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WRspice: documentation updates for mmjco, TJM and JJ, implicit print.
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81 changes: 60 additions & 21 deletions wrspice/help/spCommands.hlp
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Expand Up @@ -136,34 +136,66 @@ qhelp
quit
version

!! commands.tex 011721
!! commands.tex 083122
!!KEYWORD
commands
!!TITLE
Built-in Commands
!!HTML
When a line is entered, it is interpreted as one of several
things. First, it may be an <a href="alias">alias</a>, in which
When a line is entered, it is interpreted in one of several
ways.

<ol>
<li>An alias<br>
First, it may be an <a href="alias">alias</a>, in which
case the line is replaced with the result after alias
substitution, and the line is re-parsed. Second, it may be the
name of a <a href="codeblock">codeblock</a>, which is a
user-defined command obtained from a script file, in which case
the codeblock is executed. Third, it may be a pre-defined
command, in which case it is executed. Fourth, it may be an
assignment statement, which consists of a vector name, an '='
symbol, and an expression, in which case it is executed as if it
were preceded by the word "<tt>let</tt>". Fifth, it may be the
name of a circuit file, in which case it is loaded as if with a <a
href="source"><b>source</b></a> command, or it may be the name of
a command script - <i>WRspice</i> searches the current <a
href="sourcepath"><tt>sourcepath</tt></a> (search path) for the
file and executes it when it is found. The effect of this is
identical to the effect of "<tt>source</tt> <i>file</i>", except
that the variables <tt>argc</tt> and <tt>argv</tt> are set.
Finally, it may be a UNIX command, in which case if the variable
<a href="unixcom"><tt>unixcom</tt></a> is set, it is executed as
substitution, and the line is re-parsed.

<p>
<li>A codeblock<br>
Second, it may be the name of a <a href="codeblock">codeblock</a>,
which is a user-defined command obtained from a script file, in
which case the codeblock is executed.

<p>
<li>A command<br>
Third, it may be a pre-defined command, in which case it is
executed.

<p>
<li>An assignment, implicit <a href="let"><b>let</b></a><br>
Fourth, it may be an assignment statement, which consists of a
vector name, an '=' symbol, and an expression, in which case it is
executed as if it were preceded by the word "<tt>let</tt>".

<p>
<li>A circuit filename, implicit <b>source</b><br>
Fifth, it may be the name of a circuit file, in which case it is
loaded as if with a <a href="source"><b>source</b></a> command, or
it may be the name of a command script -- <i>WRspice</i> searches
the current <a href="sourcepath"><tt>sourcepath</tt></a> (search
path) for the file and executes it when it is found. The effect
of this is identical to the effect of "<tt>source</tt>
<i>file</i>", except that the variables <tt>argc</tt> and
<tt>argv</tt> are set.

<p>
<li>An operating system command<br>
Sixth, it may be a command known to the hosting operating system,
in which case if the variable <a
href="unixcom"><tt>unixcom</tt></a> is set, it is executed as
though it were typed to the operating system shell.

<p>
<li>An expression list, implicit <b>print</b><br>
Finally, if the command line can be recognized as a list of
expressions, the <a href="print"><b>print</b></a> command is
invoked on the line.
</ol>




The following table lists all built-in commands understood by
<i>WRspice</i>.
<p>
Expand Down Expand Up @@ -2020,7 +2052,7 @@ load command
rawfilefmt
iocmds

!! commands.tex 092816
!! commands.tex 083122
!!KEYWORD
print
!!TITLE
Expand All @@ -2035,6 +2067,13 @@ print command
of the given <a href="explists">expressions</a> to the standard
output.

<p>
If command line input can be recognized as an expression list, the
print command will be invoked implicitly. In this case, the line
cannot contain directives or a format string, This saves a bit of
typing when using the <i>WRspice</i> command line as a calculator,
for example.

<p>
The default is to use exponential format for all values, with the
number of digits given by the <a href="numdgt"><tt>numdgt</tt></a>
Expand Down
184 changes: 183 additions & 1 deletion wrspice/help/spMain.hlp
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Expand Up @@ -3505,7 +3505,7 @@ printtoraw
proc2mod
wrspiced

!! utilities.tex 051222
!! utilities.tex 090222
!!KEYWORD
mmjco
!!TITLE
Expand Down Expand Up @@ -3903,6 +3903,188 @@ The <tt>mmjco</tt> Utility: Tunnel Junction Model Calculator
of <tt>mitmojco.py</tt> gave different values, and neither matched the
values provided in the amplitudes folder.

