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User Guide

Output Files


IMD writes checkpoints in step intervals given by the parameter checkpt_int. A checkpoint is a complete configuration file, whose name has the form <outfiles>.<n>.chkpt, where <n> is a running number. Together with every checkpoint file, an iteration file <outfiles>.<n>.itr is written, which contains the current values of certain parameters, such as the current stepnumber, box size, external temperature and external pressure. A simulation can be restarted from every checkpoint. If checkpt_int is zero, no checkpoints are written. A header is prepended to the checkpoint file. Each header line begins with a # so that IMD or gnuplot will not have any problems reading such files. In the case of more than one processor and parallel_output is one the header is written to the separate file <outfiles>.<n>.head. A single file can be generated with or catfiles.csh from the utilities.

Properties File

In intervals of eng_int steps, IMD writes certain properties to a file <outfiles>.eng, one line each time. The properties written are, in this order, the current simulation time, the potential energy per atom, the kinetic energy per atom (which is normalized such that it is identical to the actual system temperature), the pressure and the volume. If the simulation ensemble is npt_axial, and the preprocessor flag PAXTEST is set, this is followed by the axial pressures and box dimensions.


IMD can be directed to write out distributions of several quantities. To compute the distribution of the kinetic energy, say, the system (or part of it) is divided into an array of rectangular boxes, called bins. For each such bin, the average value of the kinetic energy of the atoms it contains is computed. The whole array of values for all bins constitutes the distribution, and is written to a file. For other quantities, one proceeds analogously. The writing of the distributions of all supported quantities is controlled by the following common parameters:

dist_int interval for distribution writing
dist_dim dimensions of distribution array
dist_ll lower left corner in user coords
dist_ur upper right corner in user coords

Distributions are written every dist_int timestep, they have dimensions dist_dim, and only atoms within a rectangular box between the lower left corner dist_ll and the upper right corner dist_ur are considered. If the latter two parameters are missing, the default is to take the whole system, but this works only for rectangular simulation boxes. It is stronly recommended to always specify these parameters.

In addition to these parameters, the writing of the distribution of each supported quantity can individually be switched on and off with a flag, which also specifies the format in which the distribution is written. If the flag is 0, the distribution is not written (default). If the flag is 1, the distribution is written in binary floats, which is the recommended format. A flag value of 2 means writing the distribution in ASCII with bin coordinates, and 3 in ASCII without bin coordinates.

Currently, distributions of the following quantities are are supported:

Flag name Quantity
dist_Epot_flag potential energy
dist_Ekin_flag kinetic energy
dist_presstens_flag pressure tensor (option stress, all components in one file)
dist_Ekin_long_flag longitudinal kinetic energy (shock wave simulation)
dist_Ekin_trans_flag transversal kinetic energy (shock wave simulation)
dist_Ekin_comp_flag transversal kinetic energy difference between
transverse directions for anisotropic samples
(shock wave simulation)
dist_press_flag scalar pressure (requires option stress)
dist_pressoff_flag off-diagonal entries of the pressure tensor (shock
wave simulation)
dist_shock_shear_flag shear stress (shock wave simulation)
dist_shear_aniso_flag shear stress difference between transverse directions
for anisotopic samples (shock wave simulation)
dist_dens_flag local density (shock wave simulation)
dist_vxavg_flag local sample velocity

Writing Selected Atoms

The option disloc allows to selectively write certain particles to special files. These files are useful to see dislocations.

A differential energy map (DEM) file consists of all particles for which the difference of the potential energy and a (particle specific) reference potential energy exceeds a certain threshold min_dpot. These particles are written the file <outfile>.dem.<n> containing lines of the form

     type x y z dE_pot.

A displacement map (DSP) file shows the displacement of each atom in relation to a reference configuration. Every dsp_intth step the atoms are written to a file <outfile>.dsp.<n>, containing lines of the form

     type x y z dx dy dz.
where dx, dy and dz denote the displacement. At the step update_ort_ref (default 0), the current configuration is copied into the reference configuration. This overwrites the reference configuration read from the reference file, which can be avoided if update_ort_ref is set to a negative value. In any case, a reference file is always read. It must be specified in the parameter reffile. Each line of the reference file must describe the same atom as the corresponding line in the configuration file. This is checked using the atom number.