We give here a list of all possible options, and describe what
their purpose is and how they are used.
 2d

2d simulation rather than 3d. The option 3d also exists  it is
the default.
 cna

This option enables IMD to perform the CommonNeighbour
Analysis (CNA) during a simulation. The CNA is done in the same
way as in the utility program imd_cna.
The CNA starts at step cna_start (default: 0) and ends at
cna_end (default: maxsteps). The CNA is performed
every cna_int steps. The nearest neighbour distance for
common neighbours must be given by the parameter cna_rcut.
Using the parameter cna_write, a list of (up to eight)
fourdigit pair types
ijkl can be given. Atoms belonging to these pair types are
written to the files
<outfiles>.<n>.<ijkl>.cna.
For fcclike crystal structures, the option cna enables IMD to
write atoms belonging to a specific crystallinity into files
<outfiles>.<n>.crist which are written every
cna_int steps. Four types of crystallinity can be selected:
0 
atoms belonging to the fcc structure 
1 
atoms belonging to the hcp structure 
2 
12fold coordinated atoms not belonging to the fcc or hcp structure 
3 
not 12fold coordinated atoms 
Using the parameter cna_crist, a list of up to four types of
crystallinity can be given. The format of the .crist files is the one
of IMD configuration files where the 10th column represents the type of
crystallinity.
Note: The writing of .cna files is disabled when the parameter
cna_crist is used.
 rigid

This option enables IMD to combine atoms of one or several virtual
types into superatoms that behave like rigid bodies. Superatoms
are defined in the parameter file with the IMD parameter
rigid in the following form:
rigid v_1 v_2 ... v_n i j (k)
Here, v_1, v_2, ..., v_n
(n<=total_types) are virtual types that are combined into a
superatom. The integers i, j(, k) take on
the values 0 or 1. They define a restricted motion of the atoms of the
superatoms. For example, in a 3d simulation, 1 0 1 means
rigid motion in x and z direction while in y
direction, the constituent atoms of the superatom can move
freely. Hence, 1 1 1 means complete rigidity and
0 0 0 no rigidity at all (no superatom).
It is possible to
define up to total_types different (nonintersecting)
superatoms.
Note:Only translational motion of the superatoms is
possible; rotational motion is suppressed.
The option rigid
is currently implemented only for the ensembles nve, mik, and nvt.
 nbl

This option enables the usage of neighbor lists, which can
be reused for a certain number of steps. The neighbor list of an
atom includes the indices (cell and atom number within cell) of all
those atoms, whose distance at the moment of creation of the
list is within the interaction cutoff radius, or exceeds it by not
more than nbl_margin (which is a parameter). The neighbor
lists include all interacting particles, and thus remain valid,
as long as no atom has moved by more than nbl_margin.
If this is no longer the case, the neighbor lists are recomputed.
The advantage of neighbor lists is, that the number of atom pairs
for which the distance has to be computed is reduced by up to a
factor 6, which substantially reduces the computation time (
by up to 40%). The disadvantage is, that neighbor lists require a
considerable amount of memory, which is why they are made optional.
The speedup depends on the value of nbl_margin. The larger
it is, the longer the neighbor list remains valid  and the more
distances have to be computed at each step. A value of some 15%
of a typical nearest neighbor distance seems to be a good starting
point. The neighbor list then has to be recomputed every 1020
steps.
The maximal number of atom pairs in the neighbor list is determined
as a rough estimate times a factor nbl_size, a parameter
which defaults to 1.1. If the neighbor list turns out to
be too small, IMD aborts with an error message. This may happen if
the density of the system increases significantly, e.g. in an
NPT simulation. In such a case, nbl_size can be set
to a larger value, like 1.2. Note that the memory
requirement is directly proportional to nbl_size.
Limitations: Neighbor lists are currently implemented only
in 3d, and only for pair and
EAM interactions. In principle, they
could also be implemented in 2d and for angledependent interactions,
but for these the benefit is less important (neighbor lists are
already in use for some parts of the computation).
Epitax is also not supported with
neighbor lists  they make little sense, if the number of particle
can change at any time.
 nmoldyn

