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minor corrections; fixed several examples; clarified some wording

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Robert Harrison 1998-03-07 02:11:49 +00:00
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12
doc/user/functionality.tex
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@ -16,15 +16,11 @@ the first derivatives.
\begin{itemize}
\item Self Consistent Field (SCF) or Hartree Fock (RHF, UHF, high-spin
ROHF). Code to compute analytic second derivatives is being tested.
ROHF).
\item Gaussian Density Functional Theory (DFT), using many local and
non-local exchange-correlation potentials (RHF and UHF).
non-local exchange-correlation potentials (RHF or UHF).
\item MP2 semi-direct using frozen core and RHF and UHF reference.
\item Coupled-cluster single and double excitations (CCSD), with RHF
reference\footnote{CCSD analytic gradients were not yet complete at
the time of writing}.
\item Complete active space SCF (CASSCF).
\end{itemize}
@ -33,11 +29,11 @@ The following methods are available to compute energies only. First
and second derivatives are computed by finite difference of the
energies.
\begin{itemize}
\item MP3, MP4, CCSD(T), with RHF reference.
\item MP3, MP4, CCSD, CCSD(T), CCSD+T(CCSD), with RHF reference.
\item Selected-CI with second-order perturbation correction.
\item MP2 fully-direct with RHF reference.
\item Resolution of the identity integral approximation MP2 (RI-MP2), with
RHF and UHF reference.
RHF or UHF reference.
\end{itemize}
For all methods, the following operations may be performed:

3
doc/user/geometry.tex
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@ -593,8 +593,7 @@ The \verb+ZCOORD+ input parameters are defined as follows:
the atoms.
\end{itemize}
\section{Freezing internal coordinates or atom coordinates
in geometry optimizations}
\section{Freezing coordinates in geometry optimizations}
\label{sec:activeatoms}
Internal coordinates may have been specified by means of a user

172
doc/user/getstart.tex
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@ -35,7 +35,7 @@ module-specific directives (i.e., compound directives) can appear in
any order, with the exception of the \verb+TASK+ directive (see
sections \ref{sec:inputstructure} and \ref{sec:task}) which is used to
invoke an NWChem module. All input for a given task must
proceed the \verb+TASK+ directive. This input specification rule
precede the \verb+TASK+ directive. This input specification rule
allows the concatenation of multiple tasks in a single NWChem input
file.
@ -97,12 +97,14 @@ something like the following;
\end{verbatim}
The default name for the input file is \verb+nwchem.nw+. If an input
file name \verb+input_file+ is specified without an extension, the code
assumes \verb+.nw+ as a default extension, and the input filename becomes \verb+input_file.nw+. If the code cannot
locate a file named either \verb+nwchem.nw+ or \verb+input_file.nw+, an
error is reported and execution terminates. The following
section presents two input files to illustrate the directive syntax and
input file format for NWChem applications.
file name \verb+input_file+ is specified without an extension, the
code assumes \verb+.nw+ as a default extension, and the input filename
becomes \verb+input_file.nw+. If the code cannot locate a file named
either \verb+input_file+ or \verb+input_file.nw+ (or \verb+nwchem.nw+
if no file name is provided), an error is reported and execution
terminates. The following section presents two input files to
illustrate the directive syntax and input file format for NWChem
applications.
\section{Simple Input File --- SCF geometry optimization}
\label{sec:simplesample}
@ -163,21 +165,21 @@ both standard output and standard error.
\label{sec:realsample}
A more complex sample problem is the optimization of a positively
charged water molecule at the MP2 level of theory, followed by a
computation of frequencies at the optimized geometry. A preliminary
SCF geometry optimization is performed using a computationally
inexpensive basis set (STO-3G). This yields a good starting guess for
the optimal geometry, and any Hessian information generated will be
used in the next optimization step. Then the optimization is finished
using second-order M{\o}ller-Plesset perturbation theory and a basis
set with polarization functions. The final task is to calculate the
vibrational frequencies. The input file to accomplish these three
charged water molecule using second-order M{\o}ller-Plesset
perturbation theory (MP2), followed by a computation of frequencies at
the optimized geometry. A preliminary SCF geometry optimization is
performed using a computationally inexpensive basis set (STO-3G).
