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faps 1.5 documentation
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I
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J
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M
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N
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P
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W
Symbols
-d, --daemon
faps command line option
-i, --interactive
faps command line option
-j <$JOB_TYPE>, --job-type=<$JOB_TYPE>
faps command line option
-m, --import
faps command line option
-n, --no-submit
faps command line option
-o <CMDOPTS>, --option=<CMDOPTS>
faps command line option
-p, --plain
faps command line option
-q, --quiet
faps command line option
-s, --silent
faps command line option
-v, --verbose
faps command line option
A
a (faps.Cell attribute)
absl_postproc() (faps.Structure method)
add_freeform_structure() (backend.cif_file.CifFileBackend method)
(backend.sql.AlchemyBackend method)
add_symmetry_structure() (backend.cif_file.CifFileBackend method)
(backend.sql.AlchemyBackend method)
AlchemyBackend (class in backend.sql)
aligned_to() (faps.Guest method)
alpha (faps.Cell attribute)
angle_between() (in module faps)
Atom (class in faps)
atomic_number (faps.Atom attribute)
atomic_numbers (faps.Structure attribute)
B
b (faps.Cell attribute)
backend (module)
backend.cif_file (module)
backend.sql (module)
base_structure (backend.sql.FreeFunctionalisedStructure attribute)
(backend.sql.SymFunctionalisedStructure attribute)
beta (faps.Cell attribute)
binding_sites (module)
binding_sites.absl (module)
bond_length_check() (faps.Structure method)
C
c (faps.Cell attribute)
calc_surface_area() (faps.PyNiss method)
calculate_binding_sites() (in module binding_sites.absl)
calculate_properties() (faps.PyNiss method)
calculate_pxrd() (faps.PyNiss method)
calculate_zeo_properties() (faps.PyNiss method)
Cell (class in faps)
cell (faps.Cell attribute)
charges_from_egulp() (faps.Structure method)
charges_from_gulp() (faps.Structure method)
charges_from_repeat() (faps.Structure method)
check_close_contacts() (faps.Structure method)
check_connectivity() (faps.Structure method)
cif_bond_dist() (in module faps)
cif_file (backend.sql.FreeFunctionalisedStructure attribute)
(backend.sql.SymFunctionalisedStructure attribute)
CifFileBackend (class in backend.cif_file)
com (faps.Guest attribute)
commandline() (config.Options method)
compress_files() (in module faps)
compressed_open() (in module cube)
(in module faps)
config (module)
coordination (faps.Atom attribute)
count_ordered_types() (in module faps)
covalent_radius (faps.Atom attribute)
crystal_system (faps.Cell attribute)
Cube (class in cube)
cube (module)
D
del_fractional_coordinate() (faps.Atom method)
dihedral() (in module faps)
direction3d() (in module binding_sites.absl)
dot3() (in module faps)
dump_state() (faps.PyNiss method)
E
element (faps.Atom attribute)
elements (module)
email() (faps.PyNiss method)
environment variable
absl_compress_files
absl_cutoff
absl_delete_files
absl_exe
absl_radius
absl_sigma
absl_write_smooth_cube
charge_method
dedicated_queue
default_cell
dft_code
dispersion
dl_poly_exe
egulp_exe
egulp_grid
egulp_grid_parameters
egulp_potential
egulp_potential_difference
egulp_typed_atoms
email
equation_of_state
esp_resolution
fastmc_compress_files
fastmc_delete_files
fastmc_exe
fastmc_keep_unfolded_cubes
fastmc_ncpu
ff_opt_code
find_maxima
fold
gromacs_compress_files
gromacs_delete_files
gromacs_exe
gromacs_metal_geometry
gromacs_verbose
grompp_exe
guests
,
[1]
gulp_exe
gulp_terse
import
infer_types_from_bonds
initial_structure_format
interactive
kpoints
mc_code
mc_cutoff
mc_eq_steps
mc_history_freq
mc_jobcontrol
mc_numguests_freq
mc_pressure
mc_probability_plot
mc_probability_plot_spacing
mc_prod_steps
mc_state_points
mc_supercell
mc_temperature
mc_zero_charges
mdrun_exe
no_absl
no_charges
no_dft
no_force_field_opt
no_gcmc
no_properties
no_submit
optim_all
optim_cell
optim_h
order_atom_types
plain
platon_exe
platon_pxrd
potcar_dir
psf_dir
qeq_fit
qeq_parameters
