cleanup

.pytest_cache/.gitignore

@@ -0,0 +1,2 @@
+# Created by pytest automatically.
+*

.pytest_cache/CACHEDIR.TAG

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+Signature: 8a477f597d28d172789f06886806bc55
+# This file is a cache directory tag created by pytest.
+# For information about cache directory tags, see:
+#	https://bford.info/cachedir/spec.html

.pytest_cache/README.md

@@ -0,0 +1,8 @@
+# pytest cache directory #
+
+This directory contains data from the pytest's cache plugin,
+which provides the `--lf` and `--ff` options, as well as the `cache` fixture.
+
+**Do not** commit this to version control.
+
+See [the docs](https://docs.pytest.org/en/stable/how-to/cache.html) for more information.

.pytest_cache/v/cache/lastfailed

@@ -0,0 +1 @@
+{}

.pytest_cache/v/cache/nodeids

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+[
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_cast_energies_to_floats",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_change_energy_units_to_meV",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_format_axis",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_format_defect_name",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_format_ticks",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_get_displacement_dict",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_all_defects_incorrect_output_path",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_all_defects_min_e_diff",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_all_defects_nonexistent_defect_folder",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_colorbar_SnB_naming_w_site_num",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_colorbar_displacement",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_colorbar_fake_defect_name",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_colorbar_legend_label_linecolor_title_saveplot",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_colorbar_max_distance",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_colorbar_with_rattled_and_imported",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_from_other_charge_states",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_keywords",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_not_enough_markers",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_only_rattled",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_only_rattled_and_rattled_dist_from_other_charge_states",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_rattled_and_dist_from_other_chargestates",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_value_error",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_datasets_without_saving",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_add_colorbar",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_fake_output_directories",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_include_site_num_in_name",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_missing_unperturbed_energy",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_unrecognised_name",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_without_colorbar",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defect_without_title_units_in_meV",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_plot_defects_output",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_purge_data_dict",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_remove_high_energy_points",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_save_plot",
+  "tests/test_plotting.py::PlottingDefectsTestCase::test_verify_data_directories_exist"
+]

.pytest_cache/v/cache/stepwise

@@ -0,0 +1 @@
+[]

build/lib/SnB_input_files/castep.param

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+# Example CASTEP .param file
+# For keyword description, see https://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/content/modules/castep/keywords/
+
+# Geometry optimization parameters
+GEOM_METHOD: BFGS
+GEOM_CONVERGENCE_WIN : 4
+GEOM_ENERGY_TOL : 0.00005 eV
+GEOM_FORCE_TOL : 0.05 ev/ang
+GEOM_MAX_ITER : 300
+
+# Exchange-correlation parameters
+XC_FUNCTIONAL : HSE06
+
+# Electronic minimization parameters
+SMEARING_SCHEME : Gaussian
+ELEC_ENERGY_TOL : 0.00005 eV
+ELECTRONIC_MINIMIZER: CG
+MAX_SCF_CYCLES: 50
+
+# Basis set parameters
+BASIS_PRECISION: FINE # 0.1 eV/atom

