Boris Mantisi. Contents. Context 2. How to install APoGe 3. How APoGe works 4. Input File 5. Crystal File 8. How to use APoGe 10

Transcription

1 Boris Mantisi Contents Context 2 How to install APoGe 3 How APoGe works 4 Input File 5 Crystal File 8 How to use APoGe 10

2 Context Polycrystalline structure plays an important role in the macroscopic properties of a solid material. We propose a new code to generate a polycrystalline material at the atomic scale. Generated polycrystalline systems are based on a random spatial distribution of initial germs, to which a random orientation is given. Many kind of crystals are available from Metallic (Cu, Al, Ni) to oxides (Forsterite, Calcite, silica polymorphs). Initially the code was devoted to study geophysical issues; the known use of it is now linked to mechanics, grain growth or even catalysis challenges. APoGe is a FORTRAN 90 code and works only on serial CPU. Page 2/10 Context

3 How to Install APoGe - Linux A bash script called Compile.sh is provided to install properly APoGe. It is not necessary to link any library with the code. The code was designed and tested with gfortran compiler, but one can modify Compile.sh and use its favourite fortran compiler. To install the code with gfortran, place into the src folder and type: bash Compile.sh The code is under a GNU General Public Licence version 3, One needs to agree on the License before installing the code (More information on The bash script generates then an executable called APoGe.exe that can be run typing:./apoge.exe It will generate a configuration following the parameters given in the input.dat file. Page 3/10 How to Install APoGe - Linux

4 How APoGe works The code uses a geometrical criterion based on the unit cell structure (UCS) of the material under investigation. The algorithm follows a growth process, which considers two kinds of chemical entities (An entity is the unit cell of the considered crystal or a subunit of this unit cell). Chemical entities that do exist (RE for real entities) and chemical entities that can potentially exist (VE for virtual entities) as first neighbours of REs. The initial state is a distribution of REs (germs) to which we assign a random location and a random orientation in the simulation box. These germs are the first RE in the box. A virtual grid mapped on the crystal symmetry is associated with each germ. The second step is the crystal growth of these initial germs from their associated grid. For that, VE are defined as nearest neighbour of RE on their grid, and then algorithm pick up randomly a VE and declares it as RE. The new RE implies first to delete VEs (i.e VEs from other germs) closer than the minimum distance between entities defined from the UCS and second to declare new VE following the grid of the last defined RE. The process is stopped when the grids are filled taking into account that entities of different grids can not overlap. An important task of the code is to deal with the configurations where entities belonging to different grains become close to one another. The growth process is very efficient since all random pick up are accepted, because VE have been defined such that they do not overlap with any other RE. To avoid boundary effects during the simulation, the code considers periodic boundary conditions when writing RE and VE. The code has been written to generate many different configurations of several hundred of thousand of atoms. Any loop on all atoms at each building step would be a lost of time. We reduce the computational time using sub boxes paving the simulation cell with sizes of a few angstroms. Then all atoms or entities are labelled in a sub box and the check for non-overlapping is done using nearest neighbour boxes. This is the main feature which renders the code so efficient (A two dimensional box containing around atoms is generated in less than one minute). The size of small boxes is related to the nearest neighbour distances within the unit cell of the crystal under investigation. This method applies to any crystal structure. The code is described in Computational Materials Sciences journal. If you use it in a paper please cite: B. Mantisi Computational Materials Sciences Vol. 118, p. 245 (2016). Page 4/10 How APoGe works

