Index

electron_masses

Description | Description | Description | Description | Description | Description | Description | Description

[cpu_time_elapsed]

At the end of

[Dynamics_iter]

For a dynamics calculation

[Dynamics_iter_header]

For a dynamics calculation

[elec]

Fixed quantities relating to

[elec_header]

Fixed quantities relating to

[energy_force_elec]

Particle energies and forces

[energy_force_elec_header]

Particle energies and forces

[energy_force_nuc]

Particle energies and forces

[energy_force_nuc_header]

Particle energies and forces

[Minimize_iter]

For a minimization calculation

[Minimize_iter_header]

For a minimization calculation

[nuc]

Fixed quantities relating to

[nuc_header]

Fixed quantities relating to

[num_electrons]

Fixed quantities relating to

[num_nuclei]

Fixed quantities relating to

[position_elec]

Particle positions

[position_elec_header]

Particle positions

[position_nuc]

Particle positions

[position_nuc_header]

Particle positions

[pressure_flexible]

At the end of

[pressure_rigid]

At the end of

[restraint_angle]

Restraints

[restraint_angle_header]

Restraints

[restraint_coordinate]

Restraints

[restraint_coordinate_header]

Restraints

[restraint_dihedral]

Restraints

[restraint_dihedral_header]

Restraints

[restraint_distance]

Restraints

[restraint_distance_header]

Restraints

[restraint_line]

Restraints

[restraint_line_header]

Restraints

[restraint_plane]

Restraints

[restraint_plane_header]

Restraints

[restraint_tether]

Restraints

[restraint_tether_header]

Restraints

[total_dipole]

At the end of

[total_energy]

At the end of

[total_time_elapsed]

At the end of

[velocity_elec]

Particle velocities

[velocity_elec_header]

Particle velocities

[velocity_nuc]

Particle velocities

[velocity_nuc_header]