queue
quiet
repeat_compress_files
repeat_delete_files
repeat_exe
repeat_ncpu
run_all
serial_memory
siesta_accuracy
siesta_compress_files
siesta_delete_files
siesta_exe
siesta_ncpu
siesta_to_cube
silent
spin
surface_area_probe
surface_area_resolution
surface_area_save
surface_area_uniform_sample
symmetry
tar_after
tar_extract_before
threaded_codes
threaded_memory
trjconv_exe
update_opts
vasp_compress_files
vasp_custom_incar
vasp_delete_files
vasp_exe
vasp_ncpu
vasp_to_cube
verbose
zeo++
zeo++_exe
eos (module)
eos.peng_robinson (module)
error_name (cube.Cube attribute)
esp_grid (faps.PyNiss attribute)
esp_reduced (faps.PyNiss attribute)
esp_to_cube() (faps.PyNiss method)
extract_atoms() (in module cube)
F
faps (module)
faps command line option
-d, --daemon
-i, --interactive
-j <$JOB_TYPE>, --job-type=<$JOB_TYPE>
-m, --import
-n, --no-submit
-o <CMDOPTS>, --option=<CMDOPTS>
-p, --plain
-q, --quiet
-s, --silent
-v, --verbose
fastmc_postproc() (faps.Structure method)
fix_vasp_wrapped_types() (in module faps)
fold_and_maxima() (faps.Structure method)
folded_name (cube.Cube attribute)
format_tp_path() (in module faps)
fpos() (faps.Atom method)
fractional (faps.Atom attribute)
FreeFunctionalisedStructure (class in backend.sql)
from_cif() (faps.Atom method)
(faps.Structure method)
from_file() (faps.Structure method)
from_gromacs() (faps.Structure method)
from_gulp_output() (faps.Structure method)
from_lines() (faps.Cell method)
from_pdb() (faps.Atom method)
(faps.Cell method)
(faps.Structure method)
from_siesta() (faps.Atom method)
(faps.Structure method)
from_vasp() (faps.Atom method)
(faps.Structure method)
from_xyz() (faps.Atom method)
(faps.Structure method)
fullname (backend.sql.SymFunctionalisedStructure attribute)
functional_group_id (backend.sql.Functionalisation attribute)
functional_groups (backend.sql.FreeFunctionalisedStructure attribute)
FunctionalGroup (class in backend.sql)
Functionalisation (class in backend.sql)
functionalisations (backend.sql.FunctionalGroup attribute)
(backend.sql.SymFunctionalisedStructure attribute)
G
gamma (faps.Cell attribute)
gcmc_supercell (faps.Structure attribute)
gen_neighbour_list() (faps.Structure method)
gen_supercell() (faps.Structure method)
gen_types_from_bonds() (faps.Structure method)
get() (config.Options method)
get_atomic_number() (faps.Atom method)
get_cell() (faps.Cell method)
get_fractional_coordinate() (faps.Atom method)
get_gcmc_supercell() (faps.Structure method)
get_params() (faps.Cell method)
getbool() (config.Options method)
getfloat() (config.Options method)
getint() (config.Options method)
gettuple() (config.Options method)
gfloat() (in module faps)
Guest (class in faps)
guests
I
id (backend.sql.FreeFunctionalisedStructure attribute)
(backend.sql.FunctionalGroup attribute)
(backend.sql.Functionalisation attribute)
(backend.sql.SymFunctionalisedStructure attribute)
ifpos() (faps.Atom method)
imcon (faps.Cell attribute)
import_old() (faps.PyNiss method)
in_cell() (in module cube)
incar_extend() (in module faps)
index (faps.Atom attribute)
inverse (faps.Cell attribute)
ipos() (faps.Atom method)
is_exe() (in module job_handler)
is_linear() (faps.Guest method)
is_metal (faps.Atom attribute)
is_reversible() (faps.Guest method)
J
job_dispatcher() (faps.PyNiss method)
job_handler (module)
JobHandler (class in job_handler)
L
load_defaults() (config.Options method)
load_guest() (faps.Guest method)
load_job_defaults() (config.Options method)
load_job_type() (config.Options method)
load_site_defaults() (config.Options method)
logo (module)
lorentz_berthelot() (in module faps)
M
main() (in module faps)
matrix_rotate() (in module faps)
maxima() (cube.Cube method)
min_dist() (in module faps)
min_distance() (in module faps)
min_vect() (in module binding_sites.absl)
minimum_image() (in module faps)
minimum_supercell() (faps.Cell method)
minimum_width (faps.Cell attribute)
mk_connectivity_ff() (in module faps)
mk_dl_poly_control() (in module faps)
mk_egulp_ini() (in module faps)
mk_egulp_params() (in module faps)
mk_gcmc_control() (in module faps)
mk_gromacs_mdp() (in module faps)