5 Input File The input file has to be named input.dat. Each line starts with a keyword following by its desired value. All the keywords are listed and described below: dimension Growth dimension. Be careful in 2-dimensions: APoGe allows to generate grains of different crystalline structures, because of periodic boundary conditions along the direction perpendicular to the plane of growth, mixing two different crystalline structures would lead the simulation to non realistic results. Thus the code do not take into account potential errors due to this initial conditions. example: dimension 3 Allowed values: 2 or 3. default value: 3. n_cryst Number of crystalline structures to consider. This command has to be mentioned before the structure keyword, otherwise the default value will be taken to generate the structure. Several kinds of crystals are not recommended for 2D growth. example: n_cryst 1 default value: 1. structure Considered crystal(s). Each elementary structures are stored in the Crystal folder. The extension of the file has to be ".apg". example: structure Alcfc (refers to the Alcfc.apg file in the Crystal folder) default value: no, has to be mentioned. box_length Size of the box within the crystal will grow. For 2D growth, the length perpendicular to the growth plane has to be mentioned, it will be the nearest value of a modulo of unit cell length. Specifying "1.0" will take only one unit cell. This kind of structure can be considered as pillars. User can specify the perpendicular axis using the rot_axis keyword. box_length Page 5/10 Input File

6 rot_axis For two dimensions simulations, the rotational axis is the one out of the plane of growth. example: rot_axis 1 Allowed values: 1, 2 or 3 stands respectively for x, y or z. Default value: 3. write_lmp Write the output file in lammps data file format. Allowed value : 0 or 1. (respectively for "do not write" or "write" the file) default value : 0. write_cfg Write the output file in cfg format readable for AtomEye visualisation program. Allowed value : 0 or 1. (respectively for "do not write" or "write" the file) default value : 0. write_xyz Write the output file in xyz format. Allowed value : 0 or 1. (respectively for "do not write" or "write" the file) default value : 1. NoCharge Write in the Lammps output file the charge for each atoms. This is not necessary for metals EAM potentials for examples, and this can be deactivated using the value 1 as argument of this keyword. Allowed value : 0 or 1. (respectively for "do not write" or "write" the file) default value : 0. n_germs Number of initial germs to consider. If the box will contains only one type of crystals, then the user has to mention the number of grains he wants in the box. However, if the box will contains several kind of crystals, then the user need to mention the total number of grains, and the number of grain of each type in the same order than the arguments given in the structure keyword. example: n_germs 10 example: n_germs (13 grains in total, 10 of first type and 3 of second type.) Page 6/10 Input File

7 example: n_germs (13 grains in total, 8 of first type, 2 of second type and 3 of third type.) init_space Initial space required between germs before starting growth. The code spatially replace initial germs while the distance is not respected. default value : 10.0 Page 7/10 Input File

8 Crystal File APoGe need non-standard files as input for crystalline structures. In the first version of the code, some examples are given, however it can be useful to know how to build any crystal. This part is devoted to the crystal files descriptions. File description. The file is composed in 4 parts, which are preceded by a comment describing it. These four parts are described below: (l. 2) Number of atoms in the given unit cell, number of entities, number of atoms in each entities, number of chemical species and number of neighbour of each entities to consider in the growth process. (l. 4) Size of the elementary cell respectively along x, y and z. (l. 6) Properties of each species: indicative number, Chemical symbol, atomic mass, charge. (from l. 8) Atoms positions: Number associated to the chemical specie, x, y and z coordinates in the same units than the box length given at l. 4. Let us recall that an entity is a set of atoms which are neutral in charge, and the base building block to generate the crystal. An entity may contain one or several atoms. If the entity is to difficult to build, then the entire elementary unit cell can be considered as an unique entity. Few notes are required to carefully build the unit cell. First, the last parameter on the first line (number of neighbour of each entities) totally drives the growth. The best choice is to take the number of entities in the first neighbour shell. Whatever the unit chosen for the box length and the coordinates, they have to be correlated. Informations about the atomic mass and the charge are use when writing output files in Lammps format. The user may specify 0, that won t affect the grain growth. The coordinates have to be specified entity by entity. The code reads the n atoms in the first entity, then the n atoms in the second entity and so on and so on. It is also compulsory to have the same number of atoms in each entity. Build your own crystal. All given structures have been adapted from Mincryst data base. The difficulty is to create the crystal file giving coherent entities, i.e. neutral packet of atoms close together. This implies to redefine Page 8/10 Crystal File

9 coordinates of some atoms out of the unit cell. However the barycentre of the entity remains inside the unit cell. Page 9/10 Crystal File

10 How to use APoGe Because picture means sometimes more than sentences... Page 10/10 How to use APoGe