This yields a good starting guess for the optimal geometry, and any
Hessian information generated will be used in the next optimization
step. Then the optimization is finished using MP2 and a basis set
with polarization functions. The final task is to calculate the
MP2 vibrational frequencies. The input file to accomplish these three
tasks is as follows:
\begin{verbatim}
start h2o_freq
title; H2O+ frequencies with MP2 and 6-31g**
charge 1
geometry units angstroms
O 0.0 0.0 0.0
@ -185,44 +187,35 @@ geometry units angstroms
H 0.0 1.0 0.0
end
charge 1
basis "starting basis"
basis
H library sto-3g
O library sto-3g
end
basis "final basis"
scf
uhf; doublet
print low
end
title; H2O+ : STO-3G UHF geometry optimization
task scf optimize
basis
H library 6-31g**
O library 6-31g**
end
scf
uhf
doublet
print low
end
set "ao basis" "starting basis"
task scf optimize
set "ao basis" "final basis"
scf
vectors input atomic
print none
end
title; H2O+ : 6-31g** UMP2 geometry optimization
task mp2 optimize
mp2
print none
end
mp2; print none; end
scf; print none; end
title; H2O+ : 6-31g** UMP2 frequencies
task mp2 freq
eof
\end{verbatim}
The \verb+START+ directive (Section \ref{sec:start}) tells NWChem that
@ -242,86 +235,47 @@ actually necessary, however.) The {\tt CHARGE} directive defines the
total charge of the system. This calculation is to be done on an ion
with charge +1.
The next two directives are the {\tt BASIS} directives. The names for
the basis sets are arbitrary, and they may be chosen so that they will
serve as a helpful mnemonic for later reference in subsequent input
directives.
The multiple lines of the first {\tt SCF} directive in the {\tt scf
\ldots end} block specify details about the SCF calculation to be
performed. Unrestricted Hartree-Fock is chosen here (by specifying
the keyword {\tt uhf}), rather than the default, restricted open-shell
high-spin Hartree-Fock (ROHF). This is necessary for the subsequent
MP2 calculation, because only UMP2 is currently available for
open-shell systems (see Section \ref{sec:functionality}). For
open-shell systems, the spin multiplicity has to be specified (using
{\tt doublet} in this case), or it defaults to {\tt singlet}. The
print level is set to {\tt low} to reduce the output from the SCF
module to a minimum during the geometry optimization (to avoid verbose
output for the starting basis calculations).
The final step in setting up the input for the SCF calculation is to
specify that the \verb+"starting basis"+ should be used. This is
accomplished by means of the \verb+SET+ directive, which specifies
that the \verb+"ao basis"+ is the \verb+"starting basis"+. All
molecular orbital (MO) methods look for the \verb+"ao basis"+ in which
to expand the MOs. In the previous example with the nitrogen
molecule, it was not necessary to use the \verb+SET+ directive in this
manner, since the \verb+BASIS+ directive used the default name (which
is \verb+"ao basis"+). An alternative approach, which avoids the
necessity of assigning the starting basis set name, would be to defer
definition of the final basis until after the first SCF calculation is
complete.
A small basis set (STO-3G) is specified for the intial geometry
optimization. Next, the multiple lines of the first {\tt SCF}
directive in the {\tt scf \ldots end} block specify details about the
SCF calculation to be performed. Unrestricted Hartree-Fock is chosen
here (by specifying the keyword {\tt uhf}), rather than the default,
restricted open-shell high-spin Hartree-Fock (ROHF). This is
necessary for the subsequent MP2 calculation, because only UMP2 is
currently available for open-shell systems (see Section
\ref{sec:functionality}). For open-shell systems, the spin
multiplicity has to be specified (using {\tt doublet} in this case),
or it defaults to {\tt singlet}. The print level is set to {\tt low}
to avoid verbose output for the starting basis calculations.
