chfl_atom
type¶chfl_atom
¶A chfl_atom
is a particle in the current chfl_frame
. It stores the
following atomic properties:
The atom name is usually an unique identifier (H1
, C_a
) while the
atom type will be shared between all particles of the same type: H
,
Ow
, CH3
.
The initialization routine for chfl_atom
are:
Type fields: |
|
---|
chfl_atom%
init
(name[, status])¶Initialize this atom with the given name
, and set the atom type to
name
.
Parameters: | character (len=*) :: atom name |
---|---|
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 . |
chfl_atom%
copy
(atom[, status])¶Initialize this atom with a copy of atom
.
Parameters: | atom [chfl_atom] :: atom to copy |
---|---|
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 . |
chfl_atom%
from_frame
(frame, i[, status])¶Initialize this atom with a copy the atom at index i
from a frame
.
Parameters: |
|
---|---|
Options: | status [integer,optional, kind=chfl_status] :: status code of the
operation. If it is not equal to |
chfl_atom%
from_topology
(topology, i[, status])¶Initialize this atom with a copy the atom at index i
from a
topology
.
Parameters: |
|
---|---|
Options: | status [integer,optional, kind=chfl_status] :: status code of the
operation. If it is not equal to |
chfl_atom%
mass
(mass[, status])¶Get the mass of tah atom in mass
. The mass is in atomic mass units.
Parameters: | mass [real] :: atom mass |
---|---|
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 . |
chfl_atom%
set_mass
(mass[, status])¶Set the mass of the atom to mass
. The mass should be in atomic mass
units.
Parameters: | mass [real] :: new atom mass |
---|---|
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 . |
chfl_atom%
charge
(charge[, status])¶Get the charge of the atom in charge
. The charge is in number of the
electron charge e.
Parameters: | charge [real] :: The atom charge |
---|---|
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 . |
chfl_atom%
set_charge
(charge[, status])¶Get the charge of the atom to charge
. The charge should be in number of
the electron charge e.
Parameters: | charge [real] :: new atom charge |
---|---|
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 . |
chfl_atom%
name
(name, buffsize[, status])¶Get the name of an atom in the string buffer name
.
The buffer size must be passed in buffsize
. This function will truncate
the name to fit in the buffer.
Parameters: |
|
---|---|
Options: | status [integer,optional, kind=chfl_status] :: status code of the
operation. If it is not equal to |
chfl_atom%
set_name
(name[, status])¶Set the name of an atom to name
.
Parameters: | character (len=*) :: new atom name |
---|---|
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 . |
chfl_atom%
full_name
(name, buffsize[, status])¶Get the full name of an atom
from its type in the string buffer
name
.
The buffer size must be passed in buffsize
. This function will truncate
the name to fit in the buffer.
Parameters: |
|
---|---|
Options: | status [integer,optional, kind=chfl_status] :: status code of the
operation. If it is not equal to |
chfl_atom%
type
(type, buffsize[, status])¶Get the type of an atom in the string buffer type
.
The buffer size must be passed in buffsize
. This function will truncate
the type to fit in the buffer.
Parameters: |
|
---|---|
Options: | status [integer,optional, kind=chfl_status] :: status code of the
operation. If it is not equal to |
chfl_atom%
set_type
(type[, status])¶Set the type of an atom to type
.
Parameters: | character (len=*) :: new atom type |
---|---|
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 . |
chfl_atom%
vdw_radius
(radius[, status])¶Get the Van der Waals radius of an atom from the atom type in radius
.
If the radius in unknown, this function set radius
to 0.
Parameters: | radius [real] :: Van der Waals radius |
---|---|
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 . |
chfl_atom%
covalent_radius
(radius[, status])¶Get the covalent radius of an atom from the atom type in radius
.
If the radius in unknown, this function set radius
to 0.
Parameters: | radius [real] :: covalent radius |
---|---|
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 . |
chfl_atom%
atomic_number
(number[, status])¶Get the atomic number of an atom from the atom type in number
.
If the atomic number in unknown, this function set number
to 0.
Parameters: | number [integer] :: atomic number |
---|---|
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 . |
chfl_atom%
set_property
(name, property[, status])¶Add a new property
with the given name
to this atom.
If a property with the same name already exists, this function override the existing property with the new one.
Parameters: |
|
---|---|
Options: | status [integer,optional, kind=chfl_status] :: status code of the
operation. If it is not equal to |
chfl_atom%
free
([status])¶Destroy an atom, and free the associated memory
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 . |
---|