`chfl_frame` type¶

type chfl_frame¶

A chfl_frame contains data from one simulation step: the current unit cell, the topology, the positions, and the velocities of the particles in the system. If some information is missing (topology or velocity or unit cell), the corresponding data is filled with a default value.

Type fields:

% init [subroutine] :: chfl_frame%init()
% copy [subroutine] :: chfl_frame%copy()
% atoms_count [function] :: chfl_frame%atoms_count()
% add_atom [subroutine] :: chfl_frame%add_atom()
% atom [function] :: chfl_frame%atom()
% remove [subroutine] :: chfl_frame%remove()
% resize [subroutine] :: chfl_frame%resize()
% add_bond [subroutine] :: chfl_frame%add_bond()
% remove_bond [subroutine] :: chfl_frame%remove_bond()
% clear_bonds [subroutine] :: chfl_frame%clear_bonds()
% add_residue [subroutine] :: chfl_frame%add_residue()
% distance [function] :: chfl_frame%distance()
% angle [function] :: chfl_frame%angle()
% dihedral [function] :: chfl_frame%dihedral()
% out_of_plane [function] :: chfl_frame%out_of_plane()
% positions [function] :: chfl_frame%positions()
% velocities [function] :: chfl_frame%velocities()
% add_velocities [subroutine] :: chfl_frame%add_velocities()
% has_velocities [subroutine] :: chfl_frame%has_velocities()
% cell [subroutine] :: chfl_frame%cell()
% set_cell [subroutine] :: chfl_frame%set_cell()
% topology [function] :: chfl_frame%topology()
% set_topology [subroutine] :: chfl_frame%set_topology()
% guess_bonds [subroutine] :: chfl_frame%guess_bonds()
% step [function] :: chfl_frame%step()
% set_step [subroutine] :: chfl_frame%set_step()
% set [subroutine] :: chfl_frame%set()
% get [function] :: chfl_frame%get()
% properties_count [function] :: chfl_frame%properties_count()
% list_properties [subroutine] :: chfl_frame%list_properties()
% free [subroutine] :: chfl_frame%free()

subroutine chfl_frame%init([status])¶

Initialize this frame as an empty frame. This subroutine allocate memory which must be released with chfl_frame%free().

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_frame%copy(frame[, status])¶

Initialize this frame with a copy of frame. This subroutine allocate memory which must be released with chfl_frame%free().

Parameters:: frame [type(chfl_frame)] :: frame to copy
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_frame%atoms_count([status])¶

Get the current number of atoms in the frame in natoms.

Parameters:: natoms [integer] :: number of atoms in the frame
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_frame%add_atom(atom, position[, velocity, status])¶

Add a chfl_atom and the corresponding position and velocity data to this frame. velocity can be absent if no velocity is associated with this frame.

Parameters:

atom [type(chfl_atom)] :: atom to add to the frame
position (3) [real] :: atom position

Options:

velocity (3) [real,optional] :: atom velocity
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_frame%atom(index[, status])¶

Get access to the atom at the given index in this frame.

Any modification to the atom will be reflected in the frame. The frame will be kept alive, even if chfl_frame%free() is called, until chfl_atom%free() is also called on the atom returned by this function.

The atom returned by this function is a pointer that points directly inside the frame, and will be invalidated if any of the following function is called on the frame:

chfl_frame%resize()
chfl_frame%add_atom()
chfl_frame%remove()
chfl_frame%set_topology()

Calling any function on an invalidated pointer is undefined behavior. Even if the pointer if invalidated, it stills needs to be released with chfl_atom%free().

Return:: type (chfl_atom)
Parameters:: index [integer] :: Index of the atom in the frame
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_frame%remove(index[, status])¶

Remove the atom at the given index in the frame.

This modify all the atoms indexes after index, and invalidate any pointer obtained using chfl_frame%positions() or chfl_frame%velocities().

Parameters:: index [integer] :: index of the atom to remove
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_frame%resize(natoms[, status])¶

Resize the positions, velocities and topology in the frame, to have space for natoms atoms.

This function may invalidate any pointer to the positions or the velocities if the new size is bigger than the old one. In all the cases, previous data is conserved. This function conserve the presence or absence of velocities.

Parameters:: natoms [integer] :: the new number of atoms in the frame
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_frame%add_bond(i, j[, bond_order, status])¶

Add a bond between the atoms at indexes i and j in the frame’s topology, and optionaly set the bond_order. By default, a bond order of CHFL_BOND_UNKNOWN is used.

Possible bond orders are represented by an integer of kind chfl_bond_order.

Parameters:

i [integer] :: atomic index of the first atom of the bond
j [integer] :: atomic index of the second atom of the bond

Options:

bond_order [integer(chfl_bond_order)] :: order of the bond
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_frame%remove_bond(i, j[, status])¶

Remove any existing bond between the atoms at indexes i and j in the frame’s topology.

This function does nothing if there is no bond between i and j.

Parameters:

i [integer] :: atomic index of the first atom
j [integer] :: atomic index of the second atom

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_frame%clear_bonds([status])¶

Remove all bonds in this frame.

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_frame%add_residue(residue[, status])¶

Add a copy of residue to this frame’s topology.

The residue id must not already be in the topology, and the residue must contain only atoms that are not already in another residue.

Parameters:: residue [type(chfl_residue)] :: residue to add in the topology
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_frame%distance(i, j[, status])¶

Get the distance between the atoms at indexes i and j in this frame, accounting for periodic boundary conditions and expressed in angstroms.

Return:

real

Parameters:

i [integer] :: atomic index of the first atom of the pair
j [integer] :: atomic index of the second atom of the pair

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_frame%angle(i, j, k[, status])¶

Get the angle formed by the atoms at indexes i, j and k in this frame, accounting for periodic boundary conditions, and expressed in radians.

