p2ptrans¶

Command line¶

Usage:

p2ptrans [-h] [-I INITIAL_STRUCTURE] [-F FINAL_STRUCTURE] [-n N_CELLS] [-i] [-d] [-p FILENAME] [-c CRYSTFILE]
         [-o OUTDIR] [-u USEDIR] [-m] [-s] [-r] [-a] [-v] [-t] [-f N_STEPS] [--version]

Optional arguments:

`-h, --help`	Show help message and exit
`-I, --initial INITIAL_STRUCTURE`
	Initial crystal structure. It must be a POSCAR.
`-F, --final FINAL_STRUCTURE`
	Final Structure structure. It must also be a POSCAR.
`-n, --ncell N_CELL`
	Minimum number of cells to tile DEFAULT: 300

-cn N_CELL: If specified, number of cells used for the final mapping after tmat has been adjusted to be commensurate with both structures. If not specified, the mapping stays the same.

`-i, --interactive`
	Enable interactive display
`-d, --disp`	Save figures
`-p, --param FILENAME`
	Name of the parameter file (see detail in Extra parameters). DEFAULT: p2p.in Caution: if a file named p2p.in exists in the current directory, p2ptrans will read it.
`-c, --crystal CRYSTFILE`
	Name of the parameter file for crystallography analysis DEFAULT: cryst.in
`-o, --outdir OUTDIR`
	Output directory DEFAULT: current directory
`-u, --use USEDIR`
	Use previously calculated data in USEDIR
`-m, --minimize`	Force new optimization even if data is available
`-s, --switch`	Map the larger cell on the smaller cell instead of the opposite
`-r, --noprim`	Do not try to find the primitive cell of the input structures
`-a, --anim`	Produce an animation of the transition (slow)
`-v, --vol`	Make the two (stoichiometric) cells equal in volume (not tested)
`-t, --test`	Test the input file and prepare the run. You can continue this run with the -u USEDIR -r option
`-f N_STEPS, --frames N_STEPS`
	Number of intermediate structures to create
`--version`	Show installed version of p2p

Extra Parameters¶

More parameters can be specified to p2ptrans via a parameter file. This file is in the Fortran namelist format. By default any file named p2p.in in the current directory will be read. The name of the parameter file can be changed using the -p option. The syntax of this file is the following:

&input
init_class = 1.0d0
tol = 1.0d-4
tol_std = tol*1.0d-3
tol_class = 1.0d-3
fracA = 0.09d0
fracB = 0.3d0
n_iter = 1000
n_ana = 300
n_conv = 5
n_class = 30
n_adjust = 10
max_vol = 4.0d0
free = .false.
check = .false.
savebest = trim(outdir)//"/best.dat"
usebest = .false.
remap = .true.
/

This is file contains all the default parameters, if an entry is not specified, it will take the value shown above.

Init_class

Initial separation tolerance for displacement classes. At the initial classification step, if the norm of the difference between two vectors is larger than init_class they will be classified in different groups.

tol

Convergence criterion for the gradient descent

tol_std

Convergence criterion for the std minimization

tol_class

Convergence criterion for the classification abs(std - previous std)

fracA

Fraction of the mapped structure that constitutes core atoms

fracB

Fraction of the mapping structure that constitutes mapping atoms

n_iter

Number of random starts

n_ana

Maximum number of iterations in the gradient descent

n_conv

Maximum number of remappings per minimization

n_class

Maximum number of classification iterations

n_adjsut

Maximum number of unconstrained post-processing minimization iterations

max_vol

Maximum volume of the random starting tmat when using the unrestricted minimization (free = .true.)

free

Use unrestricted minimization. Not limited to rigid rotations. The optimal result is the one for which the sum of the unstrained distance and the strained (unrestricted) distance is minimal so that overly stretched results, where skipping is likely to occur, are penalized.

check

Use the mapping given by the order of the input structures directly (do not map atoms).

savebest

Name of the file to save the optimal result to at the end of the minimization, before the post-processing steps.

remap

If true, allows remapping during the post-processing steps.