nMoldyn is a
postprocessor which computes from an MD trajectory various correlation
functions, especially ones which can be measured by inelastic neutron
scattering. The functionality of nMoldyn is described in J. Comput. Chem.
24, 657667 (2003). The option nmoldyn enables IMD to
write an MD trajectory to a single file, which can subsequently be
converted with the utility program
imd2nc.py to the netCDF format
required by nMoldyn.
IMD writes every nmoldyn_int timesteps a configuration to
the .nmoldyn trajectory file. The writing interval determines
the maximal frequency available in the correlation functions, whereas
the length of the trajectory determines the lowest frequency. It is
usually not required to write at every step, but only every 10 steps
or so, depending on the frequency range required. If the flag
nmoldyn_veloc=1, the velocities are also included in the
trajectory file, otherwise they are computed numerically from the
positions. This is accurate enough only for very small values of
nmoldyn_int. For larger nmoldyn_int it is
recommended to write also the velocities (this is the default).
The nMoldyn trajectory files can get rather large. Especially for
single particle correlation functions it is not necessary to have
the trajectories of all atoms, but only those of a representative
subset. For this reason, IMD writes only atoms with virtual types
smaller than ntypes to the trajectory file. By giving part
of the atoms larges virtual types, excessively large trajectory
files can be avoided.
Note: With the nmoldyn option, the atoms must be
numbered such, that with increasing number the virtual type does not
decrease (i.e., smaller virtual types come first). Moreover, the
numbering must start at zero, and must have no gaps.
 dsf

The option dsf allows to compute the dynamical structure factor
in an MD simulation, using an NVE integrator. Every dsf_int
steps, IMD computes the spacial Fourier transform for a number of
kvectors, and writes it to a .dsf File. The value of
dsf_int determines the maximal frequency in the resulting
time series, whereas the resolution in kspace is determined by
the size of the sample (the density of the reciprocal lattice).
The temporal Fourier transform of the autocorrelation of time series
in the .dsf file is then computed with the postprocessor
dynsf.
The weights of the different atom types, usually the coherent scattering
length, is given by the parameter dsf_weight, which requires
ntypes values. The spacial Fourier transform is computed for
dsf_nk series of kvectors, each of which is given in the
following format:
dsf_k k0_x k0_y k0_z kdir_x kdir_y kdir_z n
representing the series of kvectors k0 + i * kdir, i=0,...,n.
dsf_nk must be specified before any dsf_k entry,
and there must be exactly dsf_nk such entries. The kvectors
are given with respect to the reciprocal basis of the box vectors.
 msqd

This option enables the computation of the mean square
displacements (MSQDs) (for each atom type and each direction
separately). It shares its parameters with the option corr. The
computation of the MSQDs is started at step correl_start,
and ends at step correl_end. The reference positions are
first stored at step correl_start, and then they are reset
every correl_int steps (or never, if
correl_int=0, which is the default). The MSQDs are
computed every correl_ts steps between
correl_start and correl_end, and are written to
the file <outfiles>.msqd, preceeded by the current
simulation time. The format of the msqd file is:
time d2x_1 d2y_1 [d2z_1] [d2x_2 d2y_2 [d2z_2]] ...
where d2x_n is the mean square displacement of particles
of type n in x direction, etc. With the options
msqd_ntypes (default 1) and msqd_vtypes (default
0) you can choose, whether you want mean square displacements for
real types only or for all virtual types separately. If you choose
both options, the leading columns are for real types, the rear ones
are for the virtual types.
The parameters correl_start and correl_end can
be used to switch this option on and off during a multiphase
simulation.
 corr

