This document describes the Silo file browser, an application program built on the Silo library for interactive viewing of Silo database files.
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The schnauzer is a small terrier with a wiry coat; the browser is a utility built on Silo for reading scientific database files. The browser command line is
browser [switches] [--]
[files]...
The browser recognizes the following command line switches. Single letter switches that don't require an argument can be grouped together (so ‘-l -q’ is the same as ‘-lq’). When a single-letter switch takes an argument the argument can appear either immediately after the letter or as the next argument such as ‘-l3’ or ‘-l 3’. Long format switches are introduced by double hyphens and if they take an argument it must follow an equal sign such as ‘--eval=exit’. Command-line options take effect before the initialization file is read, but also override any settings made in that file.
Invoking the browser with the switch ‘--help’ will show a complete list of command-line switches and their descriptions.
-A tolerance--absolute=tolerance-R tolerance--absolute=tolerance-V--version-d words--diff=wordsdiff function of the
browser. The words should be a comma-separated list of key words
which will be assigned to the $diff browser variable. See its
documentation for details.
-e expression--eval=expression-E list--exclude=list$exclude variable is set to the comma-separated list
of names and/or datatypes supplied as an argument to this switch. The
switch may appear more than once. The names in the $exclude list
will be excluded from recursive diff operations. See
documentation for $exclude for details.
-f initfile--file=initfile-h--help-l [value]--lowlevel[=value]$lowlevel browser
variable, which causes the browser to load database objects as type
DBobject even if the object is some other composite Silo datatype
like DBquadvar. If value is specified then it will be
assigned to the $lowlevel variable; otherwise the value ‘1’
is assigned.
-c [value]--checksums[=value]$checksums browser
variable, which controls browser's use of checksums during read.
-n lines--height=linesioctl calls, but this switch can be used to override that
choice. The setting is valid only until the browser receives a
SIGWINCH signal and queries the terminal size.
-q--quiet$verbosity variable to zero.
-o--obase=format$obase to format,
which should be ‘16’ for hexadecimal, ‘8’ for octal, ‘2’
for binary, or anything else for the default decimal format. It controls
how integer, floating-point, character, and string data are
displayed. The default is that these types of data are displayed with a
type-dependent printf format string which is user defined (e.g.,
$fmt_int).
-r [boolean]--rdonly[=boolean]$rdonly browser
variable, which causes the browser to open all subsequent files in
read-only mode. Files that only have Unix read permission are always
opened in read-only mode, but the browser issues a warning if the user
had asked for read-write permission. If no argument is given for this
switch then true is assumed. The default if this switch does not appear
is false.
-s [boolean]--single[=boolean]DBForceSingle with a value
of one or zero depending on whether the argument is true or false. If no
argument is given then it is assumed to be true. Calling
DBForceSingle with a non-zero value causes most drivers to return
floating point data with the C float type rather than the default
double type.
-v--verbose$verbosity variable to two.
-w columns--width=columnsioctl calls, but this switch overrides that
choice.
--debug[=boolean]If Silo database file names are specified then the files are opened in
the order specified and associated with file symbols $1,
$2, etc. These are opened before the initialization file is read,
which happens before any --eval statements are executed. However,
the command-line options are reevaluated after the initialization file
is read.
The browser command syntax is quite simple, consisting of function calls, operators, atoms, and lists. Comments begin with a hash mark and continue to the end of the line (except in strings). White space is generally ignored except as a token separator. Statements can be continued across multiple lines, but a backslash must escape the linefeed if the partial statement looks syntactically complete.
A function call is a parenthetical expression where the first element is
the name of the function and the subsequent elements are the arguments
to that function. Most functions evaluate all their arguments but
others evaluate only some (or none). For example, the Assign
function doesn't evaluate its first argument, but rather assignes the
evaluated second argument to the l-value specified by the first
argument. The parentheses can be omitted from around the top-level
function call. Say ‘help func’ (or ‘(help func)’) for a list
of all functions.
Most browser operators are infix, binary operators. They take two operands, one on each side of the operator, and call some function which is bound to the operator. For example the expression ‘foo=1’ is equivalent to ‘(Assign foo 1)’. The ‘{}’ operator takes any number of arguments which appear between the open and close curly braces. Say ‘help operators’ for a list of all operators.
