Physical System Module#

class nexus.physical_system.Matter(*vars, **kwargs)[source]#

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
is_element
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
new_particles
not_implemented
obj
path_exists
random_key
select_random
serial
set
set_elements
set_optional
set_particle_collection
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

particle_collection = Ac Ion Ac_227 Ion Ag Ion Ag_107 Ion Ag_109 Ion Al Ion Al_27 Ion Am Ion Am_241 Ion Am_243 Ion Ar Ion Ar_36 Ion Ar_38 Ion Ar_40 Ion As Ion As_75 Ion At Ion At_210 Ion At_211 Ion Au Ion Au_197 Ion B Ion B_10 Ion B_11 Ion Ba Ion Ba_130 Ion Ba_132 Ion Ba_134 Ion Ba_135 Ion Ba_136 Ion Ba_137 Ion Ba_138 Ion Be Ion Be_9 Ion Bh Ion Bh_272 Ion Bi Ion Bi_209 Ion Bk Ion Bk_247 Ion Bk_249 Ion Br Ion Br_79 Ion Br_81 Ion C Ion C_12 Ion C_13 Ion C_14 Ion Ca Ion Ca_40 Ion Ca_42 Ion Ca_43 Ion Ca_44 Ion Ca_46 Ion Ca_48 Ion Cd Ion Cd_106 Ion Cd_108 Ion Cd_110 Ion Cd_111 Ion Cd_112 Ion Cd_113 Ion Cd_114 Ion Cd_116 Ion Ce Ion Ce_136 Ion Ce_138 Ion Ce_140 Ion Ce_142 Ion Cf Ion Cf_249 Ion Cf_250 Ion Cf_251 Ion Cf_252 Ion Cl Ion Cl_35 Ion Cl_37 Ion Cm Ion Cm_243 Ion Cm_244 Ion Cm_245 Ion Cm_246 Ion Cm_247 Ion Cm_248 Ion Cn Ion Cn_285 Ion Co Ion Co_59 Ion Cr Ion Cr_50 Ion Cr_52 Ion Cr_53 Ion Cr_54 Ion Cs Ion Cs_133 Ion Cu Ion Cu_63 Ion Cu_65 Ion Db Ion Db_268 Ion Ds Ion Ds_281 Ion Dy Ion Dy_156 Ion Dy_158 Ion Dy_160 Ion Dy_161 Ion Dy_162 Ion Dy_163 Ion Dy_164 Ion Er Ion Er_162 Ion Er_164 Ion Er_166 Ion Er_167 Ion Er_168 Ion Er_170 Ion Es Ion Es_252 Ion Eu Ion Eu_151 Ion Eu_153 Ion F Ion F_19 Ion Fe Ion Fe_54 Ion Fe_56 Ion Fe_57 Ion Fe_58 Ion Fl Ion Fl_289 Ion Fm Ion Fm_257 Ion Fr Ion Fr_223 Ion Ga Ion Ga_69 Ion Ga_71 Ion Gd Ion Gd_152 Ion Gd_154 Ion Gd_155 Ion Gd_156 Ion Gd_157 Ion Gd_158 Ion Gd_160 Ion Ge Ion Ge_70 Ion Ge_72 Ion Ge_73 Ion Ge_74 Ion Ge_76 Ion H Ion H_1 Ion H_2 Ion H_3 Ion He Ion He_3 Ion He_4 Ion Hf Ion Hf_174 Ion Hf_176 Ion Hf_177 Ion Hf_178 Ion Hf_179 Ion Hf_180 Ion Hg Ion Hg_196 Ion Hg_198 Ion Hg_199 Ion Hg_200 Ion Hg_201 Ion Hg_202 Ion Hg_204 Ion Ho Ion Ho_165 Ion Hs Ion Hs_270 Ion I Ion I_127 Ion In Ion In_113 Ion In_115 Ion Ir Ion Ir_191 Ion Ir_193 Ion K Ion K_39 Ion K_40 Ion K_41 Ion Kr Ion Kr_78 Ion Kr_80 Ion Kr_82 Ion Kr_83 Ion Kr_84 Ion Kr_86 Ion La Ion La_138 Ion La_139 Ion Li Ion Li_6 Ion Li_7 Ion Lr Ion Lr_262 Ion Lu Ion Lu_175 Ion Lu_176 Ion Lv Ion Lv_293 Ion Mc Ion Mc_288 Ion Md Ion Md_258 Ion Md_260 Ion Mg Ion Mg_24 Ion Mg_25 Ion Mg_26 Ion Mn Ion