Io read block

thmd.io.read_block

Classes:

• LmpLogFile –

  Create an Object of LOG file.

• LmpRDF –

  class to read Radial Distribution Fuction (RDF) file from Lammps compute

• LmpAveChunk –

  class to read Radial Distribution Fuction (RDF) file from Lammps compute

• PlumHistogram –

  Create an Object of DUMP file

Functions:

• average_df_list –

  compute average of list of DataFrame

LmpLogFile(logfile=None)

Create an Object of LOG file.

Notes

• run 0 without data

Udpate

• 2024-10-10: use Polars DataFrame instead of Pandas Series

Parameters:

• logfile (str, default: None ) –

  file_name of LOG file

Returns:

• Obj ( LmpLogFile ) –

  LmpLogFile object

Methods:

• read_log –

  Read LAMMPS logfile

read_log(logfile)

Read LAMMPS logfile Args: logfile (str): input LOG file

Returns:

• Obj ( LmpLogFile ) –

  LmpLogFile object

LmpRDF(file_name: str)

class to read Radial Distribution Fuction (RDF) file from Lammps compute

Attributes:

• file_name (str) –

  file name

• frame (DataFrame) –

  3d pandas Frame (multi-row-index DataFrame)

Methods:

• ReadRDF –

  read RDF file

• AverageRDF –

  the Average RDF

initiate object

Parameters:

• file_name (str) –

  file_name

Returns:

• Obj ( LmpAveChunk ) –

  LmpAveChunk object

Examples:

RDF = LmpAveChunk('rdf.txt')

Methods:

• read_RDF –

  Args:

• compute_AveRDF –

  compute average of RDF over all frames

read_RDF(file_name: str)

Parameters:

• file_name (str) –

  input RDF file

Returns:

• Obj ( LmpRDF ) –

  LmpRDF object

compute_AveRDF()

compute average of RDF over all frames

Returns:

• df ( DataFrame ) –

  Average of RDF

LmpAveChunk(file_name)

class to read Radial Distribution Fuction (RDF) file from Lammps compute

Attributes:

• file_name (str) –

  file name.

• frame (DataFrame) –

  3d pandas Frame (multi-row-index DataFrame).

Methods:

• ReadRDF –

  read RDF file

• AverageRDF –

  the Average RDF

initiate object

Parameters:

• file_name (str) –

  file_name

Returns:

• Obj ( LmpAveChunk ) –

  LmpAveChunk object

Examples:

RDF = LmpAveChunk('LmpAveChunk.txt')

Methods:

• read_AveChunk –

  Args:

• compute_AveChunk –

  compute average of RDF over all frames

read_AveChunk(file_name)

Parameters:

• file_name (str) –

  input RDF file

Returns:

• Obj ( LmpAveChunk ) –

  LmpAveChunk object

compute_AveChunk()

compute average of RDF over all frames

Returns:

• df ( DataFrame ) –

  Average of RDF

PlumHistogram(file_name)

Create an Object of DUMP file

Methods:

• read_histogram –

  read Histogram file

• average_histogram –

  the Average Histogram

• AreaHisto –

  Area under pdf curve

• find_tail –

  find limit of histogram

• find_center –

  find center of histogram

Examples:

from thmd.io.read_block import PlumHistogram
RDF = PlumHistogram(file_name='myRDF.txt')

initiate object

Parameters:

• file_name (str) –

  file_name

Returns:

• Obj ( PlumHistogram ) –

  PlumHistogram object

Methods:

• read_histogram –

  Args:

• compute_average_histogram –

  compute average of histogram over all frames

• areaHisto –
• fit_std_gaussian –

  Fit the average-histogarm to Standard Gaussian function

• find_tail –

  Find tail of distribution function

• find_center –

  Find tail of distribution function

read_histogram(file_name: str)

Parameters:

• file_name (str) –

  input HISTOGRAM file

Returns:

• Obj ( PlumHistogram ) –

  update PlumHistogram object

compute_average_histogram()

compute average of histogram over all frames

Returns:

• df ( DataFrame ) –

  DataFrame of avergave histogram

areaHisto()

fit_std_gaussian()

Fit the average-histogarm to Standard Gaussian function

Returns:

• amp, miu, sigma) (tuple –

  parameters of Gaussian function

find_tail(tol=0.0001, gridSize=1e-06)

Find tail of distribution function

Parameters:

• tol (float, default: 0.0001 ) –

  tolerance

• gridSize (float, default: 1e-06 ) –

  size of grid

Returns:

• left_tail ( float ) –

  limit on the left side

• right_tail ( float ) –

  limit on the right side

find_center(gridSize=1e-06)

Find tail of distribution function

Parameters:

• gridSize (float, default: 1e-06 ) –

  size of grid

Returns:

• Xcenter ( float ) –

  center of the distribution function

average_df_list(list_df: list[pl.DataFrame]) -> pl.DataFrame

compute average of list of DataFrame

Parameters:

• list_df (list) –

  list of DataFrame

Returns:

• df ( DataFrame ) –

  Average of list of DataFrame