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 write Atomeye (.cfg) files, as well as read and write VASP (POSCAR/OUTCAR) files 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 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} .

• This is followed 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 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 \mathbf{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 $NP+1$) has the following format.

$s_{x_{i}}\ s_{y_{i}}\ s_{z_{i}}$

They are the scaled coordinates of atom $i$.

If we let $\mathbf {s} _{i}=(s_{x_{i}},s_{y_{i}},s_{z_{i}})^{T}$ be the scaled coordinate vector of atom $i$ and let $\mathbf {r} _{i}=(x_{i},y_{i},z_{i})^{T}$ be the real coordinate vector, then they are related to each other by,

$\mathbf {r} _{i}=\mathbf {H} \cdot \mathbf {s} _{i}$

where 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{H}} is the matrix described in the previous sub-section.

The default setting is sufficient for quasi-static (energy minimization) simulations involving a single species without any fixed atoms.

Use writevelocity

If we want to save a restart file from Molecular Dynamics simulations, we need to save atomic velocities. This can be turned on by setting writevelocity = 1, as in the following command.

 finalcnfile = myfile.cn  writevelocity = 1  writecn

The command for reading this file is the same as before. MD++ will automatically detect the format of the saved .cn files.

When writevelocity = 1, 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 s_{x_i} \ s_{y_i} \ s_{z_i} \ vs_{x_i} \ vs_{y_i} \ vs_{z_i} }

The last three numbers are the scaled velocities 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} . They are related to the real velocities in the same way as the scaled coordinates are related to the real coordinates.

Use writeall

If the simulation contains more than one species, or if some atoms are fixed, these kinds of information can only be saved if we set writeall = 1, as in the following command.

 finalcnfile = myfile.cn  writeall = 1  writecn

If writeall = 1, atomic velocities will be written to file regardless of the value of the writevelocity varible.

When writeall = 1, 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 s_{x_i} \ s_{y_i} \ s_{z_i} \ vs_{x_i} \ vs_{y_i} \ vs_{z_i} \ {\rm epot[}i{\rm ]} \ {\rm fixed[}i{\rm ]} \ {\rm topol[}i{\rm ]} \ {\rm species[}i{\rm ]} \ {\rm group[}i{\rm ]} \ {\rm image[}i{\rm ]}}

The last 6 numbers are additional attributes 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} in MD++.

• 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 {\rm epot[}i{\rm ]}} is the local potential energy 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} . The sum 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 {\rm epot[}i{\rm ]}} for all atoms equals to the potential energy of the system.

• 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 {\rm fixed[}i{\rm ]}} has the default value 0. If it equals to 1, then 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} is fixed. Its position will not change in energy minimization or Molecular Dynamics simulations. If it equals to -1, then this atom is "removed". It will not be included in the evaluation of potential energy, and it will not exert any force on other atoms. (This is a useful way to remove an atom without changing the indices of other atoms.)

• 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 {\rm topol[}i{\rm ]}} stores the central symetry deviation (CSD) parameter 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} or other parameters computed by visualization algorithms. By default, it is not computed. To turn on the calculation of this field in energy minimzation or MD simulations, set plot_color_axis = 2. You can also ask MD++ to compute the 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 {\rm topol[}i{\rm ]}} value for the current configuration by calling calcentralsymmetry.

• 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 {\rm species[}i{\rm ]}} stores the element type 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} . For a binary system, 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 {\rm species[}i{\rm ]}} is either 0 or 1. For a ternary system, 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 {\rm species[}i{\rm ]}} is either 0, 1 or 2. The interatomic potential function uses this field to decide which function to use, e.g. to compute the interaction between two given atoms.

• 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 {\rm group[}i{\rm ]}} specifies which group 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} belongs to. By default, 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 {\rm group[}i{\rm ]} = 0} for all atoms. One way to define a group of atoms is to use commands fixatoms_by_position or fixatoms_by_ID, followed by setfixedatomsgroup and freeallatoms. Once a group (or several groups) of atoms are defined, we can use commands movegroup, setgroupcomvel, addFext_to_group, relax_by_group to manipulate them.

• 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 {\rm image[}i{\rm ]}} has the default value -1. If it is not -1, it means 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} is not a real atom but a (periodic) image of another atom, whose index is stored in 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 {\rm image[}i{\rm ]}} . This means that if 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 {\rm image[}i{\rm ]}} moves in one step of the simulation, MD++ will move 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} by the same amount before going to the next step.