Mn_55 Ion Mo Ion Mo_100 Ion Mo_92 Ion Mo_94 Ion Mo_95 Ion Mo_96 Ion Mo_97 Ion Mo_98 Ion Mt Ion Mt_276 Ion N Ion N_14 Ion N_15 Ion Na Ion Na_23 Ion Nb Ion Nb_93 Ion Nd Ion Nd_142 Ion Nd_143 Ion Nd_144 Ion Nd_145 Ion Nd_146 Ion Nd_148 Ion Nd_150 Ion Ne Ion Ne_20 Ion Ne_21 Ion Ne_22 Ion Nh Ion Nh_284 Ion Ni Ion Ni_58 Ion Ni_60 Ion Ni_61 Ion Ni_62 Ion Ni_64 Ion No Ion No_259 Ion Np Ion Np_236 Ion Np_237 Ion O Ion O_16 Ion O_17 Ion O_18 Ion Og Ion Og_294 Ion Os Ion Os_184 Ion Os_186 Ion Os_187 Ion Os_188 Ion Os_189 Ion Os_190 Ion Os_192 Ion P Ion P_31 Ion Pa Ion Pa_231 Ion Pb Ion Pb_204 Ion Pb_206 Ion Pb_207 Ion Pb_208 Ion Pd Ion Pd_102 Ion Pd_104 Ion Pd_105 Ion Pd_106 Ion Pd_108 Ion Pd_110 Ion Pm Ion Pm_145 Ion Pm_147 Ion Po Ion Po_209 Ion Po_210 Ion Pr Ion Pr_141 Ion Pt Ion Pt_190 Ion Pt_192 Ion Pt_194 Ion Pt_195 Ion Pt_196 Ion Pt_198 Ion Pu Ion Pu_238 Ion Pu_239 Ion Pu_240 Ion Pu_241 Ion Pu_242 Ion Pu_244 Ion Ra Ion Ra_223 Ion Ra_224 Ion Ra_226 Ion Ra_228 Ion Rb Ion Rb_85 Ion Rb_87 Ion Re Ion Re_185 Ion Re_187 Ion Rf Ion Rf_267 Ion Rg Ion Rg_280 Ion Rh Ion Rh_103 Ion Rn Ion Rn_211 Ion Rn_220 Ion Rn_222 Ion Ru Ion Ru_100 Ion Ru_101 Ion Ru_102 Ion Ru_104 Ion Ru_96 Ion Ru_98 Ion Ru_99 Ion S Ion S_32 Ion S_33 Ion S_34 Ion S_36 Ion Sb Ion Sb_121 Ion Sb_123 Ion Sc Ion Sc_45 Ion Se Ion Se_74 Ion Se_76 Ion Se_77 Ion Se_78 Ion Se_80 Ion Se_82 Ion Sg Ion Sg_271 Ion Si Ion Si_28 Ion Si_29 Ion Si_30 Ion Sm Ion Sm_144 Ion Sm_147 Ion Sm_148 Ion Sm_149 Ion Sm_150 Ion Sm_152 Ion Sm_154 Ion Sn Ion Sn_112 Ion Sn_114 Ion Sn_115 Ion Sn_116 Ion Sn_117 Ion Sn_118 Ion Sn_119 Ion Sn_120 Ion Sn_122 Ion Sn_124 Ion Sr Ion Sr_84 Ion Sr_86 Ion Sr_87 Ion Sr_88 Ion Ta Ion Ta_180 Ion Ta_181 Ion Tb Ion Tb_159 Ion Tc Ion Tc_97 Ion Tc_98 Ion Tc_99 Ion Te Ion Te_120 Ion Te_122 Ion Te_123 Ion Te_124 Ion Te_125 Ion Te_126 Ion Te_128 Ion Te_130 Ion Th Ion Th_230 Ion Th_232 Ion Ti Ion Ti_46 Ion Ti_47 Ion Ti_48 Ion Ti_49 Ion Ti_50 Ion Tl Ion Tl_203 Ion Tl_205 Ion Tm Ion Tm_169 Ion Ts Ion Ts_292 Ion U Ion U_233 Ion U_234 Ion U_235 Ion U_236 Ion U_238 Ion V Ion V_50 Ion V_51 Ion W Ion W_180 Ion W_182 Ion W_183 Ion W_184 Ion W_186 Ion Xe Ion Xe_124 Ion Xe_126 Ion Xe_128 Ion Xe_129 Ion Xe_130 Ion Xe_131 Ion Xe_132 Ion Xe_134 Ion Xe_136 Ion Xx Ion Xx_0 Ion Y Ion Y_89 Ion Yb Ion Yb_168 Ion Yb_170 Ion Yb_171 Ion Yb_172 Ion Yb_173 Ion Yb_174 Ion Yb_176 Ion Zn Ion Zn_64 Ion Zn_66 Ion Zn_67 Ion Zn_68 Ion Zn_70 Ion Zr Ion Zr_90 Ion Zr_91 Ion Zr_92 Ion Zr_94 Ion Zr_96 Ion down_electron Particle up_electron Particle #