The browser has three types of atoms: strings, numbers, and symbols. A string is a sequence of characters enclosed in single or double quotes. The normal C escaping mechanism can be used for special characters within the string. A single quote has no special significance in a double-quoted string and vice versa. Numbers are positive or negative sequences of decimal digits with an optional embedded decimal point and trailing exponent. An exponent consists of the letter `e' or `E' followed by an optional sign and one or more decimal digits. A symbol is any sequence of alphanumeric characters and may also include dollar signs, hyphens, underscores, and various other characters (although their use is discouraged).
A list consists of zero or more atoms or lists enclosed in parentheses. Evaluation of the list results in the browser looking up the functional value of the first member of the list and calling that function with the subsequent list members as arguments. Evaluation of the list can be suppressed by using curly braces instead of parentheses (e.g., ‘{1 3 5}’ is equivalent to ‘(Quote 1 3 5)')’.
The browser reads commands interactively from its standard input. If available, the GNU readline library is used allowing the user to edit commands as they are entered using Emacs or vi editing commands. To quote from the readline library (documentation is available at http://www.cs.utah.edu/csinfo/texinfo/texinfo.html):
Often during an interactive session you type in a long line of text, only to notice that the first word on the line is misspelled. The Readline library gives you a set of commands for manipulating the text as you type it in, allowing you to just fix your typo, and not forcing you to retype the majority of the line. Using these editing commands, you move the cursor to the place that needs correction, and delete or insert the text of the corrections. Then, when you are satisfied with the line, you simply press <RETURN>. You do not have to be at the end of the line to press <RETURN>; the entire line is accepted regardless of the location of the cursor within the line.
The readline library default mode is Emacs. If you prefer vi key
bindings, then create a file called .inputrc in your home
directory with the single line ‘set editing-mode vi’.
Some of the browser functions have more than one form and are overloaded to do various things depending on the number of actual arguments supplied. Arguments shown between ‘[’ and ‘]’ are optional.
array dimensions ... basetypecd dirname [filesym]close filesym ...diff objects...diff command. If called with an even number of arguments the
argument list is split in half and each argument from the first half is
compared with the corresponding argument of the second half. If called
with no arguments then the argument list will be the SILO files from the
command-line (‘$1’, ‘$2’, etc.). If called with just one
argument which is an object from the silo file ‘$1’ then that
object will be compared to an object with the same name from file
‘$2’. The behavior is influenced by the ‘$diff’ browser
variable. In general, if no differences are found then no output is
produced.
endexit.
exit [status]file filenamels or diff commands which can take file objects as
arguments. For instance, the command ‘ls (file curv2d.pdb)’ opens
the curv2d.pdb file and lists the root directory and ‘ls
(cd dirname (file curv2d.pdb))’ lists the contents of the dirname
directory of curv2d.pdb. The file is open for read-write mode
unless the $rdonly browser variable has a non-nil value or the
file has only read permission.
help [topic] [docstring]help
subcommands. With one argument it will display documentation for a help
category (e.g., help run), a browser internal variable (e.g.,
help $diff), a function (e.g., help diff), a command-line
switch (e.g., help --diff), an operator (e.g., help
"op="), or the documentation string associated with the specified
symbol. When invoked with a string argument it will print all help
categories which contain the specified string (e.g., help
"diff"). When called with two arguments it assigns the second argument
as the documentation property of the first argument, which must be a
symbol or string.
include filenamels [filesym] [objnames...]fnmatch function was not available when the browser was
compiled. If a single object name is supplied and that object is a
directory, then the contents of that directory appear. An alternative
(and shorter) way to list the contents of a subdirectory is to type the
name of the subdirectory on a line by itself (for instance,
‘dir1’).
noprintprint.
open filename [filesym]$rdonly browser variable has a non-nil value or the file has only
read permission.
no]print expression ...print command is normally not used because the browser
prints all non-null expressions by default. However, a noprint
can be used to prevent the default output.
pwd [filesym]quitexit.
typeof expressionA browser expression is composed of terms and operators. The following operators are supported and overloaded depending on the number and type of arguments.
= value. varname. fieldname. anything[ elmtnum ][ min : max ][ expr1, expr2, ... ]| command> file>> file{ expressions }: maximumCertain aspects of the browser can be configured by setting browser variables with the ‘=’ operator described above. The current value of an internal variable can be displayed by typing the variable's name. The variables are initialized with default values when the browser starts and may then be overridden by command-line options, the initialization file, or interactively. All predefined browser variables begin with a dollar sign.
