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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
A
add() (in module siman.calc_manage)
add_calculation() (in module siman.calc_manage)
add_conv() (siman.set_functions.InputSet method)
add_conv_kpoint() (siman.set_functions.InputSet method)
add_conv_tsmear() (siman.set_functions.InputSet method)
add_des() (in module siman.calc_manage)
add_impurity() (in module siman.impurity)
add_loop() (in module siman.calc_manage)
add_neb() (in module siman.neb)
add_relax() (siman.classes.MP_Compound method)
add_to_archive_database() (in module siman.database)
ads_en() (in module siman.analysis)
aims_keys (in module siman.set_functions)
angle() (in module siman.small_functions)
around_alkali() (in module siman.analysis)
assign_oxi_states() (in module siman.analysis)
B
b2s() (in module siman.small_functions)
bash_chk_file_cmd() (in module siman.small_functions)
best_miller() (in module siman.geo)
block_print() (in module siman.small_functions)
C
cal_chg_diff() (in module siman.chg.chg_func)
cal_chg_diff_files() (in module siman.chg.chg_func)
calc_ac() (in module siman.functions)
calc_bulk() (siman.classes.MP_Compound method)
calc_ec_es() (siman.classes.MP_Compound method)
calc_k_point_mesh() (in module siman.geo)
calc_kspacings() (in module siman.geo)
calc_ngkpt() (in module siman.small_functions)
calc_oxidation_states() (in module siman.analysis)
calc_recip_vectors() (in module siman.geo)
calc_redox() (in module siman.analysis)
calc_suf() (siman.classes.MP_Compound method)
calc_suf_stoich() (siman.classes.MP_Compound method)
calc_volume() (in module siman.geo)
CalcDict (class in siman.header)
calculate_voronoi() (in module siman.functions)
cat_files() (in module siman.small_functions)
cd (class in siman.classes)
check() (in module siman.monte)
check_output() (in module siman.functions)
check_poscar() (in module siman.monte)
chg_at_point() (in module siman.chg.chg_func)
chg_at_z_direct() (in module siman.chg.chg_func)
chgarith() (in module siman.chg.vasputil_chgarith_module)
chgsum() (in module siman.analysis)
choose_cluster() (in module siman.calc_manage)
CIF2CELL (in module siman.default_project_conf)
cif2poscar() (in module siman.inout)
clean_history_file() (in module siman.calc_manage)
copy() (siman.classes.MP_Compound method)
create_additional() (in module siman.calc_manage)
create_ads_molecule() (in module siman.geo)
create_antisite_defect() (in module siman.geo)
create_antisite_defect2() (in module siman.geo)
create_antisite_defect3() (in module siman.geo)
create_antisite_defect_old() (in module siman.geo)
create_c_array() (in module siman.impurity)
create_coseg_samples() (in module siman.pairs)
create_deintercalated_structure() (in module siman.geo)
create_interface_solid() (in module siman.geo)
create_phonopy_conf_file() (in module siman.calc_manage)
create_replaced_structure() (in module siman.geo)
create_segregation_cases() (in module siman.workflow_utilities)
create_single_antisite() (in module siman.geo)
create_supercell() (in module siman.geo)
create_surface() (in module siman.geo)
create_surface2() (in module siman.geo)
cubic_supercell() (in module siman.geo)
cwd() (in module siman.small_functions)
D
Description (class in siman.classes)
det_gravity() (in module siman.dos_functions)
det_gravity2() (in module siman.dos_functions)
determine_barrier() (in module siman.analysis)
determine_file_format() (in module siman.inout)
determine_symmetry_positions() (in module siman.geo)
determine_unique_final() (in module siman.neb)
determine_unique_voids() (in module siman.impurity)
determine_voids() (in module siman.impurity)
E
e_cohesive_calc() (siman.classes.MP_Compound method)
e_cohesive_from_MP() (siman.classes.MP_Compound method)
element_name_inv() (in module siman.functions)
empty_struct (class in siman.classes)
enable_print() (in module siman.small_functions)
exchange_atoms() (in module siman.monte)
exchange_with_external() (in module siman.monte)
F
fexists() (siman.SSHTools.SSHTools method)
file_exists_on_server() (in module siman.functions)
find_moving_atom() (in module siman.geo)
find_mul_mat() (in module siman.geo)
find_pairs() (in module siman.pairs)
find_polaron() (in module siman.analysis)
find_pores() (in module siman.impurity)
find_slab_width() (in module siman.geo)
find_voids() (in module siman.geo)
fit2host() (in module siman.geo)
fit_a() (in module siman.analysis)
fit_and_plot() (in module siman.picture_functions)
fit_hex() (in module siman.fit_hex)
fitplot() (in module siman.picture_functions)
flatten() (in module siman.geo)
for_phonopy() (in module siman.calc_manage)
form_en() (in module siman.analysis)
G
gb_en_ideal() (in module siman.analysis)
gb_energy_volume() (in module siman.functions)
get() (siman.SSHTools.SSHTools method)
get_common_chemical_base() (in module siman.small_functions)
