Overview

ScaleLat (Scale Lattice) is a computer program written in C ++ for performing the atomic structure analysis of multi-phase system or high entropy alloys (HEAs). The program implements an atomic cluster extraction algorithm to obtain all independent and symmetry-reduced characteristic chemical structures for the complex atomic configurations which are usually obtained from molecular dynamics or kinetic Monte-Carlo simulations for supercell containing more than 104 atoms. ScaleLat employes an efficient and unique chemical structure matching algorithm to map all extracted atomic clusters from a large supercell (>104 atoms) to a representative small one (~ 103 or less), providing the possibility to directly use the highly accurate quantum mechanic methods to study the electronic, magnetic, and mechanical properties of multi-component alloys with complex microstructures.

Nature of Problem: Very large supercells containing more than 104 atoms must be used to describe the atomic structure of complex multi-phase or high entropy alloys, and their properties are almost not possible to investigate using quantum mechanical calculations within the conventional computational facilities right now. Decreasing the total number of atoms in a smaller representing supercell which preserves all essential chemical structures of the original large supercell is the key to the problem.

Solution to the Problem: An atomic cluster extraction algorithm is realized to thoroughly analysis all essential chemical structures of multi-phase system or high entropy alloys; Utilizing the direct atom swapping method, the chemical structure matching procedure is developed to map all extracted characteristic atomic clusters of benchmark structure to the small supercell by minimizing their differences in both the types and relative proportions of atomic cluster sets.

software environment

Only supported by Ubuntu 16. The g++, gfortran and cmake compilers need to be installed in advance.

$ sudo apt-get update
$ sudo apt-get install g++
$ sudo apt-get install gfortran
$ sudo apt-get install cmake

The software OVITO can be used to visualize the results files ".movie" or ".xyz".

$ sudo apt-get install ovito

installation

Download the file ScaleLat.zip.

Run the following commands to extract and access to all of the original files:

$ unzip ScaleLat.zip 
$ sudo chmod -R 775 ScaleLat
$ cd ScaleLat

Configure, compile, and install ScaleLat with:

$ mkdir build
$ cd build
$ cmake ..
$ make

How to run examples:

$ cd example/the/folder/contains/*.sh
$ bash *.sh

Run FEcMD

There are various commands to perform the corresponding function. Perform kMC simulation:

$ ./scalelat kMC

Perform cluster extraction:

$ ./scalelat CE

Perform chemical structure matching:

$ ./scalelat MAP

Perform cluster analysis for density, size and volume of precipitates:

$ ./scalelat analysis

Perform coarse-grained analysis to get mass density distribution:

$ ./scalelat MDS

Calculate SRO

$ ./scalelat SRO

Calculate ACF

$ ./scalelat ACF

input file:

-------------parameters for run.in (## ... should be deleted in run.in): eam_file ../in/potential/Fe_Cr_Eich_2015_TBM_lammps.eam.alloy ## the atomic potential funtion MC_method vacancy ## vacancy or atom exchange cellSize 10 10 10 ## the size of cell expansion cell_order order ## order or disorder after cell expansion threshold 0.001 ## threshold, default: 0.001 NeighbourMax 20 ## the max neighbour number for the xth shell T_max 673 ## temperature [K] Nelems 2 ## the number of elements elemName Fe Cr ## elements names NLOOP 2.e10 ## loop number stepAvg 1.e5 ## average steps for calculating energy stepMovie 1.e7 ## average steps for output *.movie stepVacancy 100 ## the steps of the vacancy exchange randomly, default: 100 stepAtom 1 ## the steps of the atom exchange randomly, default: 1 nthreads 16 ## the number of cores that run in parallel seed 7 ## random seed nebrTabFac 200 ## the max neighbour number within cutoff radius

----------------------------RDF------------------------------- limitRdf 100 # The limit steps of RDF stepRdf 100000 # The average steps of RDF rangeRdf 5. # The range of RDF [Angstrom] sizeHistRdf 200 # The size of histogram

-----------------------------MAP------------------------------ clusterSize 6 6 6 # The size of cluster extraction [unit: lattice parameter] error_map 1 # the standard deviation (1) or the mean absolute error (0) pointGroup m3m # the symmetry points group cell_order disorder # order or disorder for the initial trial supercell

--------------------------Analysis---------------------------- ith_nebrR 2 # The number of shells of cluster analysis C_threshold 0.95 # The concentration threshold of cluster analysis elem_preci Cr # The element type of cluster analysis

Alloy atomic trajectory input file ‘benchmark.xyz’ format (example for HEA): 108000 ## atomic number Lattice="105.600002 0.0 0.0 0.0 105.599999 0.0 0.0 0.0 105.599999" Properties=species:S:1:pos:R:3 ## box region and the title for ovito Cr 44.0 10.56 12.320001 Cr 82.720001 95.040001 79.199997 Fe 77.440002 33.439999 15.84 Co 22.880001 88.0 29.92 Co 40.48 26.4 59.84 Ni 44.0 0.0 82.720001 … ## The following lines are 4 arrays of tabulated values: element_type position_x position_y position_z

The unit cell ‘CONTCAR’ format (example for HEA): POSCAR file written by OVITO ## title 1.0 ## scaling factor 26.3999996185 0.0000000000 0.0000000000 0.0000000000 28.1599998474 0.0000000000 0.0000000000 0.0000000000 28.1599998474 ## box region Co Cr Cu Fe Ni ## elements types 364 402 435 368 351 ## atomic number Direct ## must be fractional coordinates 0.200000003 0.000000000 0.812500000 0.333333343 0.437500030 0.000000000 0.866666734 0.125000000 0.562500000 0.733333349 0.500000000 0.937500000 0.066666663 0.250000000 0.562500000 0.733333349 0.750000060 0.187500015 … ## The following lines are 3 arrays of tabulated values: position_x position_y position_z

output file:

.xyz and .movie files can be visualized by ‘ovito’. md: this folder includes atomic trajectory files. supercell: this folder includes cell expansion files. sro.dat: SRO data. rdf.dat: RDF data. precipitates_.dat: the average size, density and volume of precipitates. precipitates_.movie: the atom structure of precipitates. CE_benchmark: this folder includes extracted clusters of the benchmark supercell. CE_trial: this folder includes extracted clusters of the small trial structure. CE/CE.dat: the number of characteristic chemical clusters. CE/CE*.xyz: characteristic chemical clusters structure. CE/concentration.dat: the atomic concentration of characteristic chemical clusters. diff.dat: STD (or MAE) of atomic concentration and clusters proportion pi. mapping.dat: characteristic chemical clusters proportion pi of the benchmark supercell and the small trial supercell. mapping.xyz: atomic structure file of the matching structure.