classmethod set_elements(elements)[source]#

classmethod set_particle_collection(pc)[source]#

classmethod new_particles(*particles, **named_particles)[source]#

is_element(name, symbol=False)[source]#

elements = {'Ac', 'Ag', 'Al', 'Am', 'Ar', 'As', 'At', 'Au', 'B', 'Ba', 'Be', 'Bh', 'Bi', 'Bk', 'Br', 'C', 'Ca', 'Cd', 'Ce', 'Cf', 'Cl', 'Cm', 'Cn', 'Co', 'Cr', 'Cs', 'Cu', 'Db', 'Ds', 'Dy', 'Er', 'Es', 'Eu', 'F', 'Fe', 'Fl', 'Fm', 'Fr', 'Ga', 'Gd', 'Ge', 'H', 'He', 'Hf', 'Hg', 'Ho', 'Hs', 'I', 'In', 'Ir', 'K', 'Kr', 'La', 'Li', 'Lr', 'Lu', 'Lv', 'Mc', 'Md', 'Mg', 'Mn', 'Mo', 'Mt', 'N', 'Na', 'Nb', 'Nd', 'Ne', 'Nh', 'Ni', 'No', 'Np', 'O', 'Og', 'Os', 'P', 'Pa', 'Pb', 'Pd', 'Pm', 'Po', 'Pr', 'Pt', 'Pu', 'Ra', 'Rb', 'Re', 'Rf', 'Rg', 'Rh', 'Rn', 'Ru', 'S', 'Sb', 'Sc', 'Se', 'Sg', 'Si', 'Sm', 'Sn', 'Sr', 'Ta', 'Tb', 'Tc', 'Te', 'Th', 'Ti', 'Tl', 'Tm', 'Ts', 'U', 'V', 'W', 'Xe', 'Xx', 'Y', 'Yb', 'Zn', 'Zr'}#

class nexus.physical_system.Particle(name=None, mass=None, charge=None, spin=None)[source]#

