Index

Symbols

<A1-lattice> <A2-lattice> <A3-lattice> <A4-lattice> <A5-lattice> <abop> <adp> <Ah-lattice> <atom-coordinates> <atom-forces> <atom-types> <atom> <atomic-distance> <atomic-energy> <atoms> <B1-lattice> <B2-lattice> <B3-lattice> <B4-lattice> <bcc-lattice> <betaSn-lattice> <BFGS> <Bh-lattice> <bulk-modulus> <C1-lattice> <C15-lattice> <ca-ratio> <cell> <Cij> <constant> <CsCl-lattice> <D8a-lattice> <deformation> <deformations> <derivative> <derived-properties> <derived-property> <dhcp-lattice> <diamond-lattice> <eam> <electron-density>, [1] <embedding-energy>, [1] <exp-A> <exp-B> <exp-gaussian> <export-functions>, [1] <expression> <f-function> <fcc-lattice> <fit-dof>, [1], [2], [3] <fitting>, [1]

<fluorite-lattice> <functions>, [1], [2] <g-function> <gaussian> <hcp-lattice> <input-var> <job> <L10-lattice> <L12-lattice> <lattice-parameter> <lennard-jones> <mapping>, [1] <meam> <morse-A> <morse-B> <morse-C> <NaCl-lattice> <name> <nlopt> <omega-lattice> <pair-interaction>, [1] <param> <pbc> <point-defect> <poly> <potentials>, [1] <pressure> <product> <properties> <pxx> <pxy> <pxz> <pyy> <pyz> <pzz> <real-precision> <relax-dof>, [1] <relax> <sc-lattice> <screening>, [1] <spa> <spline> <structures>, [1] <sum> <tersoff> <user-function> <user-structure> <validate-potentials> <verbosity> <WC-lattice> <wurtzite-lattice> <zincblende-lattice>

A

add_ase_structure() (atomicrex.Job method) add_library_structure() (atomicrex.Job method) Analytic bond-order potential (ABOP) description example, [1], [2], [3], [4] parameters Angular Dependent Potential (ADP) description parameters

Atom types atom-coordinates atomicrex module AtomicStructure (class in atomicrex)

B

Bibliography

Broyden-Fletcher-Goldfarb-Shanno (BFGS) minimizer

C

calculate_gradient() (atomicrex.Job method) calculate_hessian() (atomicrex.Job method) calculate_residual() (atomicrex.Job method) cell() (atomicrex.AtomicStructure property) cell_origin() (atomicrex.AtomicStructure property) Cluster functionals Analytic bond-order potential (ABOP) Modified embedded atom method (MEAM) Tersoff potential

Combination functions compute_energy() (atomicrex.AtomicStructure method) compute_properties() (atomicrex.AtomicStructure method) Contribution guidelines Contributions Credits

D

deactivate_property() (atomicrex.AtomicStructure method) Debugging and testing Validation of potentials Defining a function deform_simulation_cell() (atomicrex.AtomicStructure method)

Deformations example Degree of freedom derived_properties() (atomicrex.Job property) Dimer

E

Elastic constants clamped ion example, [1], [2] relaxed ion Embedded atom method (EAM) description example, [1], [2], [3] parameters Examples Analytic bond-order potential (ABOP), [1], [2], [3], [4] Deformations Elastic constants, [1], [2] Embedded atom method (EAM), [1], [2], [3] extended markup language (XML) inclusions, [1], [2], [3] Force matching Global minimizer Modified embedded atom method (MEAM) Multi-component system, [1] NLopt minimizer, [1] Pair potential Python interface, [1], [2], [3], [4], [5] Spa minimizer Stillinger-Weber potential (SW) User defined functions, [1], [2], [3], [4] User defined structures, [1], [2]

extended markup language (XML) Inclusions Inclusions; example, [1], [2], [3]

F

Fitting phase forces() (atomicrex.AtomicStructure property) Function definition Functions constant exponential screening, [1] Gaussian function Gaussian screening interpolation functions Morse potential form, [1], [2] polynomial product screening functions specialized spline sum user defined