This option enables the computation of the (spherically
averaged) van Hove selfcorrelation function (VHSCF).
The computation of the VHSCF is started at step
correl_start, and ends at step correl_end. Every
correl_int steps after correl_start, the
correlation histogram is written to files
<basename>.corr<n>.<i>, where
<n> is a running number and <i> ist
the atom type. Every correl_ts steps, correlation data is
added to the histogram.
The dimension of the correlation histogram is detemined by the
parameters correl_tmax (time direction) and
correl_rmax (radial direction). The step width of the
histogram is correl_ts in time direction, and (half) the
diagonal of the box, divided by correl_rmax, in radial
direction.
There are several modes for the output format, determined by the
parameter correl_omode:
1 for gnuplot files with 1 empty line between blocks
2 for gnuplot files with 2 empty lines between blocks
3 for large gnuplot files (fully occupied matrix) with no empty lines
4 for short files (refer to source for documentation)
(writes only a short header followed by matrix elements)
The third mode uses a further parameter, GS_rcut, which is
a cutoff radius for the data to be written.
The parameters correl_start and correl_end can
be used to switch this option on and off during a multiphase
simulation. Beware: in the current implementation, the
histogram is allocated only once at the beginning of the
simulation, and so the dimensions of the histogram must not change
during the simulation!
Known bugs:
Resetting the reference positions every correl_int
steps is fine, but why do we have to write out and clear the
histogram each time?
The time in the histogram is taken modulo correl_tmax,
but the reference positions are not reset, which spoils the whole
histogram, if correl_tmax > correl_int!
Why don't we use a radial cutoff of the histogram right away,
instead of the wiered constuction with the diagonal, which works
only for orthogonal boxes anyway? In any case, it is better not to
compute the parts of the histogram that are not needed, instead of
just not writing them out (parameter GS_rcut)!
 disloc

The disloc option enables certain features useful to detect
dislocations in quasicrystals.
If the disloc option is present, potential energy and position of each
particle can be compared to reference values. These reference values
are either read from the configuration file(which then must have a
correct header), or set to values
computed at a certain time step.
If the parameter calc_Epot_ref = 0 (default), the
reference potential energy is read from the column labelled
Epot_ref in the configuration file. Otherwise, the
potential energy at step reset_Epot_ref (default 0)
becomes the reference potential energy.
Similarly, the reference positions of the particles are set
to the actual positions at step update_ort_ref
(default 0). If update_ort_ref < 0, the reference
positions must be given in the columns labelled x_ref,
y_ref and z_ref (3D only) in the configuration
file.
If the parameter Epot_diff = 1 (default), the potential
energy written to .pic files
and to energy distribution
files is the difference of the actual potential energy and the
reference potential energy. This can be switched off by setting
Epot_diff = 0.
If dem_int > 0, particles whose potential energy
deviates from the reference energy by more than min_dpot
are written in intervals of dem_int to
differential energy map files.
Similarly, if dsp_int > 0, particles whose squared
displacement from the reference position exceeds min_dsp2
are written in intervals of dsp_int to
displacement map files.
The writing of these files can be switched off by setting the
writing intervals to zero.
 homdef

If lindef_interval is positive, the sample is linearly
deformed every lindef_interval steps. The linear deformation
is described by a full deformation matrix A, whose rows are
given by the scalar lindef_size times the vectors
lindef_x, lindef_y, and lindef_z (3d only).
The transformation x > x + A x
is applied to both the atom positions and the box vectors.
In order to prevent the box contents from just snapping back,
periodic boundary conditions are required, or boundary layers
of atoms which are moved during the deformation, but are kept fixed
otherwise.
The older interfaces for scale and shear deformations, activated
by the parameters exp_interval and hom_interval,
are deprecated and should no longer be used.
 deform

The deform option requires free boundary conditions (the
box won't be deformed, but periodic boundary conditions can be
used, e.g. when the deformation is orthogonal to the pbc (use at
own risk, take care of angular momentum). A deform step is performed
if max_deform_int is positive, and either the last deform
step was done max_deform_int steps ago, or a
relaxation integrator
is active and the sample is
sufficiently relaxed. In a deform step, all atoms of virtual type v
are shifted by the deform_shift vector for that type v. A
deform_shift for type v is specified as follows in the
parameter file:
deform_shift v shift_vector
All shift vectors are additionally multiplied with the scalar
deform_size.
During the first annealsteps steps, no deformations are
done. This mechanism can be used both for shears
(deform_shift parallel to sample boundary) and for
compressions or expansions (deform_shift perpendicular to
sample boundary). The atoms with the virtual types concerned are
usually located in two boundary layers of the sample.
Besides translations of atoms, the option deform also
allows shear transformations of atoms with a common virtual type.
In this case, the additional parameter deform_shear has to
be specified in the parameter file in the following format:
deform_shear v shear_vector
The shear transformation is given by
where the vector s is determined by deform_shear
and v is represented by the parameter deform_shift.
deform_shift, which should be a unit vector, has now the
meaning of the shear direction. The base point b of the
shear transformation can be specified through the parameter
deform_base which is the origin of the simulation box by
default. This point determines the invariant plane of the shear
transformation. deform_base has to be given in the
parameter file in the format
deform_base v base_point
 fbc

