Pseudopotential Module

nexus.pseudopotential.pp_elem_label(filename, guard=False)

class nexus.pseudopotential.PseudoFile(filepath=None)

Bases: DevBase

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
check_required
check_types
check_types_optional
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
copy
copy_from
copy_to
data_repr
delete
delete_optional
delete_required
dict
extract
extract_optional
get
get_optional
get_path
get_required
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
random_key
read
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

read(filepath)

class nexus.pseudopotential.gamessPPFile(filepath=None)

Bases: PseudoFile

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
check_required
check_types
check_types_optional
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
copy
copy_from
copy_to
data_repr
delete
delete_optional
delete_required
dict
extract
extract_optional
get
get_optional
get_path
get_required
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
random_key
read
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

read(filepath)

class nexus.pseudopotential.Pseudopotentials(*pseudopotentials)

Bases: DevBase

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
addpp
check_required
check_types
check_types_optional
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
copy
copy_from
copy_to
data_repr
delete
delete_optional
delete_required
dict
extract
extract_optional
get
get_optional
get_path
get_required
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
pseudos_by_atom
random_key
readpp
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

addpp(*pseudopotentials)

readpp(*ppfiles)

pseudos_by_atom(*ppfiles)

class nexus.pseudopotential.PPset

Bases: DevBase

Methods

__call__(label, **code_pps)	Call self as a function.
append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
get(label, code, system)
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
check_required
check_types
check_types_optional
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
copy
copy_from
copy_to
data_repr
delete
delete_optional
delete_required
dict
extract
extract_optional
get_optional
get_path
get_required
has_set
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
random_key
select_random
serial
set
set_optional
set_path
shallow_copy
supports_code
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

instance_counter = 1

known_codes = {'gamess', 'pwscf', 'qmcpack', 'vasp'}

default_extensions = gamess                list                   pwscf                 list                   qmcpack               list                   vasp                  list                

supports_code(code)

has_set(label)

get(label, code, system)

class nexus.pseudopotential.Pseudopotential(filepath=None, format=None)

Bases: DevBase

Attributes:

formats

Methods

append(value)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
first()
keys()
list(*keys)
open_log(filepath)
save([fpath])
sorted_keys()
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
check_required
check_types
check_types_optional
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
convert
copy
copy_from
copy_to
data_repr
delete
delete_optional
delete_required
dict
extract
extract_optional
get
get_optional
get_path
get_required
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
plot
random_key
read
read_text
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_core_from
transfer_from
transfer_to
tree
tuple
values
write
write_text

requires_format = False

formats = None

transfer_core_from(other)

read(filepath, format=None)

write(filepath=None, format=None)

read_text(text, format=None, filepath=None)

write_text(format=None)

convert(format)

plot(r=None, show=True)

class nexus.pseudopotential.SemilocalPP(filepath=None, format=None, name=None, src=None)

Bases: Pseudopotential

Methods

add_L2(v)
add_local(l, v)
add_nonlocal(l, v)
angular_channels()
append(value)
change_local(local)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
evaluate_L2([r, rpow, rmin, rret])
evaluate_channel([r, l, rpow, rmin, rret, ...])
evaluate_comp(r, l, vcomp[, rpow, rmin, rret])
evaluate_comp_rV(r, l, vcomp)
evaluate_component([r, l, rpow, rmin, rret, ...])
evaluate_local([r, rpow, rmin, rret])
evaluate_nonlocal([r, l, rpow, rmin, rret])
expand_L2(lmax)
first()
get_L2()
keys()
list(*keys)
numeric_channel([l, rmin, rmax, npts, rpow, ...])
open_log(filepath)
promote_local()
remove_L2()
remove_component(l[, guard])
remove_local()
remove_nonlocal([l])
save([fpath])
set_channel(l, v)
set_component(l, v[, guard])
sorted_keys()
transfer_core_from(other)
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
assert_numeric
check_required
check_types
check_types_optional
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
convert
copy
copy_from
copy_to
data_repr
delete
delete_optional
delete_required
dict
extract
extract_optional
find_r_rng
find_rcut
get
get_component
get_local
get_nonlocal
get_optional
get_path
get_required
has_L2
has_component
has_local
has_nonlocal
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
plot
plot_L2
plot_channels
plot_components
plot_nonlocal_polar
plot_positive_definite
random_key
read
read_text
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
update_rcut
values
write
write_casino
write_qmcpack
write_text