All input up to this point affects only the settings in the runtime
database. The program takes its information from this database, so
the sequence of directives up to the first \verb+TASK+ directive is
irrelevant. An exchange of order of the different blocks or
directives would not affect the result. The {\tt TASK} directive,
however, must be specified last of all in the list of input directives
for a given problem. The {\tt TASK} directive invokes the program and
directs the code to perform the specified calculation using the
parameters set in the preceding directives. In this case, the first
task is an SCF calculation with geometry optimization, specified with
the input {\tt scf} and {\tt optimize}. (See Section \ref{sec:task}
for a list of available tasks and operations.)
however, must be specified after all relevant input for a given
problem. The {\tt TASK} directive causes the code to perform the
specified calculation using the parameters set in the preceding
directives. In this case, the first task is an SCF calculation with
geometry optimization, specified with the input {\tt scf} and {\tt
optimize}. (See Section \ref{sec:task} for a list of available
tasks and operations.)
After the completion of any task, settings in the database are used
in subsequent tasks without change, unless they are overridden by new
input directives. In this example, there are several important
changes between the first task (\verb+task scf optimize+) and the
second task (\verb+task mp2 optimize+). The {\tt "ao basis"} is set
to a better basis (i.e., {\tt "final basis"}), using the \verb+SET+
directive. The SCF output will be completely discarded (as a result of the
{\tt print none} input in the {\tt SCF} directive), which means that
no SCF output will be produced unless an error occurs. The SCF starting
guess vectors are reset to be the atomic guess, since the STO-3G
vectors are no longer appropriate (see Section \ref{sec:vectors} for
details on the different possible starting guesses).
The second {\tt TASK} directive invokes an MP2 optimization, instead
of the SCF optimization.
After the completion of any task, settings in the database are used in
subsequent tasks without change, unless they are overridden by new
input directives. In this example, before the second task (\verb+task
mp2 optimize+), a better basis set (6-31G**) is defined and the title
is changed. The second {\tt TASK} directive invokes an MP2 geometry
optimization.
Once the MP2 optimization is completed, the geometry obtained in the
calculation is used to perform a frequency calculation. This task is
invoked by the keyword \verb+freq+ in the final \verb+TASK+ directive,
\verb+task mp2 freq+. The second derivatives of the energy are
calculated as numerical derivatives of analytical gradients. The
gradients as such are not of interest in this case, so the amount of
output from the {\tt mp2} module is reduced with the \verb+PRINT+
directive.
The {\tt EOF} directive marks the end of the input to be read. It is
not necessary to specify the end-of-file as an explicit directive at
the actual end of the file. However, using the directive allows
additional lines in the file that will not be processed as input. For
example, the user might want to add a description of the
calculation(s) specified in the input or notes on the purpose of the
task(s), or other informational comments. The {\tt eof} directive can
also be used to remove a task (or series of tasks) from the
calculation without actually removing the relevant input directives
from the file. Any lines in the file that occur after the {\tt eof}
directive are ignored by the program.
intermediate energies and gradients as such are not of interest in
this case, so output from the SCF and MP2 modules is disabled with the
\verb+PRINT+ directives.
\section{Input Format and Syntax for Directives}
\label{sec:syntax}

4
doc/user/intro.tex
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@ -1,7 +1,7 @@
\label{sec:intro}
NWChem is a computational chemistry package designed to run on
high-performance parallel supercomputers and workstation clusters.
high-performance parallel supercomputers.
Code capabilities include the calculation of molecular electronic
energies and analytic gradients using Hartree-Fock self-consistent field (SCF) theory, Gaussian
density function theory (DFT), and second-order perturbation theory.
@ -14,7 +14,7 @@ NWChem is scalable, both in its ability to treat large problems
efficiently, and in its utilization of available parallel computing
resources. The code uses the parallel programming tools TCGMSG and
the Global Array (GA) library developed at PNNL for the High Performance
Computing and Communication Initiative (HPCCI) grand-challenge
Computing and Communication (HPCC) grand-challenge
software program and the Environmental Molecular Sciences Laboratory
(EMSL) Project. NWChem has been optimized to perform calculations on
large molecules using large parallel computers, and it is unique in

5
doc/user/nwarch.tex
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@ -127,8 +127,9 @@ example above, the \verb+SET+ directive is as follows:
\end{verbatim}
NWChem will automatically check for such indirections when loading
geometries. The other database object, \verb+"basis set"+, functions
in a similar fashion, using the default name \verb+"ao basis"+.
geometries. Storage of data associated with basis sets, the other
database resident object, functions in a similar fashion, using the
default name \verb+"ao basis"+.
