p2pint¶

Command Line¶

Usage:

p2pint [-h] [-B BOTTOM_STRUCTURE] [-T TOP_STRUCTURE] [-n N_CELL] [-N N_ITER] [-i] [-d]
           [-p FILENAME] [-o OUTDIR] [-u USEDIR] [-m] [-t] [-b] [-s SYM] [-l LAYERS]
           [-v VACUUM] [-w WIDTH] [--version]

Optional arguments:

`-h, --help`	Show help message and exit
`-B, --bottom BOTTOM_STRUCTURE`
	Structure at the bottom (substrate), miller indices and chemistry rule. This structure will not be strained. Format: BOTTOM_STRUCTURE [h,k,l] 1 EL11 [EL12 …] [2 EL21 [EL22 …] …] Example: POSCAR_A [0,0,1] 1 Si
`-T, --top TOP_STRUCTURE`
	Structure at the top, miller indices and chemistry rule. This structure will be strained. Format: TOP_STRUCTURE [h,k,l] 1 EL11 [EL12 …] [2 EL21 [EL22 …] …] Ex: POSCAR_B [1,1,0] 1 C
`-n, --ncell NCELL`
	Number of cells to tile DEFAULT: 100

-cn N_CELL: Number of cells used for the final mapping after tmat has been adjusted to be commensurate with both structures. DEFAULT: N_CELL

`-N, --niter N_ITER`
	Number of random initial deformation matrices. DEFAULT: 1000
`-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.
`-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
`-t, --test`	Test the input file and prepares the run, you can continue this run with the -u USEDIR option
`-b, --surface-only`
	Only use the first termination from the bottom and do not find primitive cells (compatible with cutsurfaces)
`-s, --sym SYM`	Maximum rotational symmetry around the axis perpendicular to the surface planes on both side of the interface. This will reduce the number of random starts (N_ITER) necessary to find the global minimum.
`-l, --layers LAYERS`
	Desired number of layers in the output interface structures
`-v, --vacuum VACUUM`
	Desired thickness of a vacuum in the output interface structures
`-w, --width WIDTH`
	Maximum width of corrugated surface to optimize. This defines a tolerance to account for atoms that are not exactly in-plane but are within WIDTH of the plane.
`--version`	Show installed version of p2p

Extra Parameters¶

More parameters can be specified to p2pint 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:

&input2d
tol = 1.0d-6
tol_std = tol*1.0d-3
tol_class = 1.0d-3
init_class = 1.0d0
fracA = 0.0d0
fracB = 0.25d0
n_ana = 300
n_conv = 5
n_class = 30
n_adjust = 10
findpeaks = .false.
free = .true.
max_vol = 0.08d0
savebest = trim(outdir)//"/best2d.dat"
usebest = .false.
remap = .true.
pot = "LJ"
param = 2.5d0
check = .false.
vecrep = 10
min_prom = 0.6d0
/

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. For interfaces matching fracA=0 by default so that one-to-one mapping is not enforced.

fracB

Fraction of the mapping structure that constitutes mapping atoms

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 in-plane strain or relative change in area during the minimization ( when free = .true.). Note that the final post-processed result may not meet this criterion.

free

Use unrestricted minimization. Not limited to rigid rotations.

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.

vecrep

For each deformation matrix (tmat) try vecrep random initial translations. The total number of random starts is n_iter * vecrep.

findpeaks

Find multiple local minima in distance, not only the absolute minimum. p2pint will find peaks in the distance vs. angle plot to determine the local minima. It will select the peaks that have a prominence greater than min_prom. Post-processing steps will be applied to all the selected minima.

min_prom

Minimum prominence of the peaks in the distance vs. angle plot to be selected for post-processing

pot

Type of potential to minimize. Currently, the choices are:

“LJ”: Lennard-Jones potential

“Euclidean”: Euclidean distance

param

Equilibrium length for the Lennard-Jones potential