These variables affect the operation of the diff function.
$diffdiff function. The default is $diff = {detail,
two_column}. This variable is set by the ‘--diff’ command-line
switch.
detaildiff function to report all
details about detected differences.
briefdiff doesn't actually display any
data. The output will consist of a single line for each file object
which differs between file A and file B. This option allows some
short circuiting of the work required for the detail mode.
summarydiff to report by a single line of output
when the two operands of the diff function are different. No
output is produced if they are the same. This option allows some short
circuiting of the work required for the brief mode.
ignore_additionsdiff will not report differences due to
data appearing in file B but not in file A.
ignore_deletionsdiff will not report differences due to
data appearing in file A but not in file B.
two_columnpdbdiff instead of diff). This setting is only applicable
for detailed output.
$excludediff function normally recurses into directories and compares
the contents of those directories. However, the $exclude variable
can be a list of character strings which specify object names and/or
types which should be excluded from recursive comparison. The object
names may include shell wildcards such as ‘*’, ‘?’, and
‘[]’. If a name pattern is relative (doesn't start with a slash) it
will be compared to the base name of the objects about to be
differenced; but if the name pattern is absolute (begins with a slash)
it will be compared to the full path names of the objects being
differenced. If the $exclude string begins with the string
‘type:’ then the following part should be one of the object types
printed by the ls function. A difference operation between two
objects is suppressed if either object matches any of the strings stored
in the $exclude list.
For example, to prevent diff from comparing any objects with the
base name ‘cycle’, or any objects whose full name is
‘/VM/typelist’, or any objects whose name ends with ‘_list’,
or any object of type ‘obj’ one would issue the following browser
command:
> $exclude = {"cycle", "/VM/typelist", "*_list", "type:obj"}
or invoke the browser with the switch
--exclude='cycle,/VM/typelist,*_list,type:obj'
$diff_int8_abs$diff_int8_rel$diff_short_abs$diff_short_rel$diff_int_abs$diff_int_rel$diff_long_abs$diff_long_rel$diff_float_abs$diff_float_rel$diff_double_abs$diff_double_reldiff function determines whether
two numeric values are the same or different. The ones that end with
‘_abs’ specify the maximum absolute difference allowed between two
values a and b. The diff command considers a
and b to be different if ‘|a-b|>abs’.
The variables that end with ‘_rel’ specify the maximum absolute
difference relative to the mean of two values. The diff command
considers a and b to be different if
‘|a-b|/|a+b| > rel/2’.
If both tests are performed then a and b are considered different if either test indicates they are different. If an abs or rel parameter is not defined (or has a non-positive value) then the corresponding test is not performed. If neither test is performed then an exact comparison is used.
All diff variables have a default value of zero and are set by
the ‘--absolute’ and ‘--relative’ command-line switches.
$heightSIGWINCH).
$widthSIGWINCH).
$verbosity$truncate$trailing$fmt_doubleprintf format string which is used to
format C double values. The default value is ‘%1.10g’.
$fmt_floatprintf format string which is used to
format C float values. The default value is ‘%1.5g’.
$fmt_intprintf format string which is used to
format integer values. The default value is ‘%d’.
$fmt_longprintf format string which is used to
format long integer values. The default value is ‘(long)%ld’.
$fmt_nullprintf format string which is printed for
null character strings. The default value is ‘(null)’.
$fmt_int8printf format string which is used to
format 8-bit integer values. The default is ‘(int8)%d’ but people
often like to change it to ‘`%c'’ to see the ASCII equivalent. Be
warned that output of non-printable ASCII characters in this manner may
not work if the terminal emulator interprets them as commands.
$fmt_shortprintf format string which is used to
format short integer values. The default value is ‘(short)%d’.
$fmt_stringprintf format string which is used to
format character string values. The default value is
‘\"%s\"’.
$obase Output of primitive data (integer, character, string, and$fmt_ variables described
above. However, by setting this variable to 16, 8, or 2 it is possible
to display primitive data in hexadecimal, octal, or binary format.