This option enables Force Boundary Conditions,
which are extra forces acting on atoms of certain
virtual types.
This is implemented for the nve and nvt ensembles, and for the
relaxation integrators.
The extra forces are specified by parameters.
For nonrelaxator ensembles (nve and nvt), the extra forces
are linearly interpolated between the values given by the
parameters extra_startforce and extra_endforce,
which take a virtual type as the first argument, and the
components of the extra force vector acting on atoms of that
virtual type as the following arguments. For different virtual
types, different extra forces can be specified. By default,
the extra forces are zero.
For relaxation integrators,
the extra forces are specified by the parameters
extra_startforce and extra_dforce in the
same format. extra_dforce specifies a force increment,
which is added to the applied force whenever the sample is
sufficiently relaxed.
The force increment is also added, if max_fbc_int > 0
and the last increment was added more than max_fbc_int
steps ago. After adding the force increment, the relaxation
continues.
Note that the parameter total_types must be read
before any extra forces.
 sock

Provide support for sockets (for visualization).
 pair

Use tabulated pair potentials. This is the default option. Its
only use currently is to enable IMD to employ additional pair
potentials in the options tersoff and ewald.
 eam

Use Embedded Atom Method potentials.
 eeam

Use extended Embedded Atom Method potentials.

keating, ttbp, stiweb, tersoff, and tersoff2

Use manybody potentials.
 ewald

Use Coulomb potential with Ewald summation
method.
 uniax

Use GayBerne potential for uniaxial
molecules.
 pacx

Link with PACX libraries in addition to MPI. Needed for
Metacomputing, but also useful if certain MPI routines are not
available. PACX is an extension of MPI which allows the
distribution of the simulation across a network of (possibly
continentwidely) separated supercomputers.
IMD uses MPI_Cart routines to set up the communication network
between the PEs. This is not possible with PACX since one
supercomputer sees only the communication nodes of the other and
not its topology. Therefore the MPI_Cart routines have been
replaced.
The PACX library is available from the PACXGroup at the RUS. A
description of PACX and how to use it can be found
here.
 shock

The option shock enables IMD to simulate shock waves.
The shock wave is generated by setting the velocities of the atoms
in routine imd_maxwell to a constant value shock_speed.
The velocity direction is in the positive xaxis.
There are several modes set by shock_mode:
 If shock_mode is set to 1 then the left part of the
sample ("flyer plate or piston") with thickness shock_strip is moved
towards the right part ("target").
 If shock_mode is set to 2 then two halves of the sample are
moved towards oneanother ("symmetric impact method").
 If shock_mode is set to 3 then the whole sample is moved
against a fixed wall ("momentum mirror method").
If the parameter shock_incr is set, then the shock wave velocity is
increased linearly from 0 to the final shock_speed.
 If shock_mode is set to 4 then the sample is compressed by two
mirrors moving at the velocities shock_speed_left and
shock_speed_right.
Up to now, we use a box which is periodic
along the y and zaxis and has free boundaries in the xdirection. Periodic
boundaries along the xdirection are also possible, but not yet implemented.
They can be realized by abusing hom_def and forgetting to rescaled the sample.
Important: Currently, the atom velocities for the
shockwave are set by the routine imd_maxwell, which is called at
the start of the simulation only. It is therefore not possible to
start a shockwave in a later phase of a multiphase simulation.
Therefore, this option is not multiphase
ready.
 laser