\section{Persistence of data and restart}
\label{sec:persist}

4
doc/user/titlepage.tex
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@ -9,11 +9,11 @@
{\bf\Huge Release \nwchemversion}\\[1.0in]
{\bf\Large High Performance Computational Chemistry Group\\
Environmental Molecular Sciences Laboratory\\
W.R.\ Riley Environmental Molecular Sciences Laboratory\\
Pacific Northwest National Laboratory\\
P.O. Box 999, Richland, WA 99352\\[0.5in]}
{\bf\Large April 1997}\\[1.0in]
{\bf\Large March 1998}\\[1.0in]
%\psfig{figure=zsm.major.ps,height=4in,width=4in}

109
doc/user/top-level.tex
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@ -37,15 +37,22 @@ The \verb+START+ directive indicates that the calculation is one in
which a new database is to be created. Any relevant information that
already exists in a previous database of the same name is destroyed.
The string variable {\tt <file\_prefix>} will be used as the prefix to
name any files created in the course of the calculation. If the user
does not specify an entry for {\tt <file\_prefix>} on the \verb+START+
directive (or omits the \verb+START+ directive 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 \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.
name any files created in the course of the calculation.
E.g., to start a new calculation on water, one might specify
\begin{verbatim}
start water
end
which would result in all files beginning with {\tt "water."}.
If the user does not specify an entry for {\tt <file\_prefix>} on the
\verb+START+ directive (or omits the \verb+START+ directive
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
\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.
The user also has the option of
specifying a unique name for the database, using the keyword {\tt
@ -200,8 +207,8 @@ other scratch files in \verb+/scratch+:
\begin{verbatim}
scratch_dir /scratch 0:/piofs/rjh
\end{verbatim}
\item Put scratch files from Process 1 in directory \verb+scr1+, those from
Process 2 in \verb+scr2+, and so forth, in a round-robin fashion, using the
\item Put scratch files from Process 0 in directory \verb+scr1+, those from
Process 1 in \verb+scr2+, and so forth, in a round-robin fashion, using the
given list of directories:
\begin{verbatim}
scratch_dir /scr1 /scr2 /scr3 /scr4 /scr5
@ -219,11 +226,13 @@ given list of directories:
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
is not specified, memory is allocated according to installation-dependent
defaults. These should generally suffice for most
calculations, since the defaults usually correspond to the total amount
of memory available on the machine. The general form of the directive
is as follows:
is not specified, memory is allocated according to
installation-dependent defaults. {\em These defaults should generally
suffice for most calculations, since the defaults usually correspond
to the total amount of memory available on the machine. It should
usually be unncessary to provide a memory directive.}
The general form of the directive is as follows:
\begin{verbatim}
MEMORY [[total] <integer total_size>] \
@ -381,10 +390,12 @@ once, by Process 0 when the input file is read.
\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, and if omitted, the
character string containing the input title will be empty. The format for
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,
and if omitted, the character string containing the input title will
be empty. Multiple {\tt TITLE} directives may appear in the input
file (e.g., the example file in Section {sec:realsample}) in which
case a task will use the one most recently specified. The format for
the directive is as follows:
\begin{verbatim}
@ -471,9 +482,12 @@ are:
``rtdb'' \> high \> Print names of RTDB entries\\
``rtdbvalues'' \> high \> Print name and values of RTDB entries\\
``ga summary'' \> medium \> Summarize GA allocations at job end \\
``ga stats'' \> high \> Print GA usage statistics at job end \\
``ma summary'' \> medium \> Summarize MA allocations at job end \\
``ma stats'' \> high \> Print MA usage statistics at job end \\
``version'' \> debug \> Print version number of all compiled routines \\
``version'' \> debug \> Print version number of all
compiled routines \\
``tcgmsg'' \> never \> Print TCGMSG debug information \\
\end{tabbing}
@ -506,15 +520,14 @@ The format of the directive is as follows:
SET <string name> [<string type default automatic>] <$type$ data>
\end{verbatim}
The entry for variable \verb+<name>+ is the name of some array or
object to be entered into the database. This must be specified
explicitly; there is no default. The variable \verb+<type>+, which is
The entry for variable \verb+<name>+ is the name of
data to be entered into the database. This must be specified; there is no default. The variable \verb+<type>+, which is
optional, allows the user to define a string specifying the type of
data in the array \verb+<name>+. The data type can be explicitly
specified as \verb+integer+, \verb+real+, \verb+double+,
\verb+logical+, or \verb+string+. If no entry for \verb+<type>+ is
specified on the directive, its value is inferred from the data type
of the {\em first} data element. In such a case, floating-point data
of the {\em first} datum. In such a case, floating-point data
entered using this directive must include either an exponent or a
decimal point, to ensure that the correct default type will be
inferred. The correct default type will be inferred for logical
@ -523,18 +536,21 @@ values if logical-true values are specified as \verb+.true.+,
\verb+.false.+, \verb+false+, or \verb+f+. One exeception to the
automatic detection of the data type is that the data type {\bf must}
be explicitly stated to input integer ranges, unless the first
elemenent in the list is an integer that is not a range (c.f.,
element in the list is an integer that is not a range (c.f.,
\ref{sec:syntax}). For example,
\begin{verbatim}
set atomid 1 3:7 21
set atomid 1 3:7 21
\end{verbatim}
will interpret the type as integer and the list input will work fine.