Bases: Matter

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
is_element
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
new_particles
not_implemented
obj
path_exists
random_key
select_random
serial
set
set_count
set_elements
set_optional
set_particle_collection
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

set_count(count)[source]#

class nexus.physical_system.Ion(name=None, mass=None, charge=None, spin=None, protons=None, neutrons=None)[source]#

Bases: Particle

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
is_element
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
new_particles
not_implemented
obj
path_exists
pseudize
random_key
select_random
serial
set
set_count
set_elements
set_optional
set_particle_collection
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

pseudize(valence)[source]#

class nexus.physical_system.PseudoIon(name=None, mass=None, charge=None, spin=None, protons=None, neutrons=None, core_electrons=None)[source]#

Bases: Ion

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
is_element
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
new_particles
not_implemented
obj
path_exists
pseudize
random_key
select_random
serial
set
set_count
set_elements
set_optional
set_particle_collection
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

class nexus.physical_system.Particles(*particles, **named_particles)[source]#

Bases: Matter

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`()
`get`(quantity)
`keys`()
`list`(*keys)
`open_log`(filepath)
`save`([fpath])
`sorted_keys`()
`warn`(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
add_particles
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
count_electrons
count_ions
data_repr
delete
delete_optional
delete_required
dict
electron_counts
extract
extract_optional
get_electrons
get_ions
get_optional
get_particle
get_path
get_required
inverse
is_element
items
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
new_particles
not_implemented
obj
path_exists
random_key
rename
select_random
serial
set
set_elements
set_optional
set_particle_collection
set_path
shallow_copy
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
values
write

add_particles(*particles, **named_particles)[source]#

get_particle(name)[source]#

get(quantity)[source]#

rename(**name_pairs)[source]#

get_ions()[source]#

count_ions(species=False)[source]#

get_electrons()[source]#

count_electrons()[source]#

electron_counts()[source]#

class nexus.physical_system.PhysicalSystem(structure=None, net_charge=0, net_spin=0, particles=None, **valency)[source]#

Bases: Matter

Methods

`ae_pp_species`()
`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`()
`large_Zeff_elem`(Zmin)
`list`(*keys)
`open_log`(filepath)
`save`([fpath])
`sorted_keys`()
`warn`(msg[, indent])	Warning from inside a Nexus class.

add
add_optional
add_particles
change_units
check_consistent
check_folded_system
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
generate_electrons
get
get_optional
get_path
get_required
get_smallest
group_atoms
has_folded
inverse
is_element
is_magnetic
is_valid
items
kf_rpa
last
list_optional
load
log
move_from
move_from_optional
move_to
move_to_optional
new_particles
not_implemented
obj
path_exists
pseudize
random_key
remove_folded
remove_folded_system
rename
select_random
serial
set
set_elements
set_optional
set_particle_collection
set_path
shallow_copy
spin_polarized_orbitals
tile
to_dict
to_obj
transfer_from
transfer_to
tree
tuple
update
update_particles
values
write

update_particles(clear=True)[source]#

update()[source]#

add_particles(**particle_counts)[source]#

generate_electrons(net_charge=0, net_spin=0)[source]#

pseudize(**valency)[source]#

check_folded_system(exit=True, message=False)[source]#

check_consistent(tol=1e-08, exit=True, message=False)[source]#

is_valid()[source]#

change_units(units)[source]#

group_atoms()[source]#

rename(folded=True, **name_pairs)[source]#

copy()[source]#

load(filepath)[source]#

tile(*td, **kwargs)[source]#

has_folded()[source]#

remove_folded_system()[source]#

remove_folded()[source]#

get_smallest()[source]#

is_magnetic()[source]#

spin_polarized_orbitals()[source]#

large_Zeff_elem(Zmin)[source]#

ae_pp_species()[source]#

kf_rpa()[source]#

nexus.physical_system.generate_physical_system(**kwargs)[source]#

nexus.physical_system.ghost_atoms(*particles)[source]#