l_channels = ('s', 'p', 'd', 'f', 'g', 'h', 'i', 'k', 'l', 'm', 'n', 'o', 'q', 'r', 't', 'u', 'v', 'w', 'x', 'y', 'z')

channel_colors = L2                    str                    d                     str                    f                     str                    g                     str                    h                     str                    i                     str                    p                     str                    s                     str                 

numeric = False

interpolatable = True

formats = ['qmcpack', 'casino']

channel_indices = L2                    int                    d                     int                    f                     int                    g                     int                    h                     int                    i                     int                    k                     int                    l                     int                    m                     int                    n                     int                    o                     int                    p                     int                    q                     int                    r                     int                    s                     int                    t                     int                    u                     int                    v                     int                    w                     int                    x                     int                    y                     int                    z                     int                 

transfer_core_from(other)

read(filepath, format=None)

has_component(l)

set_component(l, v, guard=False)

get_component(l, guard=False)

remove_component(l, guard=False)

has_local()

has_nonlocal(l=None)

has_L2()

get_local()

get_nonlocal(l=None)

get_L2()

add_local(l, v)

add_nonlocal(l, v)

add_L2(v)

remove_local()

remove_nonlocal(l=None)

remove_L2()

assert_numeric(loc)

change_local(local)

promote_local()

set_channel(l, v)

expand_L2(lmax)

angular_channels()

evaluate_comp_rV(r, l, vcomp)

find_r_rng(r, rmin)

evaluate_comp(r, l, vcomp, rpow=0, rmin=0, rret=True)

evaluate_local(r=None, rpow=0, rmin=0, rret=False)

evaluate_nonlocal(r=None, l=None, rpow=0, rmin=0, rret=False)

evaluate_L2(r=None, rpow=0, rmin=0, rret=False)

evaluate_component(r=None, l=None, rpow=0, rmin=0, rret=False, optional=False)

evaluate_channel(r=None, l=None, rpow=0, rmin=0, rret=False, with_local=True, with_L2=True)

numeric_channel(l=None, rmin=0.0, rmax=10.0, npts=10001, rpow=0, with_local=True, with_L2=True)

update_rcut(tol=1e-05, optional=False)

find_rcut(tol=1e-05, with_L2=False)

plot(r=None, show=True, fig=True, linestyle='-', channels=None, with_local=False, rmin=0.01, rmax=5.0, title=None, metric=None, color=None)

plot_components(r=None, show=True, fig=True, linestyle='-', rmin=0.01, rmax=5.0, title=None, metric=None, color=None, rpow=0)

plot_channels(r=None, channels=None, show=True, fig=True, linestyle='-', rmin=0.01, rmax=5.0, title=None, metric=None, color=None, rpow=0, with_local=True, with_L2=True)

plot_positive_definite(r=None, show=True, fig=True, linestyle='-', rmin=0.01, rmax=5.0, title=None, color='k')

plot_L2(show=True, fig=True, r=None, rmin=0.01, rmax=5.0, linestyle='-', title=None, color=None)

plot_nonlocal_polar(show=True, lmax=10, rmin=0.01, rmax=2.0, nr=100, nt=100, levels=100, label='')

write_qmcpack(filepath=None)

write_casino(filepath=None)

c = 'z'

i = 20

class nexus.pseudopotential.GaussianPP(filepath=None, format=None, name=None, src=None)

