Output File Formats in MD++

Output File Formats in MD++

This tutorial describes the formats of MD++ output files. The most frequently used file in MD++ is the configuration (.cn) file describing atomic positions (and other attributes). Also used a lot is the property (.out) file produced by Molecular Dynamics simulations. MD++ can also read and write VASP (POSCAR) and LAMMPS files.

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Configuration .cn File

In MD++, we save the current atomic configuration (in memory) to a file using the following command.

 finalcnfile = myfile.cn  writecn

(This is what we write in a .script input file. If we use .tcl input file, we need to put MD++ at the beginning of the line.)

The atomic configuration can be read into MD++ later (either in the same simulation run or in a different run) using the following command.

 incnfile = myfile.cn  readcn

Different amount of details are saved into the file, depending on two flags: writevelocity and writeall. By default, writevelocity = 0 and writeall = 0.

Overall format

The saved .cn files have the following format.

The first line is the number of atoms $NP$.

This is followed by $NP$ lines of data, each corresponding to an atom (more explanation below).

After that, there is a 3x3 matrix Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle H} whose column vectors are the three repeat vector of the supercell.

The next line contains the number of species and the name of the species. By default, the number of species is 1 and the name of the species is "Mo". The species name can be set in the input file by, e.g. element0 = "Si", element1 = "C". The species names will not be used by the simulation. Even if you forgot to set them, the simulation can still run correctly.

The last line contains two numbers: zeta and zetav. These are variables used in the Nose-Hoover thermostat. We save them to enhance reproducibility of MD simulations from a saved .cn (restart) file. These values are zero if the file is saved after quasi-static simulations.

Basic atomic information

When writeall = 0 and writevelocity = 0 (default), each line in the saved .cn file (from line 2 to line Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle NP + 1} ) has the following format.

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle sx_i, sy_i, sz_i}

They are the scaled coordinates of atom Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle i} .

If we let Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{s}_i = (sx_i, sy_i, sz_i)^T} be the scaled coordinate vector of atom Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle i} and let Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{r}_i = (x_i, y_i, z_i)^T} be the real coordinate vector, then they are related to each other by,

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://wikimedia.org/api/rest_v1/":): {\displaystyle \mathbf{r}_i = \mathbf{H} \cdot \mathbf{s}_i }

When writeall = 0 and writevelocity = 1, the saved cn files have the following format.