## IMD |
## Configuration File PostprocessingFor the postprocessing of IMD configuration files, IMD contains a group of utility programs with a common usage model:
These programs are compiled as follows: gmake imd_utility[_option][_2d]where utility is the name of the program. Some programs
support further options which can be appended to the compilation
target with the component _option. By default, a program
for 3d is compiled. Most programs support 2d versions which can be
compiled using the additional component _2d in the
compilation target.
The programs are run by giving the program name and one or more
command line options. The following options are supported by
Most of the programs produce output files. The name of these
output files are the names of the input files with program specific
suffixes. If checkpoint files are used as input files, the suffix
## imd_angleComputes angular distribution histograms of IMD configurations. The following special options can be used:
The output file name of phi g_000 g_001 ... g_00N g_011 ... g_01N ... g_0NN g_100 ... g_NNNThe first entry phi is the angle with range [0,180], and
the remaining entries are the histogram values for the different
combinations of atom types. The histogram entry g_ijk is
the normalized number of times the angle phi occurs
between the atoms of type i, j, and k
where the angle is centered at i. g_ijk is
normalized with respect to the total number of angles computed. In
the case of 2 types of particles, for example, the histogram has
the following format:
phi g_000 g_001 g_011 g_100 g_101 g_111 ## imd_cnaPerforms the Common-Neighbour Analysis (CNA) for IMD configuration files. The CNA classifies pairs of atoms according to their local
environment. (J.D.Honeycutt and H.C.Andersen, A set of four indices
The cutoff distance can be given for all pairs of atom types by
the parameter
pair type occurrence relative occurrence -------------------------------------------------------- ijkl n_ijkl t_ijkl ... ... ... ... ... ...where n_ijkl is the number of times the pair type
ijkl occurs and t_ijkl is n_ijkl divided
by the total number of pairs.
The following special options can be used:
## imd_connComputes the connection matrix. The following special option can be used:
## imd_coord
Computes coordination numbers of IMD configurations.
Bond Occurrence 00 c_00 01 c_01 ... 0N c_0N 10 c_10 ... NN c_NN The second table contains the occurrences Coordination Occurrence 0 occ_0 1 occ_1 ... cmax occ_cmax The following special options can be used:
If where the sum is over all neighbour atoms ## imd_elcoComputes the stress tensor, the tensor of the elastic moduli, and the pressure derivative of the bulk modulus of IMD configurations using the interatomic potentials. The following potentials are currently supported: - Tabulated pair potentials. This is the default.
- EAM potentials. In this case, the component
**_eam**has to be used in the compilation target. - Many-body potentials. If the components
**_tersoff**,**_stiweb**, or**_keating**are used in the compilation target, the Tersoff, the Stillinger-Weber, or the Keating potential are used, respectively. Many-body potentials only work in 3d.
By default,
The following special options can be used:
## imd_pairComputes radial distribution histograms of IMD configurations. The following special options can be used:
r d_00 d_01 ... d_0N d_11 ... d_NN f_00 f_01 ... f_0N f_11 ... f_NNThe first entry r is the radius, the remaining entries are
the histogram values for the different combinations of atom types.
The histogram entry d_ij is the number of times the
distance r occurs between atoms of types i and
j, divided by the total number of atoms, and f_ij =
d_ij/(4*pi*r^2) is a normalized radial distribution.
## imd_psCreates (vector) PostScript files from IMD configurations.
The geometrical setup of the projection (3d) is shown in the following figure.
## imd_ringComputes ring statistics of IMD configurations.
The following special options can be used:
Ring length Total occurrence Relative occurrence 3 n_3 p_3 4 n_4 p_4 . . . . . . . . . lmax n_lmax p_lmaxwhere n_i is the number of rings of length i and
p_i is n_i divided by the total number of rings
up to the length lmax. imd_ring writes the table of
the relative occurrences of the ring lengths into a file with
suffix .ring.
## imd_strainComputes the strain tensor from the atomic displacements. The displacements must be given in a file with the following format: x y (z) dx dy (dz)where x, y, z are the positions of the
atoms and dx, dy, dz are the
displacements. The displacement file must have the name
<outfiles>.dsp. Alternatively, the displacement file
can be created using the IMD option disloc. Then the restart
parameter -r<nn> should be given where
<nn> is the number of steps corresponding to the
displacement file.
The following special options can be used:
imd_strain is the displacement file
name with the suffix .strain.
The output file has the following format: n x y (z) e_xx e_yy (e_zz) (e_yz) (e_zx) e_xywhere n is a number (not the IMD atom number), x,
y, z are the coordinates, and e_ij are
the components of the strain tensor.
## imd_stressComputes the stress tensor from an IMD IMD determines the (raw) stress tensor by evaluating the virial
corresponding to the atomic forces. x y (z) s_xx s_yy (s_zz) (s_yz) (s_zx) s_xywhere x, y, z are the positions of the
atoms and s_ij are the components of the raw stress
tensor. The stress file name must have the suffix .press.
Alternatively, the raw stress file can be created using the IMD
option stress (with the parameter vector press_dim
set equal to zero). Then the restart parameter -r
<nn> should be given where <nn> is
the number of steps corresponding to the stress file.
The following special option can be used:
imd_stress is the raw stress file
name with the suffix .stress.
The output file has the following format: x y (z) s_xx s_yy (s_zz) (s_yz) (s_zx) s_xy vwhere s_ij are the components of the true stress tensor of
the atom with coordinates x, y, z and
v is the volume of the corresponding Voronoi cell.
## imd_torsionComputes torsion distribution histograms of IMD configurations. The following special options can be used:
The output file name of For every slot in the histogram, one line is written: phi g_0000 g_0001 ... g_000N g_0011 ... g_001N ... g_00NN g_0100 ... g_NNNNThe first entry phi is the angle with range [0,180], the
remaining entries are the histogram values for the different
combinations of atom types. The histogram entry g_ijkl is
the normalized number of times the torsion angle phi
occurs between the atoms of type i, j,
k, and l.
phi g_0000 g_0001 g_0011 g_0100 g_0101 g_0110 g_0111 g_1100 g_1101 g_1111 |