item electrondensity
\item giao
\item all
\item {\tt NBOFILE}
\item {\tt DIPOLE}
\item {\tt QUADRUPOLE}
\item {\tt OCTUPOLE}
\item {\tt MULLIKEN}
\item {\tt ESP}
\item {\tt EFIELD}
\item {\tt EFIELDGRAD}
\item {\tt ELECTRONDENSITY}
\item {\tt GIAO}
\item {\tt ALL}
\end{itemize}
The ``all'' keyword generates all currently available properties.
The ``{\tt ALL}'' keyword generates all currently available properties.
The request to NBOFILE does not execute the Natural Bond Analysis
The request {\tt NBOFILE} does not execute the Natural Bond Analysis
code, but simply creates an input file to be used as input to the
stand-alone NBO code. To execute the NBO analysis directly, see Section
\ref{sec:nbo}. All other properties are calculated upon
@ -68,11 +68,11 @@ request.
An additional subdirective is provided to specify the origin of the
molecular orbitals used in the calculation of the molecular
properties. This is the 'vectors' subdirective, also used in the
properties. This is the `{\tt VECTORS}' subdirective, also used in the
SCF and DFT tasks. For a full description of this subdirective
the user is refered to the description found in the SCF description.
By default, the input file used for the calculation of the properties
has the .movecs name extension.
has the \verb+.movecs+ name extension.
The user also has the option to choose the center of expansion for
the dipole, quadrupole, and octupole calculations.
@ -81,10 +81,10 @@ the dipole, quadrupole, and octupole calculations.
[CENTER ((com || coc || origin || arb <real x y z>) default coc)]
\end{verbatim}
com is the center of mass, coc is the center of charge, origin is
(0.0, 0.0, 0.0) and arb is any arbitrary point which must be accompanied
\verb+com+ is the center of mass, \verb+coc+ is the center of charge, \verb+origin+ is
(0.0, 0.0, 0.0) and \verb+arb+ is any arbitrary point which must be accompanied
by the coordinated to be used. Currently the x, y, and z coordinates
must be given in the same units as UNITS in GEOMETRY (See Section
must be given in the same units as \verb+UNITS+ in \verb+GEOMETRY+ (See Section
\ref{sec:geomkeys}).
\subsection{Nbofile}
@ -92,12 +92,12 @@ must be given in the same units as UNITS in GEOMETRY (See Section
Following the successful completion of an electronic structure
calculation, a Natural Bond Orbital (NBO) analysis may be carried out
in the following way. On restart specify the TASK as PROPERTY and
supply the sub-directive NBOFILE to the PROPERTY directive. NWChem
in the following way. On restart specify the \verb+TASK+ as \verb+PROPERTY+ and
supply the sub-directive \verb+NBOFILE+ to the \verb+PROPERTY+ directive. NWChem
will query the rtdb and construct an ASCII file,
\verb+<file_prefix>.gen+, that may be used as input to the stand alone
version of the NBO program, gennbo. \verb+<file_prefix>+ is equal to
string following the RESTART directive. The input deck may be edited
string following the \verb+RESTART+ directive. The input deck may be edited
to provide additional options to the NBO calculation, (see the NBO
user's manual for details.) The other option in to directly run the NBO
analysis (See Section \ref{sec:nbo} for more information).

