hfrusinque
commented
4 years ago after reading your documentation in this Matlab file and building on this Matlab function, I can generate a file "packing.xyzd" with the initial positions of an FCC crystal in Little-Endian format and it works at least for the ideal FCC configuration. Now, the problem is when I want to get a loose FCC configuration with a packing density lower than the FCC one (i.e. lower than ~0.74). The code stops always after reading the packing with "'packing.xyzd' was opened". I suppose one of the conditions for a valid initial configuration is that the spheres are in contact, maybe even that there is some degree of overlapping. I will try by adding some noise to the positions of the spheres to get some degree of contact/overlapping.
Here is the function to get the initial configuration so far:
function FCCLattice = FCCMake(a,V, finalDensity)
% "a" is the Lattice Parameter:
a = a; # (e.g. a=1.0)
%Set the Volume of the cube in variable V:
V = V; % (#e.g. V=3.0) This means your cube will be of dimensions VxVxV.
%%%----Code-----%%%
%Create an array that stores all your coordinates:
%First you will need to establish the number of atoms
%that the array will have, we will do this by establishing
%the known number of atoms, in this case, FCC 4xVxVxV.
N = V*V*V*4;
%This array will give a matrix of Nx3, that will store data.
FCCLattice = zeros(N,3);
%Create the vectors for the atoms position in the FCC Lattice:
FCCatoms = [0 0 0;(a/2) (a/2) 0;(a/2) 0 (a/2);0 (a/2) (a/2)];
%Set a variable to change rows in the array storing the coordinates:
n = 0;
k=0;
FCC_Density = pi/(3*sqrt(2));
R_FCC = sqrt(2)*a/4.0 #Radius for FCC
finalDensity = 0.73;
R = R_FCC*(finalDensity / FCC_Density)^(1/3) # final Radius
%Create 3 For loops to mix the positions between xyz
for x = 0:V-1
for y = 0:V-1
for z = 0:V-1
for i = 1:4
%Create a vector that translate your location in the
%coordinate system into the position in the crystal:
coordinatestranslation = a*[x y z];
%Add 1 to move one row down in the array:
n = n+1;
FCCLattice(n,:) = coordinatestranslation + FCCatoms(i,:);
end
k = k + 12 + 4;
M_xyzd(k-15) = FCCLattice(n-3,1);
M_xyzd(k-14) = FCCLattice(n-3,2);
M_xyzd(k-13) = FCCLattice(n-3,3);
M_xyzd(k-12) = 2*R;
M_xyzd(k-11) = FCCLattice(n-2,1);
M_xyzd(k-10) = FCCLattice(n-2,2);
M_xyzd(k-9) = FCCLattice(n-2,3);
M_xyzd(k-8) = 2*R;
M_xyzd(k-7) = FCCLattice(n-1,1);
M_xyzd(k-6) = FCCLattice(n-1,2);
M_xyzd(k-5) = FCCLattice(n-1,3);
M_xyzd(k-4) = 2*R;
M_xyzd(k-3) = FCCLattice(n,1);
M_xyzd(k-2) = FCCLattice(n,2);
M_xyzd(k-1) = FCCLattice(n,3);
M_xyzd(k) = 2*R;
end
end
end
floatDataType = 'float64';
LittleEndian = "ieee-le";
save packing_ascii.txt M_xyzd;
FCC_binary = fopen('packing.xyzd','wb'); # FCC_binary: File ID
fwrite(FCC_binary, M_xyzd, floatDataType, LittleEndian);
fclose(FCC_binary);
end
VasiliBaranov
Hi Vasili,
I want to approximate the rearrangement after relaxation of a loose FCC configuration, from a colloidal crystal whose strong electrostatic forces are "suddenly shut down". I would like to use your code (namely the LS algorithm). Should I provide the initial positions in "packing_init.xyzd" in Little-Endian format or can the code "deal" with ASCII as input?
PS: I normally change the format of the final positions via command line with:
hexdump -v -e '4 "%f "' -e '"\n"' < packing.xyzd > centers_in_ascii.datBest regards, Hector Rusinque PhD Candidate TU Clausthal