Basis Set Module

nexus.basisset.show_plots()

class nexus.basisset.BasisSets(*basissets)

Bases: DevBase

Methods

append(value)
bases_by_atom(*bsfiles)
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
addbs
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
readbs
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

addbs(*basissets)

readbs(*bsfiles)

bases_by_atom(*bsfiles)

class nexus.basisset.BasisFile(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
cleaned_text
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
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

cleaned_text()

class nexus.basisset.gaussBasisFile(filepath=None)

Bases: BasisFile

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
cleaned_text
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
read_file
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

angular_terms = 'spdfghiklmn'

cleaned_text()

read(filepath=None)

read_file(file)

class nexus.basisset.gamessBasisFile(filepath=None)

Bases: gaussBasisFile

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
cleaned_text
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
read_file
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

read_file(file)

nexus.basisset.process_gaussian_text(text, format, pp=True, basis=True, preserve_spacing=False)

class nexus.basisset.GaussianBasisSet(filepath=None, format=None)

Bases: DevBase

Methods

append(value)
basis_size()
class_error(message[, header, exit, trace, ...])	Report an error relating to a class.
contracted()
contracted_basis_size()
error(message[, header, exit, trace])	Report an error inside a class.
first()
incorporate(other[, tol, unique])
keys()
lbasis()
lcount()
list(*keys)
lset()
lsort()
open_log(filepath)
prim_expons()
prim_widths()
remove_channels(llist)
remove_large_prims(**keep)
remove_large_prims_rel(other, **keep)
remove_prims([comp, keep])
remove_small_prims(**keep)
remove_small_prims_rel(other, **keep)
save([fpath])
size()
sorted_keys()
uncontract([tol])
uncontracted()
uncontracted_basis_size()
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
plot
plot_prim_widths
plot_primitives
process_float
random_key
read
read_lines
read_text
select_random
serial
set
set_optional
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write
write_text

lset_full = ('s', 'p', 'd', 'f', 'g', 'h', 'i', 'j', 'k')

lstyles = d                     str                    f                     str                    g                     str                    h                     str                    i                     str                    j                     str                    k                     str                    p                     str                    s                     str                 

formats = ['gaussian', 'gamess']

crystal_lmap = {0: 's', 1: 'sp', 2: 'p', 3: 'd', 4: 'f'}

crystal_lmap_reverse = {'d': 3, 'f': 4, 'p': 2, 's': 0, 'sp': 1}

static process_float(s)

read(filepath, format=None)

write(filepath=None, format=None)

read_text(text, format=None)

read_lines(basis_lines, format=None)

write_text(format=None, occ=None)

size()

lset()

lcount()

lbasis()

lsort()

uncontracted()

contracted()

uncontract(tol=0.001)

contracted_basis_size()

uncontracted_basis_size()

basis_size()

prim_expons()

prim_widths()

remove_prims(comp=None, keep=None, **lselectors)

remove_small_prims(**keep)

remove_large_prims(**keep)

remove_small_prims_rel(other, **keep)

remove_large_prims_rel(other, **keep)

remove_channels(llist)

incorporate(other, tol=0.001, unique=False)

plot(r=None, rmin=0.01, rmax=8.0, show=True, fig=True, sep=False, prim=False, style=None, fmt=None, nsub=None)

plot_primitives()

plot_prim_widths(show=True, fig=True, sep=False, style='o', fmt=None, nsub=None, semilog=True, label=True)