26
doc/user/pspw.tex
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@ -102,7 +102,7 @@ TASK cg_pspw vib
\end{verbatim}
\subsection{STEEPEST\_DESCENT}
\subsection{\tt STEEPEST\_DESCENT}
The steepest\_descent task is used to optimize the one-electron orbitals
with respect to the total energy. In addition it can also be used to optimize
@ -207,7 +207,7 @@ sub-block.
\end{itemize}
\subsection{CONJUGATE\_GRADIENT}
\subsection{\tt CONJUGATE\_GRADIENT}
The conjugate\_gradient task is used to optimize the one-electron orbitals
with respect to the total energy. This method should be used for finer
@ -314,7 +314,7 @@ sub-block.
\subsection{Car-Parrinello}
\subsection{\tt Car-Parrinello}
The Car-Parrinello task is used to perform ab initio molecular dynamics
using the scheme developed by Car and Parrinello. In this unified ab
initio molecular dynamics scheme the motion of the ion cores is coupled to
@ -466,7 +466,7 @@ sub-block.
\subsection{PSP\_FORMATTER}
\subsection{\tt PSP\_FORMATTER}
The psp\_formatter task takes a non-separable pseudopotential defined in
one-dimension real-space in a one-dimensional psp datafile and does two
things to it. First it puts it into the semi-local form suggested by
@ -521,7 +521,7 @@ sub-block.
\subsection{WAVEFUNCTION\_INTITIALIZER}
\subsection{\tt WAVEFUNCTION\_INTITIALIZER}
The wavefunction\_initializer task is used to generate an initial wavefunction
datafile.
Input to the WAVEFUNCTION\_INITIALIZER task is contained
@ -575,7 +575,7 @@ sub-block.
Not used if a RESTRICTED calculation.
\end{itemize}
\subsubsection{Old Style Input (version 3.3) to WAVEFUNCTION\_INTITIALIZER}
\subsubsection{Old Style Input (version 3.3) to {\tt WAVEFUNCTION\_INTITIALIZER}}
For backwards compatibility, the input to the WAVEFUNCTION\_INITIALIZER
sub-block can also be of the form
@ -622,7 +622,7 @@ random components added and a sine function with random components
added respectively.
\subsection{V\_WAVEFUNCTION\_INITIALIZER}
\subsection{\tt V\_WAVEFUNCTION\_INITIALIZER}
The v\_wavefunction\_initializer task is used to generate an initial velocity
wavefunction datafile.
Input to the V\_WAVEFUNCTION\_INITIALIZER task is contained
@ -673,7 +673,7 @@ sub-block.
\subsection{WAVEFUNCTION\_EXPANDER}
\subsection{\tt WAVEFUNCTION\_EXPANDER}
The v\_wavefunction\_initializer task is used to convert a new wavefunction
file that spans a larger grid space from an old wavefunction file.
Input to the WAVEFUNCTION\_EXPANDER task is contained
@ -718,7 +718,7 @@ sub-block.
\subsection{PSP\_GENERATOR}
\subsection{\tt PSP\_GENERATOR}
A one-dimensional pseudopotential code has been integrated into NWChem.
This code allows the user to modify and develop pseudopotentials. Currently,
@ -785,7 +785,7 @@ sub-block.
\end{itemize}
\subsubsection{ATOMIC\_FILLING Block}
\subsubsection{\tt ATOMIC\_FILLING Block}
This required block is used to define the reference atom which is used
to define the pseudopotential. After the ATOMIC\_FILLING: $<$ncore$>$ $<$nvalence$>$ line
The core states are listed (one per line), and then the valence states are listed (one per line).
@ -813,7 +813,7 @@ ATOMIC_FILLING: 3 0
could be used for a pseudopotential with no valence electrons.
\subsubsection{CUTOFF Block}
\subsubsection{{\tt CUTOFF} Block}
This optional block specifies the cutoff distances used
to match the all-electron atom to the pseudopotential atom. For
Hamann pseudopotentials $r_{cut}(l)$ defines the distance
@ -850,7 +850,7 @@ CUTOFF: 2
\end{verbatim}
\subsubsection{SEMICORE\_RADIUS Option}
\subsubsection{{\tt SEMICORE\_RADIUS} Option}
Specifying the SEMICORE\_RADIUS option turns on the semicore correction approximation proposed
by Louie et al (S.G. Louie, S. Froyen, and M.L. Cohen, Phys. Rev. B, \textbf{26}, 1738, (1982)).
This approximation is known to dramatically improve results for systems containing
@ -928,7 +928,7 @@ input in detail.
along lattice vector directions.
\end{itemize}
\subsection{Analysis: Mulliken RTDB data}
\subsection{{\tt ANALYSIS}: Mulliken RTDB data}
\label{sec:pspw_analysis}
To perform Mulliken analysis information is needed from one-dimensional

4
doc/user/qmmm.tex
View file

@ -1,4 +1,4 @@
% $Id: qmmm.tex,v 1.7 2000-05-03 19:37:59 d3j191 Exp $
% $Id: qmmm.tex,v 1.8 2002-02-06 19:38:53 sohirata Exp $
\label{sec:qmmm}
@ -55,7 +55,7 @@ The QM/MM input consists of the standard NWChem input block:
The \verb+QMMM+ has the following the additional sub-directive that the user
may specify for the particular simulation. These options currently are:
\section{EATOMS}
\section{\tt EATOMS}
There is one compound input directive that must exist for the QM/MM
simulation to proceed. This sets the relative zero of energy for the
QM component of the system. It is not incorrect to leave this value as