mk_incar() (in module faps)
mk_kpoints() (in module faps)
mk_repeat() (in module faps)
mkdirs() (in module faps)
molar_volume (faps.Guest attribute)
move_and_overwrite() (in module faps)
N
name (backend.sql.FreeFunctionalisedStructure attribute)
(backend.sql.FunctionalGroup attribute)
(backend.sql.SymFunctionalisedStructure attribute)
name_from_types() (in module faps)
natoms (faps.Guest attribute)
(faps.Structure attribute)
O
Options (class in config)
order_by_types() (faps.Structure method)
other_bond_index() (in module faps)
P
parameters (module)
params (faps.Cell attribute)
parse_qeq_params() (in module faps)
peng_robinson() (in module eos.peng_robinson)
populate_groups() (backend.sql.AlchemyBackend method)
post_summary() (faps.PyNiss method)
postrun() (faps.PyNiss method)
prod() (in module faps)
PyNiss (class in faps)
R
re_init() (faps.PyNiss method)
read_file() (cube.Cube method)
remove_duplicates() (faps.Structure method)
remove_files() (in module faps)
rotate() (faps.Symmetry method)
run_absl() (faps.PyNiss method)
run_charges() (faps.PyNiss method)
run_dft() (faps.PyNiss method)
run_fastmc() (faps.PyNiss method)
run_ff_opt() (faps.PyNiss method)
run_optimise_gromacs() (faps.PyNiss method)
run_optimise_gulp() (faps.PyNiss method)
run_qeq_egulp() (faps.PyNiss method)
run_qeq_gulp() (faps.PyNiss method)
run_repeat() (faps.PyNiss method)
run_siesta() (faps.PyNiss method)
run_vasp() (faps.PyNiss method)
S
same_guests() (in module faps)
send_to_database() (faps.PyNiss method)
set_atomic_number() (faps.Atom method)
set_cell() (faps.Cell method)
set_fractional_coordinate() (faps.Atom method)
set_gcmc_supercell() (faps.Structure method)
set_params() (faps.Cell method)
site (backend.sql.Functionalisation attribute)
smoothed_name (cube.Cube attribute)
start_cif() (backend.sql.AlchemyBackend method)
state_points() (in module faps)
status (backend.sql.FreeFunctionalisedStructure attribute)
(backend.sql.SymFunctionalisedStructure attribute)
status() (faps.PyNiss method)
step_absl() (faps.PyNiss method)
step_charges() (faps.PyNiss method)
step_dft() (faps.PyNiss method)
step_force_field() (faps.PyNiss method)
step_gcmc() (faps.PyNiss method)
step_properties() (faps.PyNiss method)
store_results() (backend.sql.AlchemyBackend method)
strip_blanks() (in module faps)
Structure (class in faps)
sub_property() (faps.Structure method)
subgroup() (in module faps)
supercell() (faps.Structure method)
surface_area() (faps.Structure method)
SymFunctionalisedStructure (class in backend.sql)
Symmetry (class in faps)
symmetry (module)
symmetry_tree (faps.Structure attribute)
sys_argv_strip() (in module faps)
T
terminate() (in module faps)
to_cif() (faps.Structure method)
to_config_field() (faps.Structure method)
to_cssr() (faps.Structure method)
to_egulp() (faps.Structure method)
to_gromacs() (faps.Structure method)
to_gulp() (faps.Structure method)
to_gulp_optimise() (faps.Structure method)
to_siesta() (faps.Structure method)
to_vasp() (faps.Structure method)
to_vector_strings() (faps.Cell method)
to_zeoplusplus() (faps.Structure method)
trans_frac() (faps.Symmetry method)
translate() (faps.Atom method)
try_int() (in module faps)
try_symlink() (in module faps)
types (faps.Guest attribute)
(faps.Structure attribute)
U
uff_coordination (faps.Atom attribute)
ufloat() (in module faps)
unique() (in module faps)
unique_name (backend.sql.FreeFunctionalisedStructure attribute)
update_absl() (faps.Structure method)
update_charges() (faps.Structure method)
update_gcmc() (faps.Structure method)
update_pos() (faps.Structure method)
V
validate_gulp_output() (in module faps)
vdw_radius (faps.Atom attribute)
vecdist3() (in module binding_sites.absl)
(in module faps)
void_volume() (faps.Structure method)
volume (faps.Cell attribute)
(faps.Structure attribute)
W
weight (faps.Guest attribute)
(faps.Structure attribute)
welcome() (in module faps)
which() (in module job_handler)
write_cube() (cube.Cube method)
write_generic() (cube.Cube method)
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faps 1.5 documentation
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