build/lib/SnB_input_files/cp2k_input.inp

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+&GLOBAL
+	PROJECT relax ! files generated will be named relax.out etc
+	RUN_TYPE GEO_OPT ! geometry optimization
+	IOLEVEL MEDIUM ! reduce amount of IO
+&END GLOBAL
+
+&FORCE_EVAL
+	METHOD Quickstep
+
+	! the electronic structure part
+	&DFT
+		BASIS_SET_FILE_NAME HFX_BASIS
+		POTENTIAL_FILE_NAME GTH_POTENTIALS
+
+		CHARGE 0
+		SPIN_POLARIZED .TRUE.
+
+		&MGRID
+			CUTOFF [eV] 500 ! PW cutoff
+		&END MGRID
+
+		&QS
+			METHOD GPW
+			EPS_DEFAULT 1e-10
+			EXTRAPOLATION ASPC
+		&END QS
+		! use the GPW method (i.e. pseudopotential based
+		! calculations with the Gaussian and Plane Waves
+		! scheme)
+
+		&DFT
+			&KPOINTS
+				SCHEME GAMMA 1 1 1 ! Gamma point only
+			&END KPOINTS
+		&END DFT
+
+		&POISSON
+			PERIODIC XYZ ! the default
+		&END POISSON
+
+		&PRINT
+
+			! at the end of the SCF procedure generate cube
+			! files of the density
+			&E_DENSITY_CUBE OFF
+			&END E_DENSITY_CUBE
+
+		&END PRINT
+
+		! use the OT METHOD for robust and efficient
+		! SCF, suitable for all non-metallic systems.
+		&SCF
+			SCF_GUESS RESTART ! can be used to RESTART an interrupted calculation
+			MAX_SCF 80
+			EPS_SCF 1e-06 ! accuracy of the SCF procedure typically 1.0E-6 - 1.0E-7
+			&OT
+				PRECONDITIONER FULL_SINGLE_INVERSE
+				MINIMIZER DIIS
+			&END OT
+			! an accurate preconditioner suitable also for
+			! larger systems, the most robust choice (DIIS
+			! might sometimes be faster, but not as
+			! stable).
+
+			&OUTER_SCF ! repeat the inner SCF cycle 10 times
+				MAX_SCF 10
+				EPS_SCF 1e-06 ! must match the above
+			&END OUTER_SCF
+
+			! do not store the wfn
+			&PRINT
+				&RESTART
+				&END RESTART
+			&END PRINT
+		&END SCF
+
+		! specify the exchange and correlation treatment
+		&XC
+
+			! use a PBE0 functional
+			&XC_FUNCTIONAL
+				&PBE
+					SCALE_X 0.75
+					SCALE_C 1.0
+				&END PBE
+			&END XC_FUNCTIONAL
+			! 75% GGA exchange 100% GGA correlation
+
+			&HF
+				FRACTION 0.25
+				! 25 % HFX exchange
+				&SCREENING
+					EPS_SCHWARZ 1e-06
+					SCREEN_ON_INITIAL_P True
+				&END SCREENING
+
+				! important parameter to get stable HFX
+				! calcsneeds a good (GGA) initial guess
+				&INTERACTION_POTENTIAL
+					POTENTIAL_TYPE TRUNCATED
+					CUTOFF_RADIUS 6.0
+					T_C_G_DATA ./t_c_g.dat
+				&END INTERACTION_POTENTIAL
+
+				! for condensed phase systemsshould be less
+				! than halve the celldata file needed with the
+				! truncated operator
+				&MEMORY
+					MAX_MEMORY 4000
+					EPS_STORAGE_SCALING 0.1
+				&END MEMORY
+			&END HF
+		&END XC
+
+	&END DFT
+
+	! Description of the system
+	! Structure will be read from external file
+	&SUBSYS
+		&CELL
+			CELL_FILE_FORMAT CIF
+			CELL_FILE_NAME structure.cif
+		&END CELL
+
+		&TOPOLOGY
+			COORD_FILE_NAME structure.cif
+			COORD_FILE_FORMAT CIF
+		&END TOPOLOGY
+	&END SUBSYS
+
+&END FORCE_EVAL

build/lib/SnB_input_files/default_POTCARs.yaml

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+POTCAR_FUNCTIONAL: PBE
+POTCAR:
+  Ac: Ac
+  Ag: Ag
+  Al: Al
+  Ar: Ar
+  As: As
+  At: At_d
+  Au: Au
+  B: B
+  Ba: Ba_sv
+  Be: Be
+  Bi: Bi_d
+  Br: Br
+  C: C
+  Ca: Ca_sv
+  Cd: Cd
+  Ce: Ce
+  Cl: Cl
+  Co: Co
+  Cr: Cr_pv
+  Cs: Cs_sv
+  Cu: Cu
+  Dy: Dy_3
+  Er: Er_3
+  Eu: Eu
+  F: F
+  Fe: Fe
+  Ga: Ga_d
+  Gd: Gd
+  Ge: Ge_d
+  H: H
+  He: He
+  Hf: Hf_pv
+  Hg: Hg
+  Ho: Ho_3
+  I: I
+  In: In_d
+  Ir: Ir
+  K: K_sv
+  Kr: Kr
+  La: La
+  Li: Li_sv
+  Lu: Lu_3
+  Mg: Mg
+  Mn: Mn_pv
+  Mo: Mo_sv
+  N: N
+  Na: Na_pv
+  Nb: Nb_sv
+  Nd: Nd_3
+  Ne: Ne
+  Ni: Ni
+  Np: Np
+  O: O
+  Os: Os
+  P: P
+  Pa: Pa
+  Pb: Pb_d
+  Pd: Pd
+  Pm: Pm_3
+  Pr: Pr_3
+  Pt: Pt
+  Pu: Pu
+  Rb: Rb_sv
+  Re: Re
+  Rh: Rh_pv
+  Ru: Ru_pv
+  S: S
+  Sb: Sb
+  Sc: Sc_sv
+  Se: Se
+  Si: Si
+  Sm: Sm_3
+  Sn: Sn_d
+  Sr: Sr_sv
+  Ta: Ta_pv
+  Tb: Tb_3
+  Tc: Tc_pv
+  Te: Te
+  Th: Th
+  Ti: Ti_sv
+  Tl: Tl_d
+  Tm: Tm_3
+  U: U
+  V: V_sv
+  W: W_sv
+  Xe: Xe
+  Y: Y_sv
+  Yb: Yb_2
+  Zn: Zn
+  Zr: Zr_sv