24
doc/user/scf.tex
View file

@ -87,7 +87,7 @@ completeness. It may be necessary to specify these in order to modify
the behavior of a previous calculation (see Section \ref{sec:persist}
for restart behavior).
\section{SYM --- use of symmetry}
\section{{\tt SYM} --- use of symmetry}
\label{sec:sym}
\begin{verbatim}
@ -106,7 +106,7 @@ For example, to disable use of symmetry in Fock matrix construction:
sym off
\end{verbatim}
\section{ADAPT -- symmetry adaptation of MOs}
\section{{\tt ADAPT} -- symmetry adaptation of MOs}
\label{sec:adapt}
\begin{verbatim}
@ -127,11 +127,11 @@ could result in incorrect energies and poor convergence of the
calculation. It is thus advisable when specifying \verb+ADAPT OFF+ to
also specify \verb+SYM OFF+ (Section \ref{sec:sym}).
\section{TOL2E --- integral screening threshold}
\section{{\tt TOL2E} --- integral screening threshold}
\label{sec:tol2e}
\begin{verbatim}
TOL2E <real tol2e default min(10^-7 , 0.01*$thresh$)>
TOL2E <real tol2e default min(10e-7 , 0.01*$thresh$)>
\end{verbatim}
The variable \verb+tol2e+ is used in determining the integral
@ -159,7 +159,7 @@ For very diffuse basis sets, or for high-accuracy calculations it
might be necessary to set this parameter. A value of $10^{-12}$ is
sufficient for nearly all such purposes.
\section{VECTORS --- input/output of MO vectors}
\section{{\tt VECTORS} --- input/output of MO vectors}
\label{sec:vectors}
@ -682,7 +682,7 @@ the SCF input block) and before the {\tt TASK} directive.
set tolguess 1e-7
\end{verbatim}
\section{THRESH --- convergence threshold}
\section{{\tt THRESH} --- convergence threshold}
\label{sec:thresh}
\begin{verbatim}
@ -714,7 +714,7 @@ high accuracy or very weak interactions. A threshold of $10^{-10}$
should be regarded as the best that can be attained in most
circumstances.
\section{MAXITER --- iteration limit}
\section{{\tt MAXITER} --- iteration limit}
\label{sec:max}
\begin{verbatim}
@ -745,7 +745,7 @@ The following sets the maximum number of SCF iterations to 50:
maxiter 50
\end{verbatim}
\section{PROFILE --- performance profile}
\section{{\tt PROFILE} --- performance profile}
This directive allows the user to obtain timing and parallel
execution information about the SCF module. It is specified by the
@ -760,7 +760,7 @@ performance of an SCF calculation. However,
it can introduce a significant overhead
on machines that have expensive timing routines, such as the SUN.
\section{DIIS --- DIIS convergence}
\section{{\tt DIIS} --- DIIS convergence}
This directive allows the user to specify DIIS convergence rather than
second-order convergence for the SCF calculation. The form of the
@ -786,7 +786,7 @@ The default of 5 should be adequate for most applications, but may be
increased if convergence is poor. On large systems, it may be necessary
to specify a lower value for \verb+diisbas+, to conserve memory.
\section{DIRECT and SEMIDIRECT --- recomputation of integrals}
\section{{\tt DIRECT} and {\tt SEMIDIRECT} --- recomputation of integrals}
\label{sec:semidirect}
In the context of SCF calculations direct means that all integrals are
@ -1073,7 +1073,7 @@ time than it would with the unshifted Hessian.
The following sections describe the directives needed to disable the
Newton-Raphson iteration and specify level-shifting.
\section{NR --- controlling the Newton-Raphson}
\section{{\tt NR} --- controlling the Newton-Raphson}
\label{sec:nrswitch}
\begin{verbatim}
@ -1092,7 +1092,7 @@ this is as follows:
nr 0
\end{verbatim}
\section{LEVEL --- level-shifting the orbital Hessian}
\section{{\tt LEVEL} --- level-shifting the orbital Hessian}
\label{sec:level}
This directive allows the user to specify level-shifting to obtain a

2
doc/user/selci.tex
View file

@ -338,7 +338,7 @@ continuous and well defined. To do this specify
set selci:update logical .false.
\end{verbatim}
\section{Orbital locking in ci geometry optimization}
\section{Orbital locking in CI geometry optimization}
The selected CI wavefunction is not invariant to orbital rotations or
to swapping two or more orbitals. Orbitals could be swapped or rotated