However,
will be interpreted as a list of integers. However,
\begin{verbatim}
set atomid 3:7 21
set atomid 3:7 21
\end{verbatim}
will not work since the first element will be interpreted as a
string and not an integer.
string and not an integer. To work around this feature, use instead
\begin{verbatim}
set atomid integer 3:7 21
\end{verbatim}
The \verb+SET+ directive is useful for providing indirection by
associating the name of a basis set or geometry with the standard
@ -573,7 +589,7 @@ geometries. The required input lines are as follows:
This input tells the code to perform MP2 energy calculations
on an argon dimer in the first task, and then
on the argon atom in the presence of the ``ghost'' basis of the other
atom at the same geometry.
atom.
The \verb+SET+ directive can also be used as an indirect means of
supplying input to a part of the code that does not have a separate
@ -594,7 +610,7 @@ database. The general form of the directive is as follows:
\end{verbatim}
This directive cannot be used with complex objects such as geometries
and basis sets\footnote{Complex objects are stored using structured
and basis sets\footnote{Complex objects are stored using a structured
naming convention that is not matched by a simple wild card.}. A
wild-card (*) specified at the end of the string \verb+<name>+ will
cause {\em all} entries whose name begins with that string to be
@ -634,23 +650,22 @@ the calculation terminates with an error condition.
\section{{\tt TASK} --- Perform a task}
\label{sec:task}
The \verb+TASK+ directive is used to tell the code what to do with the
input. The input directives are parsed sequentially until a
\verb+TASK+ directive is encountered, as described in Section
\ref{sec:inputstructure}. At that point, the calculation or operation
specified in the \verb+TASK+ directive is performed. When that task
is completed, the code looks for additional input to process until the
next \verb+TASK+ directive is encountered, which is then executed.
This process continues to the end of the input file. NWChem expects
the last directive before the end-of-file to be a \verb+TASK+
directive. If it is not, a warning message is printed. Since the
database is persistent, multiple tasks within one job behave {\em
exactly} the same as multiple restart jobs with the same sequence of
input.
The \verb+TASK+ directive is used to tell the code what to do. The
input directives are parsed sequentially until a \verb+TASK+ directive
is encountered, as described in Section \ref{sec:inputstructure}. At
that point, the calculation or operation specified in the \verb+TASK+
directive is performed. When that task is completed, the code looks
for additional input to process until the next \verb+TASK+ directive
is encountered, which is then executed. This process continues to the
end of the input file. NWChem expects the last directive before the
end-of-file to be a \verb+TASK+ directive. If it is not, a warning
message is printed. Since the database is persistent, multiple tasks
within one job behave {\em exactly} the same as multiple restart jobs
with the same sequence of input.
There are four main forms of the the \verb+TASK+ directive. The most
common form is used to tell the code at what level of theory to
perform electronic structure calculation, and which specific
perform an electronic structure calculation, and which specific
calculations to perform. The second form is used to specify tasks
that do not involve electronic structure calculations or tasks that
have not been fully implemented at all theory levels in NWChem, such