Bases: SemilocalPP

Methods

add_L2(v)
add_local(l, v)
add_nonlocal(l, v)
angular_channels()
append(value)
append_to_component(l, coeff, expon, rpow)	This function is used to append a term to a Gaussian ECP component.
change_local(local)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
evaluate_L2([r, rpow, rmin, rret])
evaluate_channel([r, l, rpow, rmin, rret, ...])
evaluate_comp(r, l, vcomp[, rpow, rmin, rret])
evaluate_component([r, l, rpow, rmin, rret, ...])
evaluate_local([r, rpow, rmin, rret])
evaluate_nonlocal([r, l, rpow, rmin, rret])
expand_L2(lmax)
first()
get_L2()
get_basis()
get_unboundedness(db, dbs)	This function quantifies how unbounded a truncated L2 potential is.
is_truncated_L2()	Determine if the Gaussian ECP's channels follow an L2 relationship.
keys()
list(*keys)
make_L2_bounded(db, dbs[, exps0, plot])	For a truncated L2 potential, this function constructs a correction to VL2 in the unbounded region.
numeric_channel([l, rmin, rmax, npts, rpow, ...])
open_log(filepath)
ppconvert(outfile, ref[, extra])
promote_local()
read_text(text[, format, filepath])
remove_L2()
remove_component(l[, guard])
remove_local()
remove_nonlocal([l])
save([fpath])
scale_component(l, scale)	This function is used to scale a Gaussian ECP component by a factor.
set_channel(l, v)
set_component(l, v[, guard])
simplify()	This function simplifies the Gaussian ECP.
sorted_keys()
transfer_core_from(other)
transform_to_truncated_L2([keep, lmax, ...])	This function transforms a Gaussian ECP into a truncated L2 form, i.e., a form for which all channels follow an L2 relationship.
uncontract()
warn(msg[, indent])	Warning from inside a Nexus class.
write_basis([filepath, format])
write_text([format, occ])

add
add_optional
assert_numeric
check_required
check_types
check_types_optional
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
convert
copy
copy_from
copy_to
data_repr
delete
delete_optional
delete_required
dict
evaluate_comp_rV
extract
extract_optional
find_r_rng
find_rcut
get
get_component
get_local
get_nonlocal
get_optional
get_path
get_required
has_L2
has_component
has_local
has_nonlocal
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
plot
plot_L2
plot_channels
plot_components
plot_nonlocal_polar
plot_positive_definite
process_float
random_key
read
select_random
serial
set
set_basis
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
update_rcut
values
write
write_casino
write_qmcpack

requires_format = True

formats = ['qmcpack', 'casino', 'gaussian', 'gamess', 'crystal', 'numhf']

static process_float(s)

read_text(text, format=None, filepath=None)

write_text(format=None, occ=None)

get_basis()

set_basis(bs)

uncontract()

write_basis(filepath=None, format=None)

evaluate_comp_rV(r, l, vcomp)

ppconvert(outfile, ref, extra=None)

append_to_component(l, coeff, expon, rpow)

This function is used to append a term to a Gaussian ECP component. l: the angular ccomponent that the Gaussian term will be appended to coeff, expon, rpow: the coefficient, exponent, and r-power of the Gaussian term

scale_component(l, scale)

This function is used to scale a Gaussian ECP component by a factor. l: the angular component that is scaled. scale: the scaling factor

simplify()

This function simplifies the Gaussian ECP.

The simplificactions are as follows:

1. Remove all terms with coefficients that are equal to zero – unless only one term exists.

2. Within each component, look for terms that have matching exponents and r-powers, if any are present, then sum their coefficicents to make a single term. If the coefficients sum to zero, then remove the terms (unless that leaves the component empty)

is_truncated_L2()

Determine if the Gaussian ECP’s channels follow an L2 relationship.

get_unboundedness(db, dbs)

This function quantifies how unbounded a truncated L2 potential is. This is done by constructing a function that corrects VL2 in the unbounded region. Then integrating the difference between VL2 and the correcting function.

make_L2_bounded(db, dbs, exps0=None, plot=False)

For a truncated L2 potential, this function constructs a correction to VL2 in the unbounded region. Then the correction is fit to a set of Gaussian primitives that are provided in the array ‘exps0’. The fitted Gaussian primitives are then appended to the ECP, resulting in a bounded truncated L2 potential.

transform_to_truncated_L2(keep=None, lmax=None, outfile=None, inplace=True)