6
doc/user/stepper.tex
View file

@ -1,5 +1,5 @@
%
% $Id: stepper.tex,v 1.14 2000-02-04 02:38:03 edo Exp $
% $Id: stepper.tex,v 1.15 2002-02-06 19:38:53 sohirata Exp $
%
\label{sec:stepper}
@ -19,7 +19,7 @@ specified within the compound directive,
\end{verbatim}
The presence of the STEPPER compound directive automatically turns off
the default geometry optimization tool driver. Input specified for the
the default geometry optimization tool DRIVER. Input specified for the
STEPPER module must appear in the input file {\em after} the
\verb+GEOMETRY+ directive, since it must know the number of atoms that
are to be used in the geometry optimization. In the current version
@ -170,7 +170,7 @@ specified by input using a line of the following form,
%
\section{Backstepping in Stepper}
\section{Backstepping in STEPPER}
\label{sec:stepper:backstep}
If a step taken during the optimization is too large (e.g., the step
causes the energy to go up for a minimization or down for a transition

36
doc/user/top-level.tex
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@ -15,7 +15,7 @@ directives are ignored.
The following sections describe each of the top-level directives in
detail, noting all keywords, options, required input, and defaults.
\section{START and RESTART --- Start-up mode}
\section{{\tt START} and {\tt RESTART} --- Start-up mode}
\label{sec:start}
A {\tt START} or {\tt RESTART} directive is
@ -50,7 +50,7 @@ If the user does not specify an entry for {\tt <file\_prefix>} on the
altogether), the code uses the base-name of the input file as the file
prefix. That is, the variable {\tt <file\_prefix>} is assigned the
name of the input file (not its full pathname), but without the last
"dot-suffix". For example, the input file name
``dot-suffix''. For example, the input file name
\verb+/home/dave/job.2.nw+ yields \verb+job.2+ as the file prefix, if
a name is not assigned explicitly using the \verb+START+ directive.
@ -125,7 +125,7 @@ the code behaves as if the input file contained the directive,
\end{verbatim}
\section{SCRATCH\_DIR and PERMANENT\_DIR --- File directories}
\section{{\tt SCRATCH\_DIR} and {\tt PERMANENT\_DIR} --- File directories}
\label{sec:dirs}
These are start-up directives that allow the user to specify the
@ -134,7 +134,7 @@ NWChem distinguishes between permanent (or persistent) files and
scratch (or temporary) files, and allows the user the option of
putting them in different locations. In most installations, however,
permanent and scratch files are all written to the current directory
by default. What constitutes "local" disk space may also differ from
by default. What constitutes ``local'' disk space may also differ from
machine to machine.
The conventions for file storage are at the discretion of the specific
@ -211,7 +211,7 @@ given list of directories:
\end{verbatim}
\end{itemize}
\section{MEMORY --- Control of memory limits}
\section{{\tt MEMORY} --- Control of memory limits}
This is a start-up directive that allows the user to specify the
amount of memory that NWChem can use for the job. If this directive
@ -305,7 +305,7 @@ directive, the user should be aware that some of the distinctions
among these categories of memory have been blurred in their actual
implementation in the code. The memory allocator (MA) allocates both
the heap and the stack from a single memory region of size {\tt
heap+stack}, without enforcing the partition. The heap vs. stack
heap+stack}, without enforcing the partition. The heap vs.\ stack
partition is meaningful only to applications developers, and can be
ignored by most users. Further complicating matters, the global array
(GA) toolkit is allocated from within the MA space on distributed
@ -359,7 +359,7 @@ Sun & 200 \\
\end{table}
\section{ECHO --- Print input file}
\section{{\tt ECHO} --- Print input file}
\label{sec:echo}
This start-up directive is provided as a convenient way to include a
@ -375,7 +375,7 @@ the single line:
The \verb+ECHO+ directive is processed only
once, by Process 0 when the input file is read.
\section{TITLE --- Specify job title}
\section{{\tt TITLE} --- Specify job title}
This top-level directive allows the user to identify a job or series
of jobs that use a particular database. It is an optional directive,
@ -400,7 +400,7 @@ white space, it must be surrounded by double quotes. For example,
The title is stored in the database and will be used in all subsequent
tasks/jobs until redefined in the input.