This option incorporates parameters for phenomenological laser heating of
sample surfaces. At the moment, usage of the laser toolbox is
not multiphase ready.
The laser option supports three heating modes.
The first mode is
instantaneous heating at the beginning of the simulation, which is done by
setting the particle velocity randomly according to a maxwell distribution.
It can be activated by setting the parameter laser_delta_temp to a value greater
than zero, which will be used as the maximum temperature increment at the
surface.
This is equivalent to using an infinitesimally short laser pulse with a fluence
(surface energy density) of ,
with the atom number density and the
absorption constant .
corresponds to the parameter laser_delta_temp.
The second heating mode works by continuous rescaling of the atomic velocities
after every IMD timestep. The energy gain in a single time step is proportional
to the timestep itself and to a source term, which depends on time t and depth
below the surface x like , that is,
an exponential decrease in depth with a gaussian time profile. This heating
mode expects the fluence in the parameter laser_sigma_e, the time of maximum
intensity and the width of the gaussian pulse in the parameters laser_t_0 and
laser_sigma_t. To activate this mode, it is enough to assign a value larger
than zero to laser_sigma_e. By integration over time and depth one receives the
relationship .
The third heating mode works only in conjunction with the TTMintegrator for
simulations with the TwoTemperatureModel. It is automatically activated if
IMD was compiled with the ttm and laser makeoptions. It works with the same
source term and parameters as the second mode (see above), but the energy is
exclusively added to the electronic subsystem. Of course, some more parameters
are required to configure the ttm
integrator. To reduce the effects of reflected pressure waves, a
damping module was implemented in IMD
named pdecay.
 laseryz

This option is a modified version of the second heating mode from
the laser option.
In addition to rescaling the atomic velocities, an intensity profile is
applied.
The intensity profiles are controlled by the parameter laser_tem_mode,
which needs three numbers.
The first number specifies the intensity profile, 0 for Laguerre polynomials
and 1 for Hermite polynomials.
The two following numbers define order and index of the
polynomial. Example: laser_tem_mode 1 0 0 gives a profile
with a Hermite polynomial (the one at the beginning), the two zeros define the
shape of the TEMmode (Transversale ElectroMagneticMode).
To adjust the laser beam relative to the y and zaxis, one has to specify the
parameters laser_sigma_w_y and laser_sigma_w_z.
For arguments smaller than 1, the beam will be adjusted relative to the y and
zlength of the irradiated sample (i.e. laser_sigma_w_y =
0.5, laser_sigma_w_z=0.5 will center the beam).
Arguments larger than one will give absolute distances relative to the left and
bottom edge. The last parameter which needs to be specified
is laser_sigma_w0, the beam waist.
laser_offset:
The density of the sample will be calculated automatically. In order to make
this work, an offset from the laser needs to be introduced. This can be
achieved e.g. with the following awkscript:
#!/usr/bin/awk f
{
if (FNR==3)
print $1, $2+30., $3, $4, $5, $6, $7, $8, $9, $10, $11
else if (FNR>8)
print $1, $2, $3, $4+15., $5, $6, $7, $8, $9, $10, $11
else
print $1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12
}
Usage: Copy this script in a script file offset.sh and make it executable (chmod a+x offset.sh). If you copy this script in the directory with a my_sample.chkpt file as your starting sample, then typing in a bash:
./offset.sh my_sample.chkpt > offset_my_sample.chkpt
will add 15 Å to the front and back of the sample. The sample for the
simulation start should be now offset_my_sample.chkpt. To reduce the effects of refelcted
pressure waves, a damping module was implemented in IMD
named pdecay.
 sm

This option based on the model of Streitz and Mintmire (Phys. Rev. B 50,
11996 (1994)) enables IMD to compute the charges of a metal/metaloxide system.
The valencies are determined by minimization of the electrostatic energy, which
is given by the expression
.
strictly depends on nuclear coordinates and is of no
consequence for the minimization, while
,
specifies the electronegativity of each atom
and
,
the electrostatic interaction matrix with the atomic hardness or selfCoulomb
repulsion . The terms
,
and
,
are the nuclear attraction potential and the Coulomb repulsive potential,
depending on the atomicdensity distribution
(Slater 1s orbital). For a detail
examination of such integrals see Roothaan (J. Chem. Phys. 19, 1445
(1951)). Both
contain one longrange term,
which is evaluated in the origin work of Streitz and Mintmire by the standard
Ewald technique. For the computation in IMD also the Wolf summation method (J. Chem. Phys.,
110(17):82548282, 1999) is applied. The
values of are chosen
as those that minimize . This is the equivalent of
solving the system
,
subject to the constraint of netcharge neutrality . The
chemical potential follows from
the electronegativity equalization
condition. Including the constraint of netcharge neutrality, above equation
can be either splitted into two systems of linear equations:
and ,
with and ,
or can be written via block matrix notation as
.
See Modelling Simul. Mater. Sci. Eng. 16, 025006 (2008). The block vector has all elements equal
to unity. In IMD both versions are implemented and for both a conjugate
gradient solver is applied.
From the electrostatic energy additional force
contributions result:
.
Implemented by Andreas Chatzopoulos, Johannes Roth and Franz Gähler.
 transport (nvx)