$pubinit$lowlevelDBobject even if that object has some other datatype such as
DBquadvar. This variable is set by the ‘-l’ command-line
option and is useful for debugging the low layers of Silo. The default
value is zero.
If the value is two or higher then the Silo definition of DBobject
is used and the values of the comp_names and pdb_names
arrays become part of the object.
If the value is one or two then the browser translates the Silo
DBobject structure into a structure which is more user friendly
by adding additional members to the object structure. Each member has a
name from the comp_names array and a value based on the
corresponding member of the pdb_names array2.
$checksumsIf checksum checks are disabled, then if browser encounters corrupt data,
it will not know it. In particular, if checksums are disabled, the diff
operator can wind up reporting corrupted data as diffs. If checksums are
enabled, however, and the database being read includes checksums, then
browser will report errors when it encounters corrupt data and fail to
read the associated Silo object. See the associated Silo call
DBSetEnableChecksums() for more information.
$rdonlyWhen the browser starts, it looks for a file called .browser_rc in the user's home directory or a file called /usr/local/include/browser_rc3. However, an alternate startup file can be specified with the ‘--file’ browser command-line switch. The browser reads and executes each command found in the startup file.
The startup file should contain an assignment to the
$browser_version variable which will be used to check that the
version of the startup file is appropriate for the browser being
run. Mismatched version numbers result in a rather verbose warning
message (provided that the browser was even able to process the startup
file).
The $browser_version number should be assigned some real constant
like ‘3.004’ where ‘3’ is the browser major version number and
‘004’ is the browser minor version number. To determine what
version number to specify, invoke the browser as ‘browser
--version’.
The ‘=’ operator can be used to set the value of an internal browser variable or to change the value of a database object. If the left hand side of the ‘=’ is an internal variable, then the value of the internal variable is changed. Otherwise if the left hand side is a database object, its value is changed. Otherwise, a new internal variable is created and assigned an initial value.
The browser can change values for objects of type DBobject (most
objects are of this type if the browser is running in low-level mode) or
objects under the ‘var(s)’ category in a directory listing.
When changing the value of a string database object like
‘_fileinfo’, the new value will be truncated to the same length as
the old value because of limitations in the underlying Silo database
drivers. This does not apply to string fields of a DBobject.
Assigning a scalar value to an array or slice of an array results in all selected elements of the array to be set to the same value. For instance, if the type of ‘u_data’ is ‘[31, 41, 31] float’ then the statement `u_data[5]=0' sets all elements of “row” five to zero.
The browser keeps track of how many lines of output have been displayed
for the currently executing command and temporarily pauses that command
whenever output is about to scroll off the top of the screen. The
height and width of the screen is determined by the browser making
certain ioctl calls at startup and each time it gets a
SIGWINCH signal. The initial values can be set with
‘--height’ and ‘--width’ command-line switches. If the
appropriate ioctl is not available then the values of environment
variables LINES and COLUMNS will be used. If all else
fails then the browser uses zero for the number of lines (that is, no
paging of output) and 80 for the number of columns.
When the browser pauses the output, the message ‘more? ('q' to quit)’ is displayed. The following user responses are recognized:
SIGPIPE signal.
Output redirected to a file or command is not paged. If the user is not satisfied with the limited paging ability of the browser, the output from a command can be redirected to the pager of the user's choice using output redirection.
Output from any browser command can be redirected to a file or shell command by appending a redirection character and file name or shell command to the end of the command.
To save the output of a command in a file, destroying the previous contents of the file if any, append a ‘>’ and the name of the file. Unless the file name looks like a browser symbol it must be enclosed in quotes. For instance, ‘quadvar3d > saved’ saves the value of Silo database variable ‘quadvar’ in a text file named saved.
To append the output of a command to a file, append a ‘>>’ and the file name to the end of the command. Unless the file name looks like a browser symbol it must be enclosed in quotes. For example, ‘typeof quadvar3d >> saved’ appends type information to the saved file.
To send the output of a browser command to the standard input of a shell command, follow the browser command with a ‘|’ followed by the shell command in quotes. The quotes are not necessary if the shell command is a single symbol. Since paging is disabled when output is to a shell command, one way to display a result without paging is to pipe the output through the ‘cat’ command like ‘d | cat’.
