chfl_trajectory type

type  chfl_trajectory

The chfl_trajectory type is the main entry point when using chemfiles. A chfl_trajectory behave a like a file, allowing to read and/or write chfl_frame.

Type fields:
subroutine  chfl_trajectory%open(path, mode[, format, status])

Open the file at the given path using the given mode. Valid modes are 'r' for read, 'w' for write and 'a' for append.

If format is not given or an empty string, the format will be guessed from the extension.

This subroutine allocate memory which must be released with chfl_trajectory%close().

Parameters:

  • path [character(len=*)] :: path to the trajectory file

  • mode [character] :: opening mode

Options:

  • format [character(len=*)] :: format to use to read and write to the file

  • status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine  chfl_trajectory%memory_reader(data, format[, status])

Read the data memory buffer as though it were a formatted file. The format parameter is required and may contain a compression method.

This subroutine allocate memory which must be released with chfl_trajectory%close().

Parameters:

  • data [character(len=*)] :: memory to read

  • format [character(len=*)] :: format uses to read the buffer

Options:

status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine  chfl_trajectory%memory_writer(format[, status])

Write to a memory buffer as though it were a formatted file

The format parameter is required. To retrieve the memory written to by the chfl_trajectory, use chfl_trajectory%memory_buffer.

This subroutine allocate memory which must be released with chfl_trajectory%close().

Parameters:

format [character(len=*)] :: format used to write to the file

Options:

status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine  chfl_trajectory%memory_buffer(buffer[, status])

Obtain the memory buffer written to by the chfl_trajectory.

Parameters:

buffer [character(len=:),allocatable] :: buffer to fill with the data written to this trajectory

Options:

status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine  chfl_trajectory%path([status])

Get the path used to open the trajectory. If the path is longer than CHFL_STRING_LENGTH, it will be truncated.

Return:

character (len=CHFL_STRING_LENGTH)

Options:

status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

function  chfl_trajectory%nsteps([status])

Get the number of steps (the number of frames) in the trajectory.

Return:

integer

Options:

status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine  chfl_trajectory%read(frame[, status])

Read the next step of the trajectory into a frame.

If the number of atoms in frame does not correspond to the number of atom in the next step, the frame is resized.

Parameters:

frame [type(chfl_frame)] :: frame to fill with the data

Options:

status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine  chfl_trajectory%read_step(step, frame[, status])

Read a specific step of the trajectory into a frame. The first trajectory step is the step 0.

If the number of atoms in frame does not correspond to the number of atom in the step, the frame is resized.

Parameters:

  • step [integer] :: step to read

  • frame [type(chfl_frame)] :: frame to fill with the data

Options:

status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine  chfl_trajectory%write(frame[, status])

Write a single frame to the trajectory.

Parameters:

frame [type(chfl_frame)] :: frame to be writen to the file

Options:

status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine  chfl_trajectory%set_topology(topology[, status])

Set the topology associated with the trajectory. This topology will be used when reading and writing the files, replacing any topology in the frames or files.

Parameters:

topology [type(chfl_topology)] :: new topology to use

Options:

status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine  chfl_trajectory%topology_file(path[, format, status])

Set the topology associated with the trajectory by reading the first frame of the file at the given path using the file format in format; and extracting the topology of this frame.

If format is an empty string or not given, the format will be guessed from the extension.

Parameters:

path [character(len=*)] :: file to read in order to get the new topology

Options:

  • format [character(len=*)] :: format to use for the topology file

  • status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine  chfl_trajectory%set_cell(cell[, status])

Set the unit cell associated with the trajectory. This cell will be used when reading and writing the files, replacing any pre-existing unit cell.

Parameters:

cell [type(chfl_cell)] :: new cell to use

Options:

status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine  chfl_trajectory%close([status])

Close a trajectory file, and free the associated memory.

Closing a file will synchronize all changes made to the file with the storage (hard drive, network, …) used for this file.