This option enables IMD to compute the heat conductivity of a
sample. It is automatically activated by the nvx ensemble. The sample is divided
into tran_nlayers layers. The temperature of layer 0 is
initialized to starttemp + dTemp_start, and linearly moved
to starttemp + dTemp_end during the simulation. Similarly,
the temperature of layer tran_nlayers/2 (in the middle of
the sample) is initially set to starttemp  dTemp_start,
and linearly moved to starttemp  dTemp_end. The time, the
heat conductivity, and the temperatures in layers 0 to
tran_nlayers/2 is written to the file
<basename>.tempdist every tran_interval
steps.
 stress

The option stress enables the computation of the stress or
pressure tensor. This is a nonnegligible extra effort, and should
be done only when the pressure distribution or the pressure tensor
is needed. The global, scalar pressure is always computed. If the
option stress is enabled, the components of the global pressure
tensor are written to the properties file every
eng_int time steps. It is also possible to write out distributions of the scalar or
tensorial pressure, and to write out the pressure tensor
contribution of each atom every press_int time steps, by
setting the press_int parameter to a positive value.
 fnorm

Writes the average of the modulus of a (random) force component
to the .eng file. This should be a good measure for the
degree of relaxation in a
relaxation simulation.
 einstein

Writes the Einstein frequency to the .eng file. This
value can be used as inv_tau_eta for a NoseHoover
thermostat. This option is supported in NVE, NVT and NPT
simulations only.
 efilter

Only those atoms (no virtual atoms) which have a potential
energy between e_pot_lower and e_pot_upper (must be specified for
all ntypes) are written in <outfile>.ef.<n>,
where <n> is a running number. This happens every
ef_checkpt_int step.
 fefl

Option for free energy simulations using the FrenkelLadd method
(J. Chem. Phys. 81 (1984) 3188).
Runs a simulation where the native interaction (lambda=0) can be switched to an
Einstein crystal (lambda=1) with harmonic springs between the initial and the
current atom positions. Implemented by Johannes Roth.
 writef

If force_int > 0, the forces on atoms are written
every force_int steps into the file
<outfile>.wf.<n>, where <n>
is a running number. If force_all = 0, only the forces of
atoms whose virtual type differs from the real type are written
(default); otherwise, the forces of all atoms are written.
 avpos

This option enables IMD to compute the average position of the
atoms during a time interval. The averaging begins at step
avpos_start (default 0) and ends at step
avpos_end (default maxsteps). Every
avpos_int steps, the averaged positions are written in an
output file <outfile>.<n>.avp. The output file
further contains the average potential energy of the atoms. After
writing the output, the averaging begins with the actual atom
positions. The number of steps between additions of coordinates is
specified by the parameter avpos_res. For each avpos
output file, an avpos iteration file is written which has the name
<outfile>.<n>.avp.itr and contains the actual
box vectors. When an NPT ensemble is used, the averaged box vectors
are written in this file.
 quasi

This option is required for the generation of truncated
icosahedra quasicrystals, one of the few structure types IMD can
generate itself.
 nnbr

Compute coordination numbers. The cutoff radius for neighbor
counting is atom type dependent: counted as a neighbor of an
atom of type i are those atoms of type j, which are within a
cutoff radius r_ij. The cutoff radii must be specified as a
ntypes^{2}dimensional vector nb_rcutin the
parameter file.
 ordpar