Since some commands may require a long time to execute or produce a huge amount of output, the user may want to abort the command before it finishes. If the output is paged interactively to the screen then pressing ‘q’ at the ‘more?’ prompt accomplishes this. Otherwise the user can press the interrupt character (usually control-c) and the browser command will be immediately terminated and the browser will prompt for the next command. If the interrupt character is typed during command input the browser itself terminates.
If output from a browser command is being piped into a shell command and
the shell command exits (or closes its standard input) before the
browser command is finished, the browser command gets the SIGPIPE
signal and terminates.
This chapter contains some sample output from the browser.
Normally, you will specify the name of a database file on the browser command-line4 like in the following example, and sometimes it's convenient to open multiple files at the same time. Each file name listed on the command-line is given an identifier like ‘$1’, ‘$2’, etc., and most of the browser commands operate on file ‘$1’ by default.
% browser rect3d.pdb
INFO: opening `rect3d.pdb' as $1
The ls command is similar to the Unix ls command in that
it lists the contents of the current working directory. The heading
fields on the left of the equal signs apply until the next heading. The
headings are the same as those used by MeshTV. To list the contents of
some subdirectory, say ‘ls’, ‘ls dir1’,
‘print dir1’, or just ‘dir1’.
> ls
qmesh(s) = quadmesh3d
qvar(s) = d p
= t u
= v w
mat(s) = mat1
var(s) = _fileinfo _meshtv_defvars
= _meshtvinfo cycle
= d_data d_dims
= d_maxindex dtime
= mat1_dims mat1_matlist
= mat1_matnos mat1_mix_mat
= mat1_mix_next mat1_mix_vf
= mat1_mix_zone p_data
= p_dims p_maxindex
= quadmesh3d_align_nodal quadmesh3d_align_zonal
= quadmesh3d_coord0 quadmesh3d_coord1
= quadmesh3d_coord2 quadmesh3d_dims
= quadmesh3d_max_extents quadmesh3d_max_index_n
= quadmesh3d_max_index_z quadmesh3d_min_extents
= quadmesh3d_min_index quadmesh3d_zonedims
= t_data t_dims
= t_maxindex time
= u_data u_dims
= u_maxindex v_data
= v_dims v_maxindex
= w_data w_dims
= w_maxindex
To keep the size of these examples small, we've specified that at most 50 values should be printed from each array and that 25 of those values should be from the end of the array (and the other 25, from the beginning). To truncate everything say ‘$truncate=0’ and to turn truncating off say ‘$truncate=nil’.
> $truncate = 50
= 50
> $trailing = 25
= 25
The user can ask for the type of any object, including types built into the browser. If the object is a structured type (like in this example) then the type of each component of that structure is printed.
> typeof d
= struct DBquadvar {
id = +0 int
name = +4 string
units = +8 string
label = +12 string
cycle = +16 int
time = +20 float
dtime = +24 double
meshid = +32 int
datatype = +40 int (DBdatatype)
nels = +44 int
nvals = +48 int
ndims = +52 int
dims = +56 [3] int
major_order = +68 int (array order)
stride = +72 [3] int
min_index = +84 [3] int
max_index = +96 [3] int
origin = +108 int
align = +112 [3] float
mixlen = +128 int
use_specmf = +132 int (on/off)
mixvals = +124 *[1] *[0] float
vals = +36 *[1] *[36000] float
= }
An integer following a plus sign indicates that the type corresponds to a byte offset from the beginning of the innermost enclosing structure or array.
A ‘*’ means the object is a pointer to whatever type follows5.
A list of array dimensions between ‘[’ and ‘]’ mean that the object is an array and each element of the array is the type that follows the ‘]’.
The final name is always one of the browser integral types ‘string’ (same as the C ‘char*’), ‘short’, ‘int’, ‘long’, ‘float’, or ‘double’. If the integral type name is followed by parentheses then the parentheses contain the name of an underlying C ‘enum’ type or a set of related C preprocessor constants.
Some data objects override one or more standard class methods. Such objects will have flags like ‘__flag__’ which appear inside the object type.
One can also ask for the Silo definition of a named data type like ‘DBquadvar’. This prints the definition of the Silo ‘DBquadvar’ structure which is the same as printed above for the type of ‘d’ except that array sizes and some primitive types are not bound to actual values yet6.