get_file_by_version() (in module siman.inout)
get_from_database() (in module siman.database)
get_from_server() (in module siman.functions)
get_mismatch() (in module siman.small_functions)
get_st() (siman.classes.MP_Compound method)
get_structure_from_cee_database() (in module siman.calc_manage)
get_structure_from_matproj() (in module siman.calc_manage)
get_vec() (in module siman.small_functions)
get_vector() (in module siman.small_functions)
get_zr_range() (in module siman.monte)
grep_file() (in module siman.small_functions)
gunzip_file() (in module siman.small_functions)
H
headers() (in module siman.functions)
hex2rhombo() (in module siman.geo)
hkl2uvw() (in module siman.geo)
hkl_slab() (in module siman.geo)
host (siman.SSHTools.SSHTools attribute)
I
image_distance() (in module siman.geo)
image_vector() (in module siman.geo)
inherit_icalc() (in module siman.calc_manage)
inherit_iset() (in module siman.set_functions)
inherit_ngkpt() (in module siman.calc_manage)
init_default_sets() (in module siman.set_functions)
initial_run() (in module siman.monte)
InputSet (class in siman.set_functions)
insert() (in module siman.impurity)
insert_atom() (in module siman.impurity)
insert_cluster() (in module siman.impurity)
interface_en() (in module siman.analysis)
interpolate() (in module siman.geo)
invert() (in module siman.functions)
is_list_like() (in module siman.small_functions)
is_string_like() (in module siman.small_functions)
is_unique() (in module siman.small_functions)
items() (siman.header.CalcDict method)
L
latex_chem() (in module siman.small_functions)
latex_spg() (in module siman.small_functions)
list2string() (in module siman.small_functions)
load() (siman.set_functions.InputSet method)
local_surrounding() (in module siman.geo)
local_surrounding2() (in module siman.geo)
log_history() (in module siman.functions)
M
make_defect() (in module siman.workflow_utilities)
make_interface() (in module siman.impurity)
make_interface2() (in module siman.impurity)
make_neutral() (in module siman.geo)
make_sets_for_conv() (in module siman.set_functions)
makedir() (in module siman.small_functions)
MANUALLY_ADDED (in module siman.default_project_conf)
manually_remove_from_struct_des() (in module siman.calc_manage)
matrix_diff() (in module siman.analysis)
merge_dics() (in module siman.small_functions)
metropolis() (in module siman.monte_functions)
move_edge() (in module siman.geo)
move_suf_en() (siman.classes.MP_Compound method)
MP_Compound (class in siman.classes)
N
name_mod_supercell() (in module siman.calc_manage)
neb_analysis() (in module siman.analysis)
normal() (in module siman.small_functions)
O
optimize_wrapper() (in module siman.workflow_utilities)
ortho_vec() (in module siman.geo)
ortho_vec_old() (in module siman.geo)
P
PBC() (in module siman.pairs)
pickle_module_migration_script() (in module siman.header)
pkey (siman.SSHTools.SSHTools attribute)
pkeypath (siman.SSHTools.SSHTools attribute)
plot_and_annotate() (in module siman.picture_functions)
plot_bands() (in module siman.bands)
plot_bands_old() (in module siman.bands)
plot_bar() (in module siman.picture_functions)
plot_bar_simple() (in module siman.picture_functions)
plot_charge_den() (in module siman.functions)
plot_conv() (in module siman.picture_functions)
plot_dos() (in module siman.dos_functions)
plot_interaction() (in module siman.functions)
plot_mep() (in module siman.picture_functions)
polaron_analysis() (in module siman.analysis)
port (siman.SSHTools.SSHTools attribute)
prepare() (in module siman.workflow_utilities)
primitive() (in module siman.geo)
print_and_log() (in module siman.header)
printlog() (in module siman.header)
printme() (siman.set_functions.InputSet method)
process_fig_filename() (in module siman.picture_functions)
process_modified() (in module siman.workflow_utilities)
push_figure_to_archive() (in module siman.database)
push_to_server() (in module siman.functions)
put() (siman.SSHTools.SSHTools method)
Q
qe_keys (in module siman.set_functions)
R
random() (in module siman.monte_functions)
read_aims_out() (in module siman.inout)
read_atat_fit_out() (in module siman.inout)
read_charge_den_vasp() (in module siman.functions)
read_csv() (in module siman.inout)
read_cvs_database() (in module siman.database)
read_database() (in module siman.database)
read_incar() (siman.set_functions.InputSet method)
read_kpoint_labels() (in module siman.bands)
read_list() (in module siman.functions)
read_phonopy_dat_file() (in module siman.calc_manage)
read_phonopy_data() (in module siman.calc_manage)
read_poscar() (in module siman.inout)
read_string() (in module siman.functions)
read_structure() (in module siman.inout)
read_universal() (siman.set_functions.InputSet method)
read_vasp_out() (in module siman.inout)
read_vasp_sets() (in module siman.set_functions)
read_vectors() (in module siman.functions)