<h3>File Formats</h3>

<h4>TCA file formats</h4>

Tunnel current amplitude (TCA) tables are created by the
<tt>cd</tt> and <tt>cm</tt> commands. They consist of real and
imaginary parts of the pair and quasiparticle amplitudes, on a
scale of normalized potential across the structure, where the unit
value is the sum of the gap energies of the two electrodes. The
scale extends from 0 to 2 in these units.

<p>
There actually are three formats available, selectable with
options to the <tt>cd</tt> and <tt>cm</tt> commands.

<dl>
<dt>
option: <tt>-rd</tt><dd>
The file name is described in the previous section, with a suffix
"<tt>.data</tt>". This is a generic numerical format, consisting
of a comment line and six columns of numbers. The number of data
lines is the value given with the "<tt>-x</tt>" option to the
<tt>cd</tt> command, defaulting to 500. The example below
illustrates the format.
</dl>

<p>
<pre>
# X Jpair_real Jpair_imag Jqp_real Jqp_imag
0 1.00000e-03 7.50623e-01 2.85275e-04 -7.50625e-01 3.37356e-04
1 5.00601e-03 7.51136e-01 1.36358e-03 -7.51123e-01 1.62410e-03
2 9.01202e-03 7.51643e-01 2.27465e-03 -7.51594e-01 2.74301e-03
3 1.30180e-02 7.52144e-01 3.03372e-03 -7.52040e-01 3.70900e-03
...
498 1.99599e+00 4.22402e-01 -5.29166e-01 1.52235e-02 1.87539e+00
499 2.00000e+00 4.21420e-01 -5.28564e-01 1.51180e-02 1.87962e+00
</pre>

<p>
The other two options emit the data using the SPICE "rawfile"
format. This is a format developed for plot data in Berkeley
Spice3, which is supported by most plotting programs, including
Synopsys WaveView and the <a href="load"><b>load</b></a> function
of <i>WRspice</i>. The only difference is that one format ouptuts
complex numbers for two variables (pair and quasiparticle
amplitudes), while the other format outputs real values for four
variables (the real and imaginary parts of the amplitudes).

<dl>
<dt>
option: <tt>-r</tt><dd>
The file name is described in the previous section, with a suffix
"<tt>.raw</tt>". Output is in rawfile format using complex
numbers.
</dl>

<dl>
<dt>
option: <tt>-rr</tt><dd>
The file name is described in the previous section, with a suffix
"<tt>.raw</tt>". Output is in rawfile format using real numbers.
</dl>

<p>
The <a href="rawfilefmt">rawfile format</a> description can be
found in the <i>WRspice</tt> documentation.


<h4>Fit file format</h4>

A fit file contains a compacted digest of a TCA table, as
prescribed by the Odintsov, Semenov and Zorin (OSZ) algorithm.
These can be generated with the <tt>cf</tt> command. Fit files
can be used as input to simulators that contain a compatible
tunnel junction model (TJM). Presently, <i>WRspice</i> and
Synopsys HSPICE can use these files.

<p>
An example fit file is shown below.

<p>
<pre>
tcafit 4.2000e+00 1.3696e-03 1.3696e-03 0.008 500 8 0.200 3.9580e-2
-5.55136e+00, 7.35249e-02, 1.28573e+00, 1.08362e+01,-1.58776e-01, 2.87279e+01
-1.24623e-02, 1.00032e+00, 5.84894e-03,-4.50828e-04, 5.81876e-03,-2.11396e-04
-3.83312e-02, 1.00112e+00, 2.10779e-02,-3.09528e-04, 2.13882e-02, 1.13197e-03
-1.18261e-01, 9.98252e-01, 6.29481e-02, 1.95061e-03, 6.04875e-02, 1.68472e-02
-5.41049e-02, 7.52572e-07,-2.72420e-04, 5.67468e+00, 5.43002e-04, 2.37802e+00
-9.94491e-01, 6.50936e-01, 7.80341e-01, 1.14849e-01,-2.36003e-01, 9.49693e-01
-3.42835e-01, 9.60836e-01, 1.75970e-01, 1.81214e-02, 1.47672e-01, 1.40112e-01
-2.80018e-01, 6.49039e-03, 6.26863e-03, 1.81423e-01, 9.20013e-03, 3.23103e-02
</pre>

