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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



Julius 2008-04-29