Return:

real

Parameters:

i [integer] :: atomic index of the first atom of the angle
j [integer] :: atomic index of the second atom of the angle
k [integer] :: atomic index of the third atom of the angle

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_frame%dihedral(i, j, k, m[, status])¶

Get the dihedral angle formed by the atoms at indexes i, j, k and m in this frame, accounting for periodic boundary conditions, and expressed in radians.

Return:

real

Parameters:

i [integer] :: atomic index of the first atom of the angle
j [integer] :: atomic index of the second atom of the angle
k [integer] :: atomic index of the third atom of the angle
m [integer] :: atomic index of the fourth atom of the angle

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_frame%out_of_plane(i, j, k, m[, status])¶

Get the out of plane distance formed by the atoms at indexes i, j, k and m in this frame, accounting for periodic boundary conditions. The result is expressed in angstroms.

This is the distance between the atom j and the ikm plane. The atom j is the center of the improper dihedral angle formed by i, j, k and m.

Return:

real

Parameters:

i [integer] :: atomic index of the first atom of the angle
j [integer] :: atomic index of the second atom of the angle
k [integer] :: atomic index of the third atom of the angle
m [integer] :: atomic index of the fourth atom of the angle

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_frame%positions(data, size[, status])¶

Get a pointer to the positions array from the frame.

This function gives access to chemfiles internal data structure, and do not perform any copy, both when reading and writing the positions.

The pointer is invalidated if any of the following function is called:

chfl_frame%resize(),
chfl_frame%remove(),
chfl_frame%add_atom()

When the memory of the frame is released (by calling chfl_frame%free()), the pointer is released too.

This function returns a Fortran pointer, which must be used in a pointer assignement context:

program example
    use iso_fortran_env, only: real64
    use chemfiles
    implicit none
    type(chfl_frame)      :: frame
    real(real64), pointer :: positions(:, :)

    call frame%init()
    call frame%resize(122)

    positions => frame%positions()

    call frame%free()
end program

Return:: real (3, :) [pointer]
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_frame%velocities([status])¶

Get a pointer to the velocities array from the frame.

This function gives access to chemfiles internal data structure, and do not perform any copy, both when reading and writing the velocities.

The pointer is invalidated if any of the following function is called:

chfl_frame%resize(),
chfl_frame%remove(),
chfl_frame%add_atom()

When the memory of the frame is released (by calling chfl_frame%free()), the pointer is released too.

This function returns a Fortran pointer, which must be used in a pointer assignement context:

program example
    use iso_fortran_env, only: real64
    use chemfiles
    implicit none
    type(chfl_frame)      :: frame
    real(real64), pointer :: velocities(:, :)

    call frame%init()
    call frame%resize(122)
    call frame%add_velocities()

    velocities => frame%velocities()

    call frame%free()
end program

Return:: real (3, :) [pointer]
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_frame%add_velocities([status])¶

Add velocity data to this frame.

The velocities ar initialized to zero. If the frame already has velocities, this does nothing.

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_frame%has_velocities([status])¶

Check if this frame contains velocity data.

Return:: logical
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_frame%cell([status])¶

Get access to the cell of this frame

Any modification to the cell will be reflected in the frame. The frame will be kept alive, even if chfl_frame%free() is called, until chfl_cell%free() is also called on the cell returned by this function.

If chfl_frame%set_cell() is called, the cell returned by this function will point to the new cell.

Return:: type (chfl_cell)
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_frame%set_cell(cell[, status])¶

Set the chfl_cell of this frame to cell.

Parameters:: cell [type(chfl_cell)] :: new unit cell of the frame
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_frame%topology([status])¶

Get read-only access to the topology of this frame. Trying to write to the topology will give an error.

The frame will be kept alive, even if chfl_frame%free() is called, until chfl_topology%free() is also called on the topology returned by this function.

If chfl_frame%set_topology() is called, the topology returned by this function will point to the new topology.

Return:: type (chfl_topology)
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_frame%set_topology(topology[, status])¶

Set the chfl_topology of this frame to topology.

Calling this function with a topology that does not contain the right number of atom will return an error.

Parameters:: topology [type(chfl_topology)] :: new topology of the frame
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_frame%step([status])¶

Get the frame step, i.e. the frame number 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_frame%set_step(step[, status])¶

Set the frame step, i.e. the frame number in the trajectory to step.

Parameters:: step [integer] :: The new frame step
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_frame%guess_bonds([status])¶

Guess the bonds, angles and dihedrals in the frame.

The bonds are guessed using a distance-based algorithm, and then angles and dihedrals are guessed from the bonds.

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_frame%set(name, property[, status])¶

Add a new property with the given name to this frame.

If a property with the same name already exists, this function override the existing property with the new one.

property can either be a chfl_property, or any value that can be stored in a chfl_property: logical, real, string, or vector3d.

Parameters:

name [character(len=*)] :: property name
property [type(chfl_property)] :: the new property

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_frame%get(name[, status])¶

Get a copy of the property with the given name in this frame. If no property exist with this name, status will be set to CHFL_PROPERTY_ERROR.

The associated memory must be released by calling chfl_property%free().

Return:: type (chfl_property)
Parameters:: name [character(len=*)] :: property name
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_frame%properties_count([status])¶

Get the number of properties in this frame.

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_frame%list_properties(names[, status])¶

Fill the pre-allocated array names with the names of the properties in this frame. The array must have room for chfl_frame%properties_count() values of type character(len=CHFL_STRING_LENGTH).

Return:: integer
Parameters:: names (:) [character(len=CHFL_STRING_LENGTH)] :: list of properties names
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_frame%free()¶: Destroy a frame, and free the associated memory

chfl_frame type¶

`chfl_frame` type¶