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Qbox tools

A set of scripts are available in the util directory of the distribution for post-processing the output of Qbox.

Plot scripts

The following scripts are used to plot the value of various quantities during molecular dynamics simulations. These scripts use gnuplot to display results.

• etotal.plt

  Plot the total energy <etotal> during a simulation or geometry optimization. To make a plot of the total energy in the output file mdrun.r, use:
  $ ./etotal.plt mdrun.r
  To plot the energy in the range of steps 120 to 150, use:
  $ ./etotal.plt -range [120:150] md1.r
  To plot the energy for a sequence of runs md1.r, md2.r, md3.r, use:
  $ ./etotal.plt md1.r md2.r md3.r

• etotal_cmp.plt

  Compare the total energy of two simulations on the same plot. Use:
  $ ./etotal_cmp.plt md1.r md2.r

• etotal_int.plt

  Plot the value of the total energy during self-consistent iterations (tag <etotal_int>). This is used to check the quality of convergence of the electronic ground state during Born-Oppenheimer simulations.

• etotal_int_cmp.plt

  Compare the value of the total energy during non self-consistent iterations (tag <etotal_int>) from two simulations on the same plot.

• econst.plt

  Plot the constant of the motion <econst> during a simulation. This value is the sum of the Kohn-Sham energy and the ionic kinetic energy. It should be ideally constant during an MD simulation (without thermostat).

• econste.plt

  Plot both the constant of the motion <econst> and the total energy <etotal> during a simulation.

• econste_cmp.plt

  Plot both the constant of the motion <econst> and the total energy <etotal> in two simulations for comparison. Use:
  $ ./econste_cmp.plt md1.r md2.r

• econste_cp.plt

  Plot the constant of the motion <econst> the total energy <etotal> and the sum <econst>+<ekin_e>=<ekin_ec> on the same plot. This is used to monitor the quality of a Car-Parrinello simulation, checking that the kinetic energy of the electrons <ekin_e> does not grow too fast

• temp_ion.plt

  Plot the ionic temperature <temp_ion> during a simulation.

• force.plt

  Plot all components of the ionic forces during a simulation. This can be used to monitor convergence during a geometry optimization run.

• cell.plt

  Plot the components of the vectors defining the unit cell during a simulation. Used in simulations with varying cell size/shape.

• sigma.plt

  Plot the components of the stress tensor during an MD simulation (values in GPa).

• volume.plt

  Plot the volume of the unit cell during a simulation.

Analysis scripts

• qbox_distance.py

  Extract the distance between two atoms from a simulation.

• qbox_angle.py

  Extract the angle formed by three atoms from a simulation.

• qbox_torsion.py

  Extract the dihedral angle formed by four atoms from a simulation.

• qbox_xyz.py

  Create an xyz file from the trajectories in a Qbox simulation output file.

• qbox_eig.py

  Extract eigenvalues.

• qbox_dos.py

  Compute the density of states.

• qbox_msd.py

  Compute the mean square displacement of atoms of a given atomic species in an MD simulation.

• qbox_maxforce.py

  Print the x, y and z components of the largest forces acting on any atom during a simulation. Use:
  $ ./qbox_maxforce.py file.r

Post-processing shell scripts

• qbox_xyz.sh

  Extract atomic trajectories from Qbox output and print a file in xyz format. Use:
  $ ./qbox_xyz.sh md.r > md.xyz
  This script uses the xsltproc program to extract and process XML data from the Qbox output file. The xsltproc program is included in most modern Linux distributions. [Note: This script is provided as an example of XSLT script. The qbox_xyz.py script performs the same function.]

• qso2qbox.py

  Generate a Qbox input file file from a Qbox sample file.

• xyz2qbox.py

  Generate a Qbox input file file from an xyz file. The resulting file must be edited to include the correct species names and cell size

• qso2qe.py

  Generate a Quantum Espresso input file from a Qbox sample file. The resulting file must be edited to include the correct pseudopotential file names and other parameters.

• split_sample.sh

  Separate a sample XML file into two files atomset.xml and wf.xml containing the header and the wavefunction respectively. Use:
  $ ./split_sample sample.xml
  The resulting files can be edited and then reassembled into a sample using
  $ cat atomset.xml wf.xml > new_sample.xml
  This is useful when trying to edit the <atomset> part of the sample since it avoids having to edit a large file.

• sample_to_sys.sh

  Generate a sys file (to be used as input by Qbox) from a sample file. Use:
  $ ./sample_to_sys.sh sample.xml > sample.sys
  The sys file contains "atom" commands.

• sample_to_move.sh

  Generate a Qbox input file from a sample file. Use:
  $ ./sample_to_move.sh sample.xml > move.i
  The file move.i contains "move" commands, and can be used to move atoms to the positions defined in sample.xml (see the syntax of the Qbox move command).

• qbox_replicate.sh

  Generate a Qbox input file defining a supercell from an input file definint a primitive cell. Use:
  $ ./qbox_replicate.sh cell.sys n0 n1 n2 > supercell.sys
  The file supercell.sys contains Qbox commands defining a supercell obtained by replicating the cell defined in cell.sys. Replication is performed n0, n1 and n2 times in the directions of the lattice vectors a0, a1 and a2.