Particle velocities

adaptive step size

adaptive_step_size = false

adaptive_energy

adaptive_energy = 0.0001

adaptive_step_size

For a dynamics calculation

andersen_coupling

andersen_coupling = 0.1

Auger process

Auger dissociation of adamantane

beryllium atom

$\mathbf {Be}$

beryllium dihydride

$\mathbf {BeH_{2}}$

beryllium hydride

$\mathbf {BeH}$

beryllium_solid_cfg

see scripts

borane

$\mathbf {BH_{3}}$

bound_x

bound_x = -10000 10000

bound_y

bound_y = -10000 10000

bound_z

bound_z = -10000 10000

boundaries

periodic

Features

periodic, warm dense hydrogen

Pressure of warm dense

boundary

Ewald electrostatics

Ewald parameters

boundary, minimum image

Periodic boundary conditions

boundary, small vs large periodic

Periodic boundary conditions

cfgrepeat

see scripts

cfgscale

see scripts

cfgtrans

see scripts

conjugate_gradient

min = conjugate_gradient

constraints

Features

symbol

Constraints and restraints

contraints

hydrogen molecule

Hydrogen molecule

cubane

$\mathbf {Cubane}$

cutoff, pairwise

Pairwise cutoff

cutoffs

pairwise

Features

cyclopropane

$\mathbf {Cyclopropane}$

diamond_cfg

see scripts

diborane

$\mathbf {B_{2}H_{6}}$

dt

dt = 0.005

dynamics

Features | calc = single_pt | Dynamics | For a dynamics calculation

NVE

Pressure of warm dense

NVE vs NVT

thermostat = none

e_field

e_field = 0 0

e_field_freq

e_field_freq = 0

e_field_packet_duration

e_field_packet_duration = 0

eFF

command line

eFF

eFFview

The eFFview visualizer

command line

eFFview

command summary

eFFview

electron/nuclear display

Basic commands

fast graphics glitches

eFFview

ImageMagick

Saving snapshots and movies

ionized electrons

Basic commands

mouse controls

Basic commands

parameters

eFFview parameters

periodic boundaries

Basic commands

snapshots and movies

Saving snapshots and movies

spin pairing

Basic commands

timer bar

Basic commands

velocity vectors

Basic commands

electric field

Features | e_field = 0 0

electron mass

Valence electron ionization in | electron_mass = 1 | Description

Auger dissociation

Auger dissociation of adamantane

end_temperature

end_temperature = 0

error cancellation

Hydrogen atom

ethane

$\mathbf {Ethane}$

Ewald

parameters

Ewald parameters

ewald_autoset

ewald_autoset = true

ewald_k_cutoff

ewald_k_cutoff = 8

ewald_log_precision

ewald_log_precision = -6

ewald_max_re

ewald_max_re = 4.5

ewald_nuc_r

ewald_nuc_r = 1e-10

ewald_r_cutoff

ewald_r_cutoff = 7

ewald_re_cutoff

ewald_re_cutoff = 3.54

examples

core ionization in adamantane

Auger dissociation of adamantane

dendritic lithium

Dendritic forms of lithium

hydrogen atom

Hydrogen atom

hydrogen molecule

Hydrogen molecule

valence ionization in methane

Valence electron ionization in

warm dense hydrogen thermodynamics

Pressure of warm dense

file formats

input file .cfg

Input file .cfg

output file .eff

Output file .eff

restart file .cfg.restart

Restart file .cfg.restart

h2_box_cfg

see scripts

header tag

output file

Output file .eff

helium

protonated

$\mathbf {HeH^{+}}$

helium atom

$\mathbf {He}$

hydrogen atom

see examples | $\mathbf {H}$

hydrogen molecule

see examples | $\mathbf {H_{2}}$

hydrogen_cfg

see scripts

input file .cfg

see file formats

ionization

core

see examples

valence

see examples

lithium

bulk

Dendritic forms of lithium

clusters

Dendritic forms of lithium

lithium atom

$\mathbf {Li}$

lithium hydride

$\mathbf {LiH}$

lithium, dendritic

see examples

lithium_hydride_solid_cfg

see scripts

lithium_solid_cfg

see scripts

methane

$\mathbf {CH_{4}}$

min_freeze

min_freeze = none

minimization

Features | calc = single_pt | For a minimization calculation

CG vs Newton

min = conjugate_gradient

freeze nuclei/electrons

min_freeze = none

newton

min = conjugate_gradient

nose_hoover_coupling

nose_hoover_coupling = 1

num_steps

num_steps = 10000

orbital energies

Valence electron ionization in

output

every few iterations

print_every = 100

number of steps

num_steps = 10000

select print

Output

output file .eff

see file formats

output_energy_forces

output_energy_forces = none

output_position

output_position = all

output_restart

output_restart = all

output_restraints

output_restraints = all

output_velocity

output_velocity = all

Pauli repulsion

Features | Dendritic forms of lithium

periodic

periodic = none

pressure

Features

kinetic vs potential

Pressure of warm dense

rigid vs flexible

Pressure of warm dense

print_every

print_every = 100

propane

$\mathbf {Propane}$

rand_seed

rand_seed = 10000

random number seed

Random numbers

restart file .cfg.restart

see file formats

restraints

Features

list of types

Constraints and restraints

scripts

beryllium_solid_cfg

Beryllium

cfgrepeat

cfgrepeat

cfgscale

cfgscale

cfgtrans

cfgtrans

diamond_cfg

Diamond

h2_box_cfg

Hydrogen box

hydrogen_cfg

Pressure of warm dense

lithium_hydride_solid_cfg

Lithium hydride

lithium_solid_cfg

Lithium

uniform_electron_gas

Uniform electron gas

xyz2cfg

Auger dissociation of adamantane | Generating hydrocarbons

simulated annealing

Pressure of warm dense | Dendritic forms of lithium

single point calculation

Features | calc = single_pt | For a single point

single_pt

calc = single_pt

size limit

electron

size_limit_stiffness = 1

size_limit_stiffness

size_limit_stiffness = 1

start_temperature

start_temperature = 0

taper_cutoff

taper_cutoff = 1000

thermostat

Andersen

thermostat = none

Nose-Hoover

Pressure of warm dense | thermostat = none

time step

dt = 0.005

uncertainty principle

Hydrogen atom

uniform_electron_gas

see scripts

units

Units

velocities

initial

Features

velocities, Maxwell-Boltzmann

start_temperature = 0

virial expressions

Pressure of warm dense

visualizer

see eFFview

warm dense hydrogen

see examples

wavefunction

bond vs atom centered

Hydrogen molecule

xyz2cfg

see scripts