> DBquadvar
= struct DBquadvar {
id = +0 int
name = +4 string
units = +8 string
label = +12 string
cycle = +16 int
time = +20 float
dtime = +24 double
meshid = +32 int
datatype = +40 int (DBdatatype)
nels = +44 int
nvals = +48 int
ndims = +52 int
dims = +56 [self.ndims] int
major_order = +68 int (array order)
stride = +72 [self.ndims] int
min_index = +84 [self.ndims] int
max_index = +96 [self.ndims] int
origin = +108 int
align = +112 [self.ndims] float
mixlen = +128 int
use_specmf = +132 int (on/off)
mixvals = +124 *[self.nvals] *[self.mixlen]
mixvals = self.datatype
vals = +36 *[self.nvals] *[self.nels] self.datatype
= }
Giving just the name of the Silo object is short for ‘print $1.d’. Notice that the ‘vals’ array has been truncated as requested and that mixvals has no value. The subscripts in the labels to the left of the equal sign correspond to the first value on that line (an entire array in the case of ‘vals[0]’.
One can also ask for tye type of a single structure component by typing the command ‘DBquadvar.vals’.
> d
= DBquadvar: struct
id = 0
name = "d"
units = (null)
label = (null)
cycle = 48
time = 4.80000
dtime = 4.8000000000
meshid = 0
datatype = float
nels = 36000
nvals = 1
ndims = 3
dims[0] = {30, 40, 30}
major_order = row major
stride[0] = {1, 30, 1200}
min_index[0] = {0, 0, 0}
max_index[0] = {29, 39, 29}
origin = 0
align[0] = {0.50000, 0.50000, 0.50000}
mixlen = 0
use_specmf = off
mixvals = NULL
vals[0] = {{0.83957, 0.82083, 0.80304, 0.78626, 0.77056,
vals[0, 5] = 0.75601, 0.74266, 0.73059, 0.71987, 0.71055,
vals[0, 10] = 0.70269, 0.69633, 0.69153, 0.68831, 0.68669,
vals[0, 15] = 0.68669, 0.68831, 0.69153, 0.69633, 0.70269,
vals[0, 20] = 0.71055, 0.71987, 0.73059, 0.74266, 0.75601,
vals[0, 25] = ...(35950 values omitted)..., 0.75601,
vals[0, 35976] = 0.74266, 0.73059, 0.71987, 0.71055, 0.70269,
vals[0, 35981] = 0.69633, 0.69153, 0.68831, 0.68669, 0.68669,
vals[0, 35986] = 0.68831, 0.69153, 0.69633, 0.70269, 0.71055,
vals[0, 35991] = 0.71987, 0.73059, 0.74266, 0.75601, 0.77056,
vals[0, 35996] = 0.78626, 0.80304, 0.82083, 0.83957}}
The browser does not attempt to be efficient about loading objects from the database into memory since the underlying Silo library makes it difficult to do so. However, if one says ‘$lowlevel=1’ then the browser uses lower-level Silo functions to read the file. As a result, less data is moved from disk to memory.
> $lowlevel=1
= 1
> d
= struct
name = "d"
type = "quadvar"
meshid = "quadmesh"
align = "/quadmesh_align_zonal"
dims = "/d_dims"
max_index = "/d_maxindex"
value0 = "/d_data"
ndims = 3
nvals = 1
nels = 36000
origin = 0
datatype = 19
mixlen = 0
major_order = 0
cycle = 48
time = "/time"
dtime = "/dtime"
min_index = "/quadmesh_min_index"
use_specmf = -1000
Now we'll decrease the number of values printed and increase the precision that's displayed for ‘float’ values.
> $truncate = 12
= 12
> $trailing = 6
= 6
> $fmt_float = "%1.15f"
= "%1.15f"
> d.vals[0]
[0] = {0.839570403099060, 0.820833325386047,
[2] = 0.803043246269226, 0.786264479160309,
[4] = 0.770563006401062, 0.756006062030792,
[6] = ...(35988 values omitted)...,
[35994] = 0.756006062030792, 0.770563066005707,
[35996] = 0.786264479160309, 0.803043246269226,
[35998] = 0.820833325386047, 0.839570462703705}
The ‘diff’ command compares two objects and reports differences between them. The output is in groups of differences where the group is delimited at the beginning and end by a line of stars. The first half of the group displays (part of) the first argument to ‘diff’ while the part of the group after the line of dashes displays (part of) the second argument. Subobjects that differ only partially (‘stride’ in this case) appear separately before those which completely differ. The array truncating parameters apply to each array segment individually.
