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.

The initialization routine for chfl_trajectory are:

• chfl_trajectory%open();
• chfl_trajectory%with_format().

The memory liberation routine is chfl_trajectory%close().

Type fields:

% open [subroutine] :: chfl_trajectory%open() % with_format [subroutine] :: chfl_trajectory%with_format() % nsteps [subroutine] :: chfl_trajectory%nsteps() % read [subroutine] :: chfl_trajectory%read() % read_step [subroutine] :: chfl_trajectory%read_step() % write [subroutine] :: chfl_trajectory%write() % set_topology [subroutine] :: chfl_trajectory%set_topology() % topology_file [subroutine] :: chfl_trajectory%topology_file() % set_cell [subroutine] :: chfl_trajectory%set_cell() % close [subroutine] :: chfl_trajectory%close()

subroutine chfl_trajectory%open(path, mode[, 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.

Parameters:	character (len=*) :: path to the trajectory file mode [character] :: opening mode
Options:	status [integer,optional, kind=chfl_status] :: status code of the operation. If it is not equal to CHFL_SUCCESS, you can learn more about the error by using chfl_last_error.

subroutine chfl_trajectory%with_format(path, mode, format[, status])¶

Open the trajectory at the given path using a specific file format and the given mode.

This is be needed when the file format does not match the extension, or when there is not standard extension for this format. Valid modes are 'r' for read, 'w' for write and 'a' for append.

If format is an empty string, the format will be guessed from the extension.

Parameters:	character (len=*) :: path to the trajectory file mode [character] :: opening mode character :: format to use
Options:	status [integer,optional, kind=chfl_status] :: status code of the operation. If it is not equal to CHFL_SUCCESS, you can learn more about the error by using chfl_last_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 [chfl_frame] :: frame to fill with the data
Options:	status [integer,optional, kind=chfl_status] :: status code of the operation. If it is not equal to CHFL_SUCCESS, you can learn more about the error by using chfl_last_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 [chfl_frame] :: frame to fill with the data
Options:	status [integer,optional, kind=chfl_status] :: status code of the operation. If it is not equal to CHFL_SUCCESS, you can learn more about the error by using chfl_last_error.

subroutine chfl_trajectory%write(frame[, status])¶

Write a single frame to the trajectory.

Parameters:	frame [chfl_frame] :: frame to be writen to the file
Options:	status [integer,optional, kind=chfl_status] :: status code of the operation. If it is not equal to CHFL_SUCCESS, you can learn more about the error by using chfl_last_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 [chfl_topology] :: new topology to use
Options:	status [integer,optional, kind=chfl_status] :: status code of the operation. If it is not equal to CHFL_SUCCESS, you can learn more about the error by using chfl_last_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:	character (len=*) :: file to read in order to get the new topology
Options:	format [string,optional] :: format to use for the topology file status [integer,optional, kind=chfl_status] :: status code of the operation. If it is not equal to CHFL_SUCCESS, you can learn more about the error by using chfl_last_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 [chfl_cell] :: new cell to use
Options:	status [integer,optional, kind=chfl_status] :: status code of the operation. If it is not equal to CHFL_SUCCESS, you can learn more about the error by using chfl_last_error.

subroutine chfl_trajectory%nsteps(nsteps[, status])¶

Store the number of steps (the number of frames) from the trajectory in nsteps.

Parameters:	nsteps [integer] :: number of steps
Options:	status [integer,optional, kind=chfl_status] :: status code of the operation. If it is not equal to CHFL_SUCCESS, you can learn more about the error by using chfl_last_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.

Options:	status [integer,optional, kind=chfl_status] :: status code of the operation. If it is not equal to CHFL_SUCCESS, you can learn more about the error by using chfl_last_error.