read_xyz() (in module siman.inout)
red_prec() (in module siman.small_functions)
remove_atoms() (in module siman.geo)
remove_closest() (in module siman.geo)
remove_half() (in module siman.geo)
remove_half_based_on_symmetry() (in module siman.geo)
remove_one_atom() (in module siman.geo)
remove_vacuum() (in module siman.geo)
remove_x() (in module siman.geo)
remove_x_based_on_symmetry() (in module siman.geo)
removed_atoms() (in module siman.geo)
replace_x_based_on_symmetry() (in module siman.geo)
replic() (in module siman.geo)
res() (in module siman.calc_manage)
res_loop() (in module siman.calc_manage)
return_atoms_to_cell() (in module siman.functions)
return_xred() (in module siman.small_functions)
rgbline() (in module siman.bands)
rhombo2hex() (in module siman.geo)
rms_between_structures() (in module siman.geo)
rms_between_structures2() (in module siman.geo)
rms_pos_diff() (in module siman.geo)
rotate() (in module siman.functions)
rotate_align_with_vector() (in module siman.geo)
rotation_matrix() (in module siman.functions)
rotation_matrix_from_vectors() (in module siman.functions)
run() (siman.SSHTools.SSHTools method)
run_on_server() (in module siman.functions)
run_win_cmd() (in module siman.header)
run_wrapper() (in module siman.workflow_utilities)
runBash() (in module siman.header)
S
salary_inflation() (in module siman.functions)
scale_cell_by_matrix() (in module siman.geo)
scale_cell_uniformly() (in module siman.geo)
server_cp() (in module siman.functions)
set_add_nbands() (siman.set_functions.InputSet method)
set_attrp() (siman.set_functions.InputSet method)
set_compare_with() (siman.set_functions.InputSet method)
set_ngkpt() (siman.set_functions.InputSet method)
set_oxidation_states_guess() (in module siman.analysis)
set_params_dict() (siman.set_functions.InputSet method)
set_potential() (siman.set_functions.InputSet method)
set_relaxation_type() (siman.set_functions.InputSet method)
setting_sshpass() (in module siman.small_functions)
setup() (siman.SSHTools.SSHTools method)
sget() (siman.SSHTools.SSHTools method)
show_head (in module siman.default_project_conf)
siman (module)
siman.3d_plot (module)
siman.analysis (module)
siman.bands (module)
siman.calc_manage (module)
siman.chg (module)
siman.chg.chg_func (module)
siman.chg.vasputil_chgarith_module (module)
siman.classes (module)
siman.database (module)
siman.default_project_conf (module)
siman.dos_functions (module)
siman.fit_hex (module)
siman.functions (module)
siman.geo (module)
siman.header (module)
siman.helper_for_writing_beatiful_code (module)
siman.impurity (module)
siman.inout (module)
siman.monte (module)
siman.monte_functions (module)
siman.neb (module)
siman.pairs (module)
siman.picture_functions (module)
siman.set_functions (module)
siman.small_functions (module)
siman.SSHTools (module)
siman.workflow_utilities (module)
sl_misfit() (in module siman.geo)
smart_structure_read() (in module siman.inout)
smoother() (in module siman.functions)
SSHTools (class in siman.SSHTools)
stoichiometry_criteria() (in module siman.geo)
stoichiometry_criteria2() (in module siman.geo)
suf_en() (in module siman.analysis)
suf_en_polar_layered() (in module siman.analysis)
supercell() (in module siman.geo)
symmetry_criteria() (in module siman.geo)
symmetry_criteria_at() (in module siman.geo)
symmetry_multiply() (in module siman.geo)
T
test_transform_miller() (in module siman.geo)
toabinit() (siman.set_functions.InputSet method)
toJSON() (siman.set_functions.InputSet method)
TracePrints (class in siman.small_functions)
transform_miller() (in module siman.geo)
triangle_area_points() (in module siman.geo)
two_cell_to_one() (in module siman.geo)
U
unique_elements() (in module siman.functions)
update() (siman.set_functions.InputSet method)
update_des() (in module siman.calc_manage)
user (siman.SSHTools.SSHTools attribute)
uvw2hkl() (in module siman.geo)
V
vasp_run() (in module siman.monte)
vec_l() (in module siman.small_functions)
voltage_profile() (in module siman.analysis)
W
words() (in module siman.functions)
wrapper_cp_on_server() (in module siman.functions)
wrapper_create_coseg() (in module siman.pairs)
wrapper_create_coseg_C1() (in module siman.pairs)
wrapper_create_coseg_CSL7s() (in module siman.pairs)
wrapper_create_coseg_T1s() (in module siman.pairs)
wrapper_create_coseg_T2() (in module siman.pairs)
wrapper_create_pairs_H() (in module siman.pairs)
write() (siman.small_functions.TracePrints method)
write_database() (in module siman.database)
write_geometry_aims() (in module siman.inout)
write_jmol() (in module siman.inout)
write_lammps() (in module siman.inout)
write_occmatrix() (in module siman.inout)
write_xyz() (in module siman.inout)
wulff() (in module siman.analysis)
X
xcart2xred() (in module siman.geo)
xred2xcart() (in module siman.geo)
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