Property .out File

An MD simulation will produce a property file if saveprop = 1 is set before the run command, as is given in the following example.

 saveprop = 1    savepropfreq = 100
 output_fmt = "curstep EPOT KATOM Tinst TSTRESSinMPa_zz H_33"
 outpropfile = prop.out openpropfile
 run 

(This is written for the .script input format. For .tcl input format, we need to add MD++ at the beginning of each line.)

In this example, one line of information is written into file prop.out every 100 MD steps. The content is specified by the output_fmt variable. Every variable that can be set in an MD++ input script can be included in output_fmt. The following is a brief explanation of the few variables included in this variable.

• curstep is the current step of the simulation.

• EPOT is the potential energy of the system.

• KATOM is the kinetic energy of all atoms. EPOT + KATOM is the total energy and should be conserved in an NVE MD simulation.

• Tinst is the instantaneous temperature in K.

• TSTRESSinMPa_zz is the zz component of the total stress given by the Virial formula, including both kinetic and potential energy terms. MD++ follows the sign convention of Parrinello-Rahman, which is opposite to many elasticity books. In MD++, a normal stress component has positive value if it is compressive.

• H_33 is the 33 component of the 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{H}} matrix.

MD++ cannot read the output .out file. This file can be plotted using other programs such as Matlab and Gnuplot.

Atomeye .cfg file

We often use Atomeye to visualize the atomic configurations from MD++ simulations. The following command writes the current configuration into Atomeye's .cfg format.

 finalcnfile = nanowire.cfg  writeatomeyecfg

By default, all atoms will be written into the .cfg file. However, we usually configure MD++ to plot only the "defect" atoms (either with a high local energy or central symmetry parameter) in the X-display window. In this case, only those atoms that would be seen in the X-display window will be written into the .cfg file. As a result, the .cfg file is usually much smaller than the .cn file. This allows us to save it more frequently (e.g. to make a movie). However, in this case we cannot restart the simulation from the .cfg file because many atoms are missing.

We can also configure MD++ to write .cfg files periodicaly in an MD simulation by setting savecfg = 1 and, e.g., savecfgfreq = 10 before calling run.

VASP POSCAR File

MD++ can write atomic configurations into VASP's POSCAR format using the writePOSCAR command. It can also read the energy and atomic forces from VASP's OUTCAR file using the readOUTCAR command. The following example illustrates how to do create a vacancy in Si crystal, call VASP to compute the energy and atomic forces and return to MD++. For convenience, the input script is written in Tcl format.

  MD++ { crystalstructure = diamond-cubic
         latticeconst = 5.431 #(A) for Si
         latticesize  = [ 1  0  0  1
                          0  1  0  1
                          0  0  1  1 ]
         makecrystal
         finalcnfile = "perf.cn" writecn
       }

  MD++ input = \[ 1 0 \] fixatoms_by_ID removefixedatoms
  MD++ finalcnfile = "si7.cn" writecn

  # use MD++'s empirical potential to compute potential energy
  MD++ eval
  MD++_PrintVar EPOT "(eV)"
  MD++_PrintVectorArray F "(eV/A)" 0 7

  # write VASP input file
  MD++ finalcnfile = "POSCAR" writePOSCAR

  # specify how to run VASP on your local computer
  MD++ command = "./vasp"

  # run VASP
  MD++ runcommand

  # read force and energy from VASP output file
  MD++ readOUTCAR
  MD++_PrintVar EPOT "(eV)"
  MD++_PrintVectorArray F "(eV/A)" 0 7

To really run this example, you need to prepare other VASP input files, such as INCAR, KPOINTS, POTCAR, etc. in your local directory. Of course, you can always copy the POSCAR file created by MD++ to a different folder for a future VASP run. This allows us to relax an atomic configuration using an empirical potential first before relaxing it using VASP.

LAMMPS File

The following command writes the current configuration into a file that can be read by LAMMPS.

 finalcnfile = myconfig.lammps  writeLAMMPS

MD++ can also read atomic configurations saved from a LAMMPS run (the "dump" file) by the following command.

 incnfile = dump.mysimulation.300K  readLAMMPS