Data File classes

SimpleDataFile

Class to handle simple data files, aka cvs files.

class pylam.SimpleDataFile(filename, header_prefix='#', delimiter=None)

Bases: pylam.base.IndexedFile

Class for a simple (csv) data file with an optional header line.

Parameters:

• filename (str) – file name
• header_prefix (str) – prefix of header line (default: #)
• delimiter (str) – string used to separate values (default: any whitespace)

Returns:

simple data file object

Return type:

SimpleDataFile

getRows(startRowIndex, endRowIndex)

Returns a part of the file as a numpy array.

Parameters:

• startRowIndex (int) – index of first data row
• endRowIndex (int) – index of last data row (included!)

Returns:

data

Return type:

numpy.ndarray

getRow(rowIndex)

Returns the data in row with index (0,1,..) as a numpy array.

Parameters:rowIndex (int) – index of data row in file Returns:data Return type:numpy.ndarray

getCol(idx)

Returns a whole column as a np.ndarray.

Parameters:idx (int) – column index Returns:column data Return type:np.ndarray

data

Returns:the whole data Return type:numpy.ndarray

header

Returns:the header line as list Return type:list

properHeader

Returns:tests if a proper header is defined Return type:bool

info()

Prints debug info to screen, e.g.:

file name        : example_data_files/simple.dat
data header      : ['Chunk', 'Coord1', 'Ncount', 'v_temp']
number of lines  : 491

columnName2Index(name)

Returns the column index for a given name as defined in the header. Therefore pylam.SimpleDataFile.properHeader must be True.

Parameters:name (str) – column name Returns:column index Return type:int

getColumnByName(name)

Returns a whole column as a np.ndarray.

Parameters:name (str) – column name Returns:column data Return type:np.ndarray

__len__()

Returns the number of data rows. (support for len())

next()

Returns the data of the next row from the file as numpy array.

FixBlockFile

class pylam.FixBlockFile(filename)

Bases: pylam.base.BlockFile

Class for LAMMPS fix data files.

Parameters:filename (str) – file name Returns:fix block data file object Return type:FixBlockFile

blockClass

Block class which is attached, here: pylam.DataBlock

alias of FixBlock

aveBlocks(bids)

Average over blocks.

Parameters:bids (list) – list of block ids to use for average Returns:numpy array containing the ‘average block’ Return type:numpy.ndarray

info()

Prints debug info to screen, e.g.:

file name        : example_data_files/chunk1D.dat
title            : Chunk-averaged data for fix TPROFILE and group all
data type        : Chunk-averaged
block header     : ['Timestep', 'Number-of-chunks', 'Total-count']
data header      : ['Chunk', 'Coord1', 'Ncount', 'v_temp']
block size       : 121
number of lines  : 491
number of blocks : 4
multi            : True

columnName2Index(name)

The index of the column with a given name.

Parameters:name (str) – name of the column (property) Returns:index of the column Return type:int

blocks2cols(colname, fix=[])

Extracts a selected column (property) from a each block and combines them.

For example, if chunk1D.dat looks like:

# Chunk-averaged data for fix TPROFILE and group all
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount v_temp
500000 121 2000
1 0.0881802 12.1949 0.842912
2 0.264541 12.09 0.842986
3 0.440901 12.0788 0.840996
...
1000000 121 2000
1 0.0881802 11.6526 0.841493
2 0.264541 11.7525 0.840792
3 0.440901 11.7087 0.842102
...
...

with

>>> import pylam
>>> FBF = pylam.FixBlockFile('chunk1D.dat')
>>> newTable = FBF.blocks2cols('v_temp', fix=['Chunk','Coord1'])
>>> newTable.write('new.dat')

new.dat will look like:

# Chunk Coord1 v_temp_0 v_temp_1 v_temp_2 v_temp_3
+1.00000000e+00 +8.81802000e-02 +8.42912000e-01 +8.41493000e-01 +8.40999000e-01 +8.43067000e-01
+2.00000000e+00 +2.64541000e-01 +8.42986000e-01 +8.40792000e-01 +8.45285000e-01 +8.40694000e-01
+3.00000000e+00 +4.40901000e-01 +8.40996000e-01 +8.42102000e-01 +8.40272000e-01 +8.44249000e-01
+4.00000000e+00 +6.17262000e-01 +8.37955000e-01 +8.37166000e-01 +8.39804000e-01 +8.38266000e-01

Parameters:

• colname – selected column to collect
• fix – common column (like, e.g. ‘Bin’)

Returns:

Table object

Return type:

pylam.base.Table

LogFile

This class provides a access to the log file (log.lammps). The thermodynamic info block(s) are made accessable as ThermoBlock objects.

class pylam.LogFile(filename)

Bases: pylam.base.BlockFile

Class for LAMMPS log files.

Parameters:filename (str) – log file name Returns:log file object Return type:LogFile

blockClass

Block class which is attached, here: pylam.ThermoBlock

alias of ThermoBlock

info(re=False)

Prints debug info to screen, e.g.:

file name:        example_data_files/log.lammps
units:            real
N atoms           1372
N runs:           3
total run time:   3682.2074 sec
total steps:      5010000

Parameters:re (bool) – recursive info for pylam.ThermoBlock