Gabriel WlazłowskiIntroduction
W-data was designed to satisfy the following requirements:
- Binary data is stored in a conceptually easy format that allows a variety of tools/languages to be used.
- Format provides storage for data with time stepping (frames / measurements / cycles).
- Data format is suitable for parallel processing (preferably with MPI I/O).
- Data is easy for processing via VisIt.
- It provides the extensible framework - new variables can be created and easily added to the existing dataset.
- Data is convenient for copy between computing systems.
- It allows for easy extraction / copy of selected variables
W-data format concept
Data set will consist of set of files, example:
test.wtxt # metadata file, this one should be indicated when opening in VisIt
test_density_a.wdat # binary file with data
test_delta.wdat # binary file with data
test_current_a.wdat # binary file with dataContent of test.wtxt may look like:
# Comments with additional info about data set
# Comments are ignored when reading by parser
nx 24 # lattice
ny 28 # lattice
nz 32 # lattice
dx 1 # spacing
dy 1 # spacing
dz 1 # spacing
datadim 3 # dimension of block size: 1=nx, 2=nx*ny, 3=nx*ny*nz
prefix test # prefix for files belonging to this data set, binary files have names `prefix_variable-name.format`
cycles 10 # number of cycles (measurements)
t0 0 # time value for the first cycle
dt -1 # time interval between cycles. If `dt` negative then time step is varying and is read from binary file `prefix__t.wdata`
# variables
# tag name type unit format
var density_a real none wdat
var delta complex none wdat
var current_a vector none wdat
# links
# tag name link-to
link density_b density_a
link current_b current_a
# consts
# tag name value unit
const eF 0.5 MeV
const kF 1 1/fmAccording to our experience, three types of variables (real, complex, vector) are sufficient and cover more less 90% of applications. However we have implemented a single precision (float in C notation) types denoted as real4, complex8 and vector4, to be consistent with the notation one can use real8, complex16 or vector8 exchengable for real, complex, vector.
Binary files store data as row arrays, called datablocks:
The size of datablock depends on variable type and data dimensionality.
-
real/real8:
blocksize=blocklength*8 Bytes -
real4:
blocksize=blocklength*4 Bytes -
complex/complex16:
blocksize=blocklength*16 Bytes -
complex8:
blocksize=blocklength*8 Bytes -
vector/vector8:
blocksize=blocklength*3*8 Bytes -
vector4:
blocksize=blocklength*3*4 Bytes
where blocklength is
- for datadim=3:
blocklength=nx*ny*nz - for datadim=2:
blocklength=nx*ny - for datadim=1:
blocklength=nx
Note that for vector variables we use following storage pattern:
To compute time associated with given cycle we use the wdata_set_time() function. Which takes as parameters wdata_metadata struct, icycle current number of cycle and current_time which will be calculated.
!Note
If dt is positive (to be precise, non negative) then we assume evenly distributed times, according to formula: current_time=t0 + icycle*dt. Hovewer if dt is negative then current_time parameter has to be calculated by the user and parsed to the function in which binary file is created and the value is stored. For more information see Example.
Let's get back to the *wtxt file.
W-data format allows for the representation of the following elements:
-
variable:
Each variable is represented by the binary file of nameprefix_varname.format. The variable description has following format:
var name type unit format
Following formats are allowed:-
wdat: default format for WSLDA codes. Binary files contain row data (no header). -
dpca: (deprecated) previous format of cold atomic codes. Binary file contains header of size 68B where additional info about file content is stored. For this format wdata lib provides only reading functionality. -
npy: binary files are numpy arrays. Functionality under construction
In order to switch WSLDA codes to writing in this format add to input file:
dataformat npy
-
-
link:
It is an alternative name for a given variable. In the case of
WSLDAcodes in many cases, we do the computation for systems that exhibit some symmetries, like spin symmetry. Then densities for spin-a and spin-b particles are exactly the same. In order to save disk space we can save only one of them:
var density_a real none wdat
and for another one set link:
link density_b density_a -
constant:
Typically besides variables, we have some constants that are useful during the data analysis process. For example, when making plots it is convenient to express variables in dimensionless form, like delta/eF. To provide user info what are values of selected constants we useconstfield:
const eF 0.5
W-data C library
Folder lib/wdata contains library that provides support for w-data processing.
List of examples demonstrating how to use this library are presented below. One can see more detailed descritption of each of it in Examples
- example-write.c: code creates artificial set of variables and writes them do wdat files.
- example-write-many.c: code creates artificial set of variables and writes them do wdat files. The differnence between the above is the non repeating parts of the code, however it introduces some limitations.
- example-write-many-t_varying.c: code creates artificial set of variables and writes them do wdat files.
- example-read.c: code reads data from wdat files (created by example-write.c).
- example-addvar.c: code adds new variable to existing data set (created by example-write.c).
In order to compile examples (optionally you will need to modify Makefile):
[wtools@dell cold-atoms]$ cd lib/wdata/
[wtools@dell lib/wdata]$ make