H5hut
src

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TABLE OF CONTENTS
--------------------

[1] Quick Guide 

--- For h5pAttrib
[2] To see number of timesteps in a h5part file
[3] To see file attributes in a h5part file
[4] To see step attributes in a h5part file
[5] To see dataset in a h5part file
[6] Providing more than one flag at once for h5pAttrib

--- For h5pToGNUplot
[7] What parameters to provide
[8] How to create an input file to GNUplot


************************************************************************************************


[1] Quick Guide 
------------------

--> -h option will display a concise help page.

$>> ./h5pAttrib -h

usage: h5pAttrib [OPTIONS] file

  OPTIONS
   -h, --help           Print help page
   -n, --nstep          Print number of steps
   -A, --fileA          Print file attributes
   -a, --stepA          Print step attributes & values for time step n
   -d, --dataset        Print data sets names & values for time step n
   -H, --header         Print shorter version without the values

  Examples:

  1) Show file attribute names & values of sample.h5part

        h5pAttrib -A sample.h5part

  2) Show step attribute names for time step 5 of sample.h5part

        h5pAttrib -a 5 -H sample.h5part
        
        
$>> ./h5pToGNUplot -h

usage: h5pToGNUplot -t TIMESTEP -1 VARIABLE#1 -2 VARIABLE#2 -i INPUTFILE [OPTIONAL_FLAGS]

  FLAGS
   -h, --help           Print help page
   -1, --1var           (REQUIRED) Takes first variable parameter
   -2, --2var           (REQUIRED) Takes second variable parameter
   -i, --input          (REQUIRED) Takes input file name
   -t, --timestep       (REQUIRED) Sets the timestep (Value -1 will result in dumping values of all timesteps.)
   -o, --output         (OPTIONAL) Takes output file name (without this flag, the program will print to stdout)
   -n, --number         (OPTIONAL) Sets number of output points
   -s, --start          (OPTIONAL) Sets the starting particle index

  Examples:

  1) Create GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54

        h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt

  2) Create GNU plot file output.txt from sample.h5part by ploting x vs px for timestep 54
     using 1200 points from particle index 76

        h5pToGNUplot -t 54 -1 x -2 px -i sample.h5part -o output.txt -s 76 -n 1200

************************************************************************************************
--- For h5pAttrib
************************************************************************************************

[2] To see number of timesteps in a h5part file
--------------------------------------------------

EXAMPLE>>

$>> ./h5pAttrib -n sample.h5part

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Printing number of timesteps for: sample.h5part ...

There are total 252 number of timesteps.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

done


[3] To see file attributes in a h5part file
----------------------------------------------

EXAMPLE>>

$>> ./h5pAttrib -A sample.h5part

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Printing file attributes for: sample.h5part ...

The number of file attributes for file sample.h5part is 0 ...
There are no file attributes.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

done


NOTE: -H option will omit the list of values of file attributes.


[4] To see step attributes in a h5part file
----------------------------------------------

EXAMPLE>>

$>> ./h5pAttrib -a 2 sample.h5part

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Printing step attributes for: sample.h5part ...

The number of step attributes for timestep #2 is 10 ...

Attribute #0 = Step
There are 1 elements in the attribute
Attribute Type is H5T_NATIVE_INT64
Printing 1 element value(s):
COUNT[0]: 2

Attribute #1 = Spos
There are 1 elements in the attribute
Attribute Type is H5T_NATIVE_DOUBLE
Printing 1 element value(s):
COUNT[0]: 0.143580

Attribute #2 = structLen
There are 1 elements in the attribute
Attribute Type is H5T_NATIVE_DOUBLE
Printing 1 element value(s):
COUNT[0]: 2.393000

.
.
.


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

done


NOTE: -H option will omit the list of values of step attributes.


[5] To see dataset in a h5part file
--------------------------------------

EXAMPLE>>

$>> ./h5pAttrib -d 2 -H sample.h5part

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Printing names of datasets for: sample.h5part ...

The number of datasets for timestep #2 is 7 ...

Dataset Name #0 = id
Dataset Type is H5T_NATIVE_INT64
Number of elements: 67587

Dataset Name #1 = px
Dataset Type is H5T_NATIVE_DOUBLE
Number of elements: 67587

Dataset Name #2 = py
Dataset Type is H5T_NATIVE_DOUBLE
Number of elements: 67587

Dataset Name #3 = pz
Dataset Type is H5T_NATIVE_DOUBLE
Number of elements: 67587

Dataset Name #4 = x
Dataset Type is H5T_NATIVE_DOUBLE
Number of elements: 67587

Dataset Name #5 = y
Dataset Type is H5T_NATIVE_DOUBLE
Number of elements: 67587

Dataset Name #6 = z
Dataset Type is H5T_NATIVE_DOUBLE
Number of elements: 67587

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

done


NOTE: -H option will omit the list of values of dataset attributes.

