Index

Symbols | A | B | C | D | E | F | G | I | J | L | M | N | O | P | R | S | T | U | V | W

Symbols

<A1-lattice>
<A2-lattice>
<A3-lattice>
<A4-lattice>
<A5-lattice>
<abop>
<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>
<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
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 attribute)
cell_origin (atomicrex.AtomicStructure attribute)
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 attribute)
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]
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, [1], [2], [3]
extended markup language (XML)
Inclusions
Inclusions; example, [1], [2], [3]

F

Fitting phase
forces (atomicrex.AtomicStructure attribute)
Function definition
Functions
Gaussian screening
Morse potential form, [1], [2]
constant
exponential screening, [1]
interpolation functions
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_parameters() (atomicrex.Job method)
get_pressure_tensor() (atomicrex.AtomicStructure method)
get_target_forces() (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)
Monte Carlo sampling

N

name (atomicrex.Job attribute)
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
Lennard-Jones potential
general pair potential
parse_input_file() (atomicrex.Job method)
pbc (atomicrex.AtomicStructure attribute)
perform_fitting() (atomicrex.Job method)
Point defects
positions (atomicrex.AtomicStructure attribute)
potential_energy (atomicrex.AtomicStructure attribute)
Potentials, [1]
common parameters
overview
potentials (atomicrex.Job attribute)
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 attribute)
Python interface
example, [1], [2], [3], [4], [5]
overview
scipy

R

Relaxation
Residual
style
sum of squares
tolerance

S

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

T

tags (atomicrex.AtomicStructure attribute)
target_forces (atomicrex.AtomicStructure attribute)
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)
Lennard-Jones potential
general pair potential
types (atomicrex.AtomicStructure attribute)

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)