Compute order parameter closely related to the potential energy.
This option is mainly useful for twodimensional binary tiling
quasicrystals. In quasicrystals the potential energy of atoms of
the same type can be quite different, depending on their neighbourhood,
so that defects can be hard to detect. The order parameter  which is
printed in the output files in place of the potential energy  narrows
the potential energy distribution and improves the visibility of
defects.
Only atoms within a sphere of a certain radius which is
specified in the ntypes^{2}dimensional vector
op_rcut contribute to the order parameter: their
potential energy, weighted by the number specified in the
ntypes^{2}dimensional vector op_weight is
added up.
Twodimensional binary tiling quasicrystals obey in their
ground state a linear relation in the numbers of neighbors.
With the choice
op_rcut 1.50 1.25 1.25 0.85
op_weight 1.00 0.25 0.50 1.00
all atoms will then have the same value of the order parameter
in the ground state, and defects become visible through deviations
from this value. In three dimensions, such a simple relation usually
doesn't exist.
 pdecay

This option allows the damping of pressure waves, which are reflected at the
back of the sample. It is usually used together with
the laser or
laseryz modules.
Four different modes exist. A mode is set via pdecay_mode, so that
e.g. pdecay_mode 2 sets mode 2. Mode 0 linearly scales down the
momenta of the atoms, mode 1 is a quadratic scale down of the momenta. The
modes 2 and 3 add a friction part to the forces. Mode 2 in a linear and mode 3
in a quadratic fashion. The value xipdecay is a constant friction
parameter, that has to be specified for mode 2 and 3. The damping zone can be
specified via the parameter ramp_fraction. The possible values
for ramp_fraction are between 0 and 0.9. They define
the damping range relative to the sample size. A ramp_fraction of
e.g. 0.4 will create a damping ramp with a size of 40% of the sample's
length, starting at the back.
Usage example:
xipdecay 4.0
pdecay_mode 2
ramp_fraction 0.4
 atdist

Determines the timeaveraged distribution of atoms in a
rectangular block of material between the lower left corner
atdist_ll and the upper right corner atdist_ur.
For this purpose, the block is divided into a rectangular array of
bins, of dimension atdist_dim. Each bin contains a counter
for each atom type, and every atdist_int time steps such a
counter is incremented if an atom of the given type is located in
that bin. This recording is started at time step
atdist_start, and stopped at time step
atdist_end. Small samples can be periodically extended in
order to fill a large enough block, using the parameters
atdist_per_ll and atdist_per_ur, which are
integer vectors specifying the lower left and upper right corners,
respectively, of the the periodic array of copies of the sample. It
is the user's responsibility to choose this array large enough. The
parameter atdist_phi, which is given in multiples of 2 Pi,
can be used to rotate the sample around the zaxis, before it is
mapped to the array of bins. Furthermore, the positions and types
of all atoms in the block are written every atdist_pos_int
time steps to files *.cpt, which can be used for visualization with
the Covise program. The resulting distribution files *.atdist can
be analysed and converted with the utility program atdist.
This option is parallelized only by OpenMP, not by MPI.
 diffpat

Determines the diffraction pattern of a rectangular block
of material between the lower left corner diffpat_ll and
the upper right corner diffpat_ur by Fast Fourier
Transform (FFT). For this purpose, the block is divided into an
array of bins, of dimension diffpat_dim. Each bin contains
a counter for each atom type, and every time step such a counter is
incremented if an atom of the given type is located in that bin.
Every diffpat_int time steps, the FFT of the resulting
distrbution is computed, its intensities are added up, and the
array is cleared. In other words, the contributions of time slices
of diffpat_int steps are added up incoherently. The
recording of the diffraction pattern is started at time step
diffpat_start, and stopped at time step
diffpat_end. The scattering strength of the different
atoms types, usually propotional to the charge of the nucleus, must
be given with the parameter diffpat_weight.
Note that the resulution of the diffraction pattern (the size of
its pixels) is inversely proportional to the size of the block of
material, whereas the dimension of the distribution array
determines the range of reciprocal space for which the diffraction
pattern is computed. Unlike to option atdist,
the sample is not periodically extended in order to fill the block.
The resulting diffraction pattern files *.diffpat can be analysed
and converted with the utility program diffpat.
This option is parallelized only by OpenMP, not by MPI. It also
requires the FFTW library, whose
location must be configured in the Makefile.
 ada