[6] Providing more than one flag at once
-------------------------------------------

When more than one flags are provided, one result after another will be displayed.

EXAMPLE>>

$>> ./h5pAttrib -H -a 1 -d 1 sample.h5part

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Printing step attributes for: sample.h5part ...

The number of step attributes for timestep #1 is 10 ...

Attribute #0 = Step
Attribute #1 = Spos
Attribute #2 = structLen
Attribute #3 = org
Attribute #4 = maxX
Attribute #5 = minX
Attribute #6 = maxP
Attribute #7 = minP
Attribute #8 = centroid
Attribute #9 = nloc
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Printing names of datasets for: sample.h5part ...

The number of datasets for timestep #1 is 7 ...

Dataset Name #0 = id
Dataset Type is H5T_NATIVE_INT64
Number of elements: 60214

Dataset Name #1 = px
Dataset Type is H5T_NATIVE_DOUBLE
Number of elements: 60214

Dataset Name #2 = py
Dataset Type is H5T_NATIVE_DOUBLE
Number of elements: 60214

Dataset Name #3 = pz
Dataset Type is H5T_NATIVE_DOUBLE
Number of elements: 60214

Dataset Name #4 = x
Dataset Type is H5T_NATIVE_DOUBLE
Number of elements: 60214

Dataset Name #5 = y
Dataset Type is H5T_NATIVE_DOUBLE
Number of elements: 60214

Dataset Name #6 = z
Dataset Type is H5T_NATIVE_DOUBLE
Number of elements: 60214

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

done

************************************************************************************************
--- For h5pAttrib
************************************************************************************************

[7] What parameters to provide
---------------------------------

When you execute the program with -h option, it displays what flags are necessary and what flags
are optional.

   -h, --help           Print help page
   -1, --1var           (REQUIRED) Takes first variable parameter
   -2, --2var           (REQUIRED) Takes second variable parameter
   -i, --input          (REQUIRED) Takes input file name
   -t, --timestep       (REQUIRED) Sets the timestep (Value -1 will result in dumping values of all timesteps.)
   -o, --output         (OPTIONAL) Takes output file name (without this flag, the program will print to stdout)
   -n, --number         (OPTIONAL) Sets number of output points
   -s, --start          (OPTIONAL) Sets the starting particle index


[8] How to create an input file to GNUplot
---------------------------------------------

EXAMPLE>>
Create input file to GNUplot that plots x vs. y.

$>> ./h5pToGNUplot -1 x -2 y -t 1 -i sample.h5part -o output.txt
$>> cat output.txt
-0.390779       -0.254793
-0.396527       -0.252781
-0.375362       -0.285137
-0.396527       -0.252781
-0.379917       -0.283147
-0.390779       -0.254793
-0.387536       -0.287346
-0.371787       -0.319797
-0.379917       -0.283147
-0.378967       -0.326058
-0.378976       -0.326078
-0.387536       -0.287346
-0.378957       -0.326069
-0.379917       -0.283147
-0.388762       -0.265390
-0.371787       -0.319797
-0.390779       -0.254793
-0.376825       -0.266804
-0.379917       -0.283147
-0.375362       -0.285137
...

Then run GNUplot...

$>> gnuplot

        G N U P L O T
        Version 4.0 patchlevel 0
        last modified Thu Apr 15 14:44:22 CEST 2004
        System: Linux 2.6.11.4-21.11-smp

        Copyright (C) 1986 - 1993, 1998, 2004
        Thomas Williams, Colin Kelley and many others

        This is gnuplot version 4.0.  Please refer to the documentation
        for command syntax changes.  The old syntax will be accepted
        throughout the 4.0 series, but all save files use the new syntax.

        Type `help` to access the on-line reference manual.
        The gnuplot FAQ is available from
                http://www.gnuplot.info/faq/

        Send comments and requests for help to
                <gnuplot-info@lists.sourceforge.net>
        Send bugs, suggestions and mods to
                <gnuplot-bugs@lists.sourceforge.net>


Terminal type set to 'x11'
gnuplot> plot "output.txt"

This will open a GNUplot window that plots output.txt.