This function transforms a Gaussian ECP into a truncated L2 form, i.e., a form for which all channels follow an L2 relationship. For a semi-local ECP, this transformation can have a significant negative impact on transferability. For an ECP that is already in a trucnated L2 form, the transformation has no affect.

class nexus.pseudopotential.QmcpackPP(filepath=None, format=None, name=None, src=None)

Bases: SemilocalPP

Methods

add_L2(v)
add_local(l, v)
add_nonlocal(l, v)
angular_channels()
append(value)
change_local(local)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
evaluate_L2([r, rpow, rmin, rret])
evaluate_channel([r, l, rpow, rmin, rret, ...])
evaluate_comp(r, l, vcomp[, rpow, rmin, rret])
evaluate_component([r, l, rpow, rmin, rret, ...])
evaluate_local([r, rpow, rmin, rret])
evaluate_nonlocal([r, l, rpow, rmin, rret])
expand_L2(lmax)
first()
get_L2()
keys()
list(*keys)
numeric_channel([l, rmin, rmax, npts, rpow, ...])
open_log(filepath)
promote_local()
remove_L2()
remove_component(l[, guard])
remove_local()
remove_nonlocal([l])
save([fpath])
set_channel(l, v)
set_component(l, v[, guard])
sorted_keys()
transfer_core_from(other)
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
assert_numeric
check_required
check_types
check_types_optional
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
convert
copy
copy_from
copy_to
data_repr
delete
delete_optional
delete_required
dict
evaluate_comp_rV
extract
extract_optional
find_r_rng
find_rcut
get
get_component
get_local
get_nonlocal
get_optional
get_path
get_required
has_L2
has_component
has_local
has_nonlocal
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
plot
plot_L2
plot_channels
plot_components
plot_nonlocal_polar
plot_positive_definite
random_key
read
read_text
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
update_rcut
v_at_zero
values
write
write_casino
write_qmcpack
write_text

requires_format = False

numeric = True

interpolatable = False

read(filepath, format=None)

evaluate_comp_rV(r, l, vcomp)

v_at_zero(l)

class nexus.pseudopotential.CasinoPP(filepath=None, format=None, name=None, src=None)

Bases: SemilocalPP

Methods

add_L2(v)
add_local(l, v)
add_nonlocal(l, v)
angular_channels()
append(value)
change_local(local)
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
error(message[, header, exit, trace])	Report an error inside a class.
evaluate_L2([r, rpow, rmin, rret])
evaluate_channel([r, l, rpow, rmin, rret, ...])
evaluate_comp(r, l, vcomp[, rpow, rmin, rret])
evaluate_component([r, l, rpow, rmin, rret, ...])
evaluate_local([r, rpow, rmin, rret])
evaluate_nonlocal([r, l, rpow, rmin, rret])
expand_L2(lmax)
first()
get_L2()
keys()
list(*keys)
numeric_channel([l, rmin, rmax, npts, rpow, ...])
open_log(filepath)
promote_local()
remove_L2()
remove_component(l[, guard])
remove_local()
remove_nonlocal([l])
save([fpath])
set_channel(l, v)
set_component(l, v[, guard])
sorted_keys()
transfer_core_from(other)
warn(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
assert_numeric
check_required
check_types
check_types_optional
class_get
class_has
class_items
class_keys
class_log
class_set
class_set_optional
class_set_single
class_warn
clear
close_log
convert
copy
copy_from
copy_to
data_repr
delete
delete_optional
delete_required
dict
evaluate_comp_rV
extract
extract_optional
find_r_rng
find_rcut
get
get_component
get_local
get_nonlocal
get_optional
get_path
get_required
has_L2
has_component
has_local
has_nonlocal
inverse
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
not_implemented
obj
path_exists
plot
plot_L2
plot_channels
plot_components
plot_nonlocal_polar
plot_positive_definite
random_key
read
read_text
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
update_rcut
values
write
write_casino
write_qmcpack
write_text

requires_format = False

numeric = True

interpolatable = False

unitmap = {'ev': 'eV', 'hartree': 'Ha', 'rydberg': 'Ry'}

read(filepath, format=None)

evaluate_comp_rV(r, l, vcomp)