This option enables IMD to perform the AngularDeviation Analysis
(ADA) during a simulation. The ADA value is added in each chkptfile
and every ada_write_int steps into a ..ada file. The
cutoff radius to identify nearest neighbors is either given as
ada_nbr_rcut or by ada_latticeConst. The parameter
ada_crystal_structure offers three different characterization schemes
ackland: Characterization according to Ackland & Jones Phys.Rev.B 73
054104 (2006), except that the nearest neighbor cutoff radius is
constant
Types: ada=0: bcc
ada=1: fcc (not written to .adafiles)
ada=2: hcp
ada=3: unassigned
ada=4: unknown (usually surface)
fcc: Modified scheme to identify defects in fcc crystals (extended
pattern as published in Begau et al. Acta Materialia 59 (2011)
934–942)
ada=0: bcc
ada=1: fcc (not written to .adafiles)
ada=2: hcp
ada=3: 12 neighbors, not fcc/hcp
ada=4: less than 12 neighbors
ada=5: more than 12 neighbors
ada=6: less than 10 neighbors
ada=7: more than 14 neighbors
bcc: Modified scheme to identify defects in bcc crystals
ada=0: bcc (not written to .adafiles)
ada=1: fcc
ada=2: hcp
ada=3: 14 neighbors, not bcc
ada=4: 1213 neighbors
ada=5: 15 neighbors
ada=6: less than 11 neighbors
ada=7: unknown
 nye

This option enables IMD to perform a Nye tensor analysis during a
simulation to numerically compute an approximation of he dislocation
Burgers vectors and the dislocation linedirection as published in
Begau et al. JMPS 60 (2012) 711–722.
Atomatically ativates the option ada as well.
For each atom classified as a defect, a pair of a (resultant) Burgers
vector and a line direction/line sense vector is computed and added to
the .chkpt and .adafiles.
Both vectors are outputted in cartesian coordinates and not in crystal
coordinates. The Nye tensor analysis only works correctly in single
crystals.
In .adafiles a compressed output format is used. If no Burgers vector
exists at one atom the column "rbv_data" consists only of the value
"0", if a Burgers vector is found, the output value is "1" followed by
six values defining the linedirection and the resultant Burgers
vector.
 monolj

Monoatomic LennardJones system. The masses are all set to 1,
and particles have no number. All this saves space, which is useful
for world records.
Editor's remark: Part of this could also be achieved by
using only one mass variable per atom type, instead of one per
atom.
 mono

Special version for one atom type. Hard coding of the number of
different atom types makes IMD faster.
 single

Do everything with single precision (default is double precision).
This saves space, which is useful for world records.
 4point

Imd uses by default a 3point Lagrange interpolation to
determine the interaction energy and the forces. This option
switches to a 4point Lagrange interpolation.
 hpo

The output is written with a higher precision.
 debug

Compile with debug flags.
 timing

This option gives an idea how much time is spent in IO.
 prof

Compile with profiling support.
 epitax

This option enables the simulation of vacuum deposition of
atoms. For more details take a look at the description of the
EPITAX implementation.
 ep

This option permits the application of an external potential. I.e. it can be
used to simulate and indentor. See Ju Li, Phys. Rev. B 67 (2003) 104105
 neb

This method can be used to calculate reaction pathways by the nudge elastic
band method (NEB). Currently, this option requires one CPU per image. The number of images is provided by the parameter
neb_nrep. The file names of the images are then coordname.0  coordname.[neb_nrep1]. NEB uses the minimization scheme provided by the ensemble, e.g. FIRE. NEB requires as further input parameter a spring constant neb_k.
The MEP should not depend on the value of neb_k, but the convergence behavior does. The neb_k should scale like one over the time step squared.
Variable spring constants can be used by specifying neb_vark_start and neb_kmax and neb_kmin. Climbing image NEB is used when neb_cineb_start and
neb_climbing_image are specified.
 rnemd

Option for computing transport properties by the MüllerPlathe
nonequilibrium exchange method, see
J. Chem. Phys. 106 (1997) 6082.
 zapp

removes the net momentum, assuming equal masses.
 clone

The purpose of this option is to work with a twodimensional system with two
degrees of freedom, but the computation runs in threedimensions. The
3*r_cutcondition for minimal cell size is establihed by "cloned" atoms which
move exactly as their parents do.