> diff d p
***************
stride[1] = {30, 1200}
---------------
stride[1] = {31, 1271}
***************
***************
name = "d"
nels = 36000
dims[0] = {30, 40, 30}
max_index[0] = {29, 39, 29}
vals[0] = {{0.839570403099060, 0.820833325386047,
vals[0, 2] = 0.803043246269226, 0.786264479160309,
vals[0, 4] = 0.770563006401062, 0.756006062030792,
vals[0, 6] = ...(35988 values omitted)...,
vals[0, 35994] = 0.756006062030792, 0.770563066005707,
vals[0, 35996] = 0.786264479160309, 0.803043246269226,
vals[0, 35998] = 0.820833325386047, 0.839570462703705}}
---------------
name = "p"
nels = 39401
dims[0] = {31, 41, 31}
max_index[0] = {30, 40, 30}
vals[0] = {{1.190943479537964, 1.218125700950623,
vals[0, 2] = 1.245107889175415, 1.271674990653992,
vals[0, 4] = 1.297584056854248, 1.322565793991089,
vals[0, 6] = ...(39389 values omitted)...,
vals[0, 39395] = 0.000000000000000, 0.000000000000000,
vals[0, 39397] = 0.000000000000000, 0.000000000000000,
vals[0, 39399] = 0.000000000000000, 0.000000000000000}}
***************
A compound array is composed of zero or more subarrays. A subarray can be printed by saying something like ‘carray.b’, but a subarray is also printed by saying just ‘b’ as long as ‘b’ is not some other type of object and ‘b’ exists in exactly one compound array.
> carray
= struct
name = "carray"
id = 0
nelems = 3
nvalues = 18
datatype = float
a[0] = {0.00000, 0.34185, 0.64252, 0.86576}
b[0] = {0.98468, 0.98496, 0.86656, 0.64374, 0.34335,
b[5] = 0.00159}
c[0] = {-0.34036, -0.64130, -0.86496, -0.98441,
c[4] = -0.98523, -0.86735, -0.64495, -0.34485}
> b
[0] = {0.98468, 0.98496, 0.86656, 0.64374, 0.34335,
[5] = 0.00159}
> b[2]
[2] = {0.86656}
If the file is opened for reading and writing (the default) then variables can be given new values. The new values are written back to the file immediately.
> _fileinfo
= "3D rectilinear test file"
> _fileinfo = "testing"
= "testing"
> _fileinfo
= "testing"
A scalar variable assigned to an array (or slice of an array) sets all the elements of that array (or slice) to the specified value. A list of values enclosed in curly braces can be assigned to an array (or slice of an array) causing each element of the array (or slice) to be set to one of the listed values.
> typeof v_data
= [31, 41, 31] float
> v_data = 0
= 0
> v_data[0, 0, 2:4]
= {0, 0, 0}
> v_data[0, 0, 2:4] = {0.111, 0.222, 0.333}
= {0.111, 0.222, 0.333}
> v_data
[0, 0, 0] = {0, 0, 0.111, 0.222, 0.333, 0,
[0, 0, 6] = ...(39389 values omitted)..., 0, 0, 0,
[30, 40, 28] = 0, 0, 0}
Pressing control-c during a browser command aborts the command, but pressing control-c when the browser is asking for input aborts the browser. It is more polite to press control-d or type ‘exit’ instead since this gives the browser a chance to properly close database files.
> $truncate = nil
> d >data_file
control-c
Command aborted.
> control-c
%
[1] In contrast, pressing the interrupt character during an interactive browser command aborts the command but not the browser.
[2] Changes
should not be made to the comp_names or pdb_names arrays
since the Silo DBobject is regenerated from the user-friendly
fields before being saved back to the file.
[3] The path name may be different depending on how the browser was compiled.
[4] Opening a file on the command line is the same as saying ‘open "rect3d.pdb" $1’ interactively.
[5] Whether or not something is a pointer is generally not important to using the browser: a 1d array of pointers to 1d arrays of integers can be treated like a ragged-edge 2d array of integers.
[6] The word ‘self’ refers to the object corresponding to the innermost structure which incloses the ‘self’.