<p>
The first line is a header, the first word of which is "<tt>tcafit</tt>".
The numbers that follow in this line are:
<ul>
<li>The temperature in Kelvin (4.2000e+00).
<li>The left electrode pair-breaking energy in ev (1.3696e-03).
<li>The right electrode pair-breaking energy in ev (1.3696e-03).
<li>The smoothing parameter value used to create the TCA table,
<tt>-s</tt> option in the <tt>cd</tt> command for example (0.008).
<li>The number of scale points used in the TCA table, <tt>-x</tt>
option in the <tt>cd</tt> command for example (500).
<li>The number of terms used in the fit table, <tt>-n</tt> option
in the <tt>cf</tt> command (8).
<li>The value of the threshold parameter used when generating the
fit parameter table, <tt>-h</tt> option of the <tt>cf</tt> command
(0.200).
<li>Normalized quasiparticle current at x=0.8, used to estimate
the sub-gap conductance (3.9580e-2).
</ul>

<p>
Following the header line are six columns of real numbers. The
number of rows is equal to the "terms", which is the <tt>-n</tt>
option to the <tt>cf</tt> command. The columns are the OSZ
parameters P.real, P.imag, A.real, A.imag, B.real, B.imag.


<h4>Sweep file format</h4>

Temperature sweep files are concatenations of fit records as
described above for a temperature range. These allow rapid
temperature modeling through interpolation in supporting
simulators (<t>WRspice</i> and Synopsys HSPICE). Sweep files are
created with the <tt>cs</tt> command.

<p>
Below is an example temperature sweep file.

<p>
<pre>
tsweep 91 0.1000 0.1000 0.008 500 8 0.200
tcafit 1.0000e-01 1.4086e-03 1.4086e-03 1.3185e-02
-8.51331e+00, 1.15164e-01, 1.29900e+00, 1.11105e+01,-4.05570e-01, 5.65607e+01
-1.06700e-02, 1.00009e+00, 3.58651e-03,-2.25268e-04, 3.57013e-03,-5.66586e-05
-2.47980e-02, 1.00072e+00, 1.14692e-02,-5.49747e-04, 1.15840e-02,-1.07382e-04
-6.31470e-02, 1.00196e+00, 2.92347e-02,-1.70767e-03, 2.93324e-02, 2.09767e-03
-1.86179e+00, 9.23541e-01, 7.52628e-01,-8.71131e-02,-4.37397e-01, 2.11473e+00
-1.56178e-01, 1.00378e+00, 6.81933e-02,-6.76474e-03, 7.04144e-02, 1.46763e-02
-3.74403e-01, 1.01258e+00, 1.53951e-01,-3.71976e-02, 1.73747e-01, 7.86682e-02
-8.73847e-01, 1.06711e+00, 2.56553e-01,-1.53780e-01, 4.86150e-01, 3.82557e-01
tcafit 2.0000e-01 1.4086e-03 1.4086e-03 1.3185e-02
-8.51331e+00, 1.15164e-01, 1.29900e+00, 1.11105e+01,-4.05570e-01, 5.65607e+01
-1.06700e-02, 1.00009e+00, 3.58651e-03,-2.25268e-04, 3.57013e-03,-5.66586e-05
...
</pre>

<p>
The first line is a file header starting with the word "<tt>tsweep</tt>".
The numbers that follow on this line are:
<ul>
<li>The number of fit records contained in this file (91).
<li>The lowest temperature K used for fit parameters in the file,
this will be used in the first fit record (0.1000).
<li>The temperature delta K used in the sweep file (0.1000).
<li>The smoothing parameter, <tt>-s</tt> option, used to create
all TCA tables (0.008).
<li>The number of scale points, <tt>-x</tt> option, used to create
all TCA tables (500).
<li>The number of terms used for each fit table, <tt>-n</tt>
option (8).
<li>The value of the threshold parameter used in each fit table
(0.200).
</ul>