build/lib/SnB_input_files/example_generate_all_config.yaml

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+## Example config file for snb-generate_all
+
+# General/distortion options
+oxidation_states:
+  Cd: 2
+  Te: -2
+distortion_increment: 0.1
+bond_distortions: [-0.6, -0.5, -0.4, -0.3, -0.2, -0.1, 0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6]
+distorted_elements:  # (Default = None, distorts nearest neighbours)
+  Int_Cd_2:
+    Cd
+dict_number_electrons_user:  # (Default = None, determined from electron change at defect site)
+  Int_Cd_2:
+    2
+
+# Rattle options
+stdev: 0.25  # Rattle standard deviation (Default = 10% of auto-determined bulk bond length)
+d_min: 2.25 # Displacements that place atoms closer than d_min are penalised. (Default = 80% of auto-determined bulk bond length)
+n_iter: 1  # Number of Monte Carlo cycles to perform. (Default: 1)
+active_atoms: None  # Atoms to apply rattle displacement to. (Default = all atoms)
+nbr_cutoff: 5  # The radial cutoff distance (in Angstroms) used to construct the list of atomic neighbours for checking interatomic distances. (Default: 5)
+width: 0.1  # Width of the Monte Carlo rattling error function, in Angstroms. (Default: 0.1)
+max_attempts: 5000  # Limit for how many attempted rattle moves are allowed a single atom; if this limit is reached an `Exception` is raised
+max_disp: 2.0  # Rattle moves that yields a displacement larger than max_disp will always be rejected. Rarely occurs, mostly used as a safety net
+seed: 42  # Seed from which rattle random displacements are generated (Default = 100*distortion_factor, e.g. 40 for -60% distortion, 100 for 0% Distortion/Rattled etc)
+local_rattle: False  # If True, rattle displacements will tail-off as we move away from the defect site. Not recommended as typically worsens performance.
+
+# Defects section: to specify charge states and defect index/frac coords
+defects:
+  vac_1_Cd:  # Name should match your defect structure file/folder
+    charges: [0, -1, -2]  # List of charge states
+    defect_coords: [0.0, 0.0, 0.0]  # Fractional coords for vacancies!
+  Int_Cd_2:
+    charges: [0, +1, +2]
+    defect_index: -1
+
+# Code specific section
+# For VASP, we can specify POTCARs like this:
+POTCAR:
+  Sn: Sn_d  # Element matching its POTCAR symbol
+  Te: Te
+# For Quantum Espresso, we can specify the pseudopotentials like:
+pseudopotentials:
+  Cd: Cd_pbe_v1.uspp.F.UPF
+  Te: Te.pbe-n-rrkjus_psl.1.0.0.UPF

build/lib/SnB_input_files/example_generate_config.yaml

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+### Example config file for snb-generate, with all options commented out
+
+## General/distortion options
+# oxidation_states:
+#   Cd: 2
+#   Te: -2
+# distortion_increment: 0.1
+# bond_distortions: [-0.6, -0.5, -0.4, -0.3, -0.2, -0.1, 0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6]
+# distorted_elements:  # (Default = None, distorts nearest neighbours)
+#   Int_Cd_2:
+#     Cd
+# dict_number_electrons_user:  # (Default = None, determines from electron change at defect site)
+#   Int_Cd_2:
+#     2
+
+## Rattle options
+# stdev: 0.25  # Rattle standard deviation (Default = 10% of auto-determined bulk bond length)
+# d_min: 2.25  # Displacements that place atoms closer than d_min are penalised. (Default = 80% of auto-determined bulk bond length)
+# n_iter: 1  # Number of Monte Carlo cycles to perform. (Default: 1)
+# active_atoms: None  # Atoms to apply rattle displacement to. (Default = all atoms)
+# nbr_cutoff: 5  # The radial cutoff distance (in Angstroms) used to construct the list of atomic neighbours for checking interatomic distances. (Default: 5)
+# width: 0.1  # Width of the Monte Carlo rattling error function, in Angstroms. (Default: 0.1)
+# max_attempts: 5000  # Limit for how many attempted rattle moves are allowed a single atom; if this limit is reached an `Exception` is raised
+# max_disp: 2.0  # Rattle moves that yields a displacement larger than max_disp will always be rejected. Rarely occurs, mostly used as a safety net
+# seed: 42  # Seed from which rattle random displacements are generated (Default = 100*distortion_factor, e.g. 40 for -60% distortion, 100 for 0% Distortion/Rattled etc)
+# local_rattle: False  # If True, rattle displacements will tail-off as we move away from the defect site. Not recommended as typically worsens performance.
+
+## CLI arguments can also be specified using the config file:
+# charge: 0  # (Default = None, assumes charge range from -2 to +2)
+# min_charge: -2  # (Default = None, assumes charge range from -2 to +2)
+# max_charge: 2  # (Default = None, assumes charge range from -2 to +2)
+# defect_index: 1 # (Default = None, determines defect position automatically)
+# defect_coords: [0, 0, 0] # (Default = None, determines defect position automatically)
+# code: VASP
+# name: Int_1_Sb  # (Default = None, automatically generated using pymatgen syntax)
+# verbose: False