8.2. DCDFTBMD

It is a menu related to the divide and conquer type density functional the strongly bound molecular dynamics method.

Purchase of add-on is necessary for using.

How to install DCDFTBMD is described in Installing Winmostar and solvers.

8.2.1. Configure

After setting, press the OK button.

The Reset button returns to the default state. Save button to save the settings. Load button loads settings saved with Save.

Extending Simulation

Run a continuation job. The keyword RESTART = TRUE is set, and the calculation restarts from the restart information.

See Run for details.

# of Threads
Specify the OpenMP parallel number.
Use MPI
Use MPI. Specify the MPI parallel number in the horizontal column.
Basic
Charge
Specify the charge of the entire system.
Multiplicity
Specify the spin multiplicity of the entire system.
Parameter Set
Select the type of parameter to use. The names of folders placed in the DFTBParam folder under the Winmostar installation folder (by default C:\winmos10\) are listed.The folder placed under the DFTBParam folder must contain parameter files such as skf. For example, a hierarchical structure of C:\winmos10\DFTBParam\mio-1-1\C-C.skf is assumed.
Open Directory for Parameter Set
Open the aforementioned DFTBParam folder.
Reload Parameter Set
Reload the aforementioned DFTBParam folder and update the list of Parameter Set.
Executable
Specifies the binary of DCDFTBMD used for the calculation. When using MPI, it is necessary to specify an MPI compatible binary such as dftb_mpiomp_mpich.00.x. The binary specified here must be passed through PATH on the remote server.
Advanced
Method

Select SCC or NCC.

THIRDFULL
Use third-order correction for SCC Hamiltonian.
DAMPXH
Use short-range damping of SCC interactions for X-H pairs.
MAXITER
Specifies the maximum number of SCC cycles.
ECONV
Specify the convergence condition of energy change. (atomic unit)
DCONV
Specify the convergence condition of the gradient change. (atomic unit)
DISP

Use empirical dispersion force correction.

DISPTYPE
Specifies the type of empirical dispersion force correction.
DC

Use divide and conquer method.

SUBTYPE
Specify how to create a subsystem.
BUFRAD
Specifies the radius of the spherical buffer area. (angstrom)
DELTAR
Grid when dividing system into cubic space with SUBTYPE = AUTO (angstrom)
OPT/FREQ
OPT

Perform structural optimization calculations.

MAXITER
Specify the maximum number of structural optimization cycles.
DCONV
Specify the convergence condition of the gradient change. (atomic unit)
FREQ
Perform harmonic vibration analysis
MO

Perform molecular dynamics calculations

NSTEP
Specify the number of steps. When Extending Simulation is checked, it is necessary to enter the sum of the number of steps of the job before continuing and the number of steps of the job to be run.
DELTAT
Specify time step (second)
BATHTEMP
Specify the heat bath temperature when using NVT and NPT ensembles. (Kelvin)
Ensemble
Specify the type of ensemble.
NVTTYPE
Specify the settings for the hot bath.
INITTEMP
Specify the initial temperature (Kelvin)
PRINT
Specify the output frequency to the file such as coordinates during simulation.
CALCPRESSURE
Calculate the pressure. Care should be taken when performing a continuous job, as it cannot be changed from the settings of the job before takeover.
Properties
PRINT
MO
Output molecular orbital coefficient (only when the number of subsystems is 1)
ATOME
Outputs the contribution from each atom to the total energy.
HS
Outputs zero-order Hamiltonian and overlap matrix (only when the number of subsystems is 1)
FORCE
Calculate energy and force.
STRESS
Calculate stress tensor and lattice vector
Options
Restore Working Directory
Click to return the working directory to its pre-execution status, such as when a continued job ends abnormally.

8.2.2. Run

To run DCDFTBMD, open Remote job. See Remote job for detailed instructions.

The execution method depends on the situation.

  • (Default) If Extending Simulation is unchecked
    Save the input file (extension dci) with the name specified by the user at the time of execution, and execute the calculation using it.
  • When Extending Simulation is checked
    Create a backup of the existing working directory associated with the input file opened in the main window, save the input file as dftb.inp in the newly created working directory, and use it to perform calculations .

The following files are generated with execution. As an example, the file/folder name when the input file is water.dci is also shown.

Type Explanation
dco file
water.dco
DCDFTMD standard output file.
A copy of dftb.out in your working folder.
Shell script
water.sh
To perform DCDFTBMD and its pre/post processing
shell script.
conf file
water_conf.sh
Contains variables used in the above shell script
file.
Working directory
water_dc_data\
working directory.

The following files are generated in the working directory. Only the main files are shown here.

Type Explanation
dftb.inp
Input file actually passed to DCDFTMD
dftb.out
Standard output file
dftb.dat
Detailed output file
traject
Trajectory file in MD calculation
restart
Restart file

Hint

** Working directory **

  • A working directory is a folder with the suffix of the name of the file opened in the main window.

    • ** The suffix depends on the type of solver. **
    • For example, for Gromacs, if the file opened in the main window is aaa.gro and the suffix is _gmx_tmp, the name of the working directory is aaa_gmx_tmp.
  • It must be on the same level as the file opened in the main window.

  • Although processing continues in the working directory with the same name for continued jobs, by default, a backup of the previous job’s working directory is created immediately before the continued job is executed.

    • The name of the backup will be the one with the lowest number in the range where there are no duplicate names. For example, if your working directory is aaa_gmx_tmp, it will be aaa_gmx_tmp1.
    • ** Unnumbered directories are always up to date. **

8.2.3. Open Log File (dco)

Open the dco (standard output) file with a text editor.

8.2.4. Open Detailed Data File (dat)

Open the detailed output file in a text editor.

8.2.5. Animation

8.2.5.1. OPT (dco)

Select a dco file and animate optimization calculation trajectory.

Please refer to Animation window for how to operate the animation.

8.2.5.2. MD (traject)

Select dci and traject files and animate MD calculation trajectory.

The main window file name does not change.

Please refer to Animation window for how to operate the animation.

You can calculate mean square displacement, self-diffusion coefficient, and radial distribution function from Tools ‣ Mean Square Displacement/Diffusion Constant and Tools ‣ Radial Distribution Function in Animation window.See Diffusion Constant/Mean Square Displacement or Radial Distribution Function for details.

8.2.6. Energy Plot

Select a log file and display graphs of various thermodynamic quantities such as energy and temperature.

See Energy Plot window for how to operate subwindows.