G

get_atoms() (atomicrex.AtomicStructure method) get_cell() (atomicrex.AtomicStructure method) get_forces() (atomicrex.AtomicStructure method) get_number_of_atoms() (atomicrex.AtomicStructure method) get_pbc() (atomicrex.AtomicStructure method) get_positions() (atomicrex.AtomicStructure method) get_potential_energy() (atomicrex.AtomicStructure method)

get_potential_lower_bounds() (atomicrex.Job method) get_potential_parameters() (atomicrex.Job method) get_potential_upper_bounds() (atomicrex.Job method) get_pressure_tensor() (atomicrex.AtomicStructure method) get_target_forces() (atomicrex.AtomicStructure method) get_types() (atomicrex.AtomicStructure method) Global minimizer example

I

Input variables Atom types Floating point precision Job name Verbosity

Installation Interpolation functions

J

Job (class in atomicrex)

Job file Job name

L

lattice-parameter Least squares

Lennard-Jones potential description parameters

M

Minimizers Broyden-Fletcher-Goldfarb-Shanno (BFGS) Global minimizer NLopt minimizer Spa minimizer Models Modified embedded atom method (MEAM) description example parameters

modify_property() (atomicrex.AtomicStructure method) module atomicrex Monte Carlo sampling

N

name() (atomicrex.Job property)

NLopt minimizer example, [1]

O

Objective function Hessian sampling, [1] weight model

Optimization algorithms Output phase output_results() (atomicrex.Job method)

P

Pair functionals Embedded atom method (EAM) Pair potential example Pair potentials general pair potential Lennard-Jones potential parse_input_file() (atomicrex.Job method) pbc() (atomicrex.AtomicStructure property) perform_fitting() (atomicrex.Job method) Point defects positions() (atomicrex.AtomicStructure property) potential_energy() (atomicrex.AtomicStructure property) Potentials, [1] common parameters overview potentials() (atomicrex.Job property) Pre-defined structures prepare_fitting() (atomicrex.Job method)

print_potential_parameters() (atomicrex.Job method) print_properties() (atomicrex.AtomicStructure method) (atomicrex.Job method) Properties, [1] atomic energy atomic forces bulk modulus derived property elastic constants energy per atom internal structural parameters lattice constants pressure stiffness tensor stress tensor properties() (atomicrex.AtomicStructure property) Python interface example, [1], [2], [3], [4], [5] overview scipy

R

Relaxation Residual style sum of squares tolerance

S

Screening functions set_positions() (atomicrex.AtomicStructure method) set_potential_parameters() (atomicrex.Job method) set_target_forces() (atomicrex.AtomicStructure method) set_types() (atomicrex.AtomicStructure method) set_verbosity() (atomicrex.Job method) Setup Simulated annealing Spa minimizer example Specialized functions Stillinger-Weber potential (SW) example Structures, [1] beta-Sn, A5 body-centered cubic (BCC), A2 C15 lattice caesium chloride (CsCl), B2 D8a lattice diamond, A4 dimer double hexagonal close packed (DHCP) face-centered cubic (FCC), A1 fluorite, C1 format conversion hexagonal close packed (HCP), A3 L10 L12 omega-phase rocksalt (NaCl), B1 simple cubic (SC), Ah tungsten carbide (WC), Bh user defined wurtzite, B4 zincblende, B3

structures() (atomicrex.Job property)

T

tags() (atomicrex.AtomicStructure property) target_forces() (atomicrex.AtomicStructure property) Tersoff potential description parameters Three-body potentials Analytic bond-order potential (ABOP) Modified embedded atom method (MEAM) Tersoff potential

Tolerance Training phase Training set Two-body potentials Embedded atom method (EAM) general pair potential Lennard-Jones potential types() (atomicrex.AtomicStructure property)

U

User defined functions example, [1], [2], [3], [4] User defined structures example, [1], [2] format conversion from external file via job file

Utility scripts

V

Validation set

Verbosity

W

Weight model

write_lammps_dump() (atomicrex.AtomicStructure method) write_poscar() (atomicrex.AtomicStructure method)