<p>
Following this header, fit records are concatenated. These are
similar to the format described above, the only difference is that
the header line is simplified to omit redundant information. The
fit record header contains the following value following the word
"<tt>tcafit</tt>".
<ul>
<li>The temperature in Kelvin (4.2000e+00).
<li>The left electrode pair-breaking energy in ev (1.3696e-03).
<li>The right electrode pair-breaking energy in ev (1.3696e-03).
<li>Normalized quasiparticle current at x=0.8, used to estimate
the sub-gap conductance (3.9580e-2).
</ul>


<h3>References</h3>

Background references from the MiTMoJCo project.
Expand Down
57 changes: 42 additions & 15 deletions wrspice/manual/commands.tex
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@@ -1,29 +1,50 @@
\chapter{{\WRspice} Commands}
\label{commands}

% spCommands.hlp:commands 011721
% spCommands.hlp:commands 083122

When a line is entered, it is interpreted as one of several things.
When a line is entered, it is interpreted in one of several ways.

\begin{enumerate}
\item{An alias}\\
First, it may be an alias, in which case the line is replaced with the
result after alias substitution, and the line is re-parsed. Second,
it may be the name of a codeblock, which is a user-defined command
obtained from a script file, in which case the codeblock is executed.
result after alias substitution, and the line is re-parsed.

\item{A codeblock}\\
Second, it may be the name of a codeblock, which is a user-defined
command obtained from a script file, in which case the codeblock is
executed.

\item{A command}\\
Third, it may be a pre-defined command, in which case it is executed.

\item{An assignment, implivit {\cb let}}\\
Fourth, it may be an assignment statement, which consists of a vector
name, an `{\vt =}' symbol, and an expression, in which case it is
executed as if it were preceded by the word ``{\vt let}''. Fifth, it
may be the name of a circuit file, in which case it is loaded as if
with a {\cb source} command, or it may be the name of a command script
-- {\WRspice} searches the current {\et sourcepath} (search path) for
the file and executes it when it is found. The effect of this is
identical to the effect of ``{\vt source} {\it file}'', except that
the variables {\et argc} and {\et argv} are set. Finally, it may be a
UNIX command, in which case if the variable {\et unixcom} is set, it
is executed as though it were typed to the operating system shell.
executed as if it were preceded by the word ``{\vt let}''.

\item{A circuit filename, implicit {\cb source}}\\
Fifth, it may be the name of a circuit file, in which case it is
loaded as if with a {\cb source} command, or it may be the name of a
command script -- {\WRspice} searches the current {\et sourcepath}
(search path) for the file and executes it when it is found. The
effect of this is identical to the effect of ``{\vt source} {\it
file}'', except that the variables {\et argc} and {\et argv} are set.

\item{An opeerating system command}\\
Sixth, it may be a command known to the hosting operating system, in
which case if the variable {\et unixcom} is set, it is executed as
though it were typed to the operating system shell.

\item{An expression list}\\
Finally, if the command line can be recognized as a list of
expressions, the {\cb print} command is invoked on the line.
\end{enumerate}


The following table lists all built-in commands understood by
{\WRspice}.
\newpage

\begin{longtable}{|l|l|}\hline
\multicolumn{2}{|c|}{\bf Control Structures}\\ \hline
Expand Down Expand Up @@ -1395,7 +1416,7 @@ \subsection{\spcmd{print}}
\index{print command}
\label{print}

% spCommands.hlp:print 092816
% spCommands.hlp:print 083122

The {\cb print} command is used to print vector data on-screen or
to a file using output redirection.
Expand All @@ -1405,6 +1426,12 @@ \subsection{\spcmd{print}}
The command prints the values of the given expressions to the standard
output.

If command line input can be recognized as an expression list, the
print command will be invoked implicitly. In this case, the line
cannot contain directives or a format string, This saves a bit of
typing when using the {\WRspice} command line as a calculator, for
example.

The default is to use exponential format for all values, with the
number of digits given by the {\et numdgt} variable. However this,
and some other presentation attributes, can be specified in the format
Expand Down
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