\section{PRINT and NOPRINT --- Print control}
\section{{\tt PRINT} and {\tt NOPRINT} --- Print control}
\label{sec:printcontrol}
The \verb+PRINT+ and \verb+NOPRINT+ directives allow the user to
@ -490,7 +490,7 @@ within the MP2 module will cause the SCF, CPHF and gradient modules
when invoked from the MP2 to default to low print. Explicit user
input of print thresholds overrides the inherited value.
\section{SET --- Enter data in the RTDB}
\section{{\tt SET} --- Enter data in the RTDB}
\label{sec:set}
This top-level directive allows the user to enter data directly into the
@ -580,7 +580,7 @@ the sample input files (see Section \ref{sec:realsample}), and
its usage with basis sets (Section \ref{sec:basis}) and geometries
(Section \ref{sec:geom}).
\section{UNSET --- Delete data in the RTDB}
\section{{\tt UNSET} --- Delete data in the RTDB}
\label{sec:unset}
This directive gives the user a way to delete simple entries from the
@ -615,7 +615,7 @@ The following example makes an entry in the database using the
\end{verbatim}
\section{STOP --- Terminate processing}
\section{{\tt STOP} --- Terminate processing}
This top-level directive provides a convenient way of verifying
an input file without actually running the calculation. It consists
@ -628,7 +628,7 @@ of the single line,
As soon as this directive is encountered, all processing ceases and
the calculation terminates with an error condition.
\section{TASK --- Perform a task}
\section{{\tt TASK} --- Perform a task}
\label{sec:task}
The \verb+TASK+ directive is used to tell the code what to do. The
@ -665,7 +665,7 @@ code execution continues with the next task.
The input options, keywords, and defaults for each of these four forms
for the \verb+TASK+ directive are discussed in the following sections.
\subsection{TASK Directive for Electronic Structure Calculations}
\subsection{{\tt TASK} Directive for Electronic Structure Calculations}
\label{sec:first_task}
This is the most commonly used version of the \verb+TASK+ directive, and
@ -752,7 +752,7 @@ theory, the \verb+TASK+ directive is
The optional keyword \verb+ignore+ can be used to allow execution to
continue even if the task fails, as discussed above.
\subsection{TASK Directive for Special Operations}
\subsection{{\tt TASK} Directive for Special Operations}
This form of the \verb+TASK+ directive is used in instances where the
task to be performed does not fit the model of the previous version
@ -783,7 +783,7 @@ below, with the corresponding entries for string variable \verb+<task>+.
This directive also recognizes the keyword \verb+ignore+, which allows
execution to continue after a task has failed.
\subsection{TASK Directive for the Bourne Shell}
\subsection{{\tt TASK} Directive for the Bourne Shell}
This form of the \verb+TASK+ directive is supported only on machines
with a fully UNIX-style operating system. This directive causes
@ -835,7 +835,7 @@ execute all but the simplest UNIX commands, it is usually much easier
to put the shell script in a file and execute the file from within
NWChem.
\subsection{TASK Directive for QM/MM simulations}
\subsection{{\tt TASK} Directive for QM/MM simulations}
This is very similar to the most commonly used version of the
\verb+TASK+ directive described in Section \ref{sec:first_task}, and
@ -885,7 +885,7 @@ level of theory the task directive input would be
The optional keyword \verb+ignore+ can be used to allow execution to
continue even if the task fails, as discussed above.
\section{CHARGE --- Total system charge}
\section{{\tt CHARGE} --- Total system charge}
\label{sec:charge}
This is an optional top-level directive that allows the user to specify

4
doc/user/vib.tex
View file

@ -1,4 +1,4 @@
% $Id: vib.tex,v 1.11 2000-11-21 01:09:53 windus Exp $
% $Id: vib.tex,v 1.12 2002-02-06 19:38:53 sohirata Exp $
\label{sec:vib}
The nuclear hessian which is used to compute the vibrational
@ -123,7 +123,7 @@ task scf frequencies
The ``VIB'' module also can generate mode animation input files in the
standard xyz file format for graphics packages like
RasMol or XMol {There are scripts to automate this for RasMol in
.../nwchem/contrib/rasmolmovie}. Each mode will have 20 xyz
{\verb+$NWCHEM_TOP/contrib/rasmolmovie+}. Each mode will have 20 xyz
files generated that cycle from the equilibrium geometry to 5 steps in
the positive direction of the mode vector, back to 5 steps in the
negative direction of the mode vector, and finally back to the