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Data analyzer

A data analyzer is provided in the analyzer directory.

vtk2dump

A file vtk2dump.f90 is provided in the directory analyzer/vtk2dump to convert at most two *.vtk files to a dump.* file. To compile it, simply

ifort vtk2dump.f90 -o vtk2dump

or

gfortran vtk2dump.f90 -o vtk2dump

To run the code, simply

./vtk2dump

The executable then reads at most three files, namely, cac_cg_#.vtk, cac_atom_#.vtk, and vtk2dump.in. From cac_cg_#.vtk, the atomic positions inside the elements are linearly interpolated from the nodes; from cac_atom_#.vtk, the atomic positions are read as is. Then both interpolated atoms and real atoms are written into a dump.# file. Here, #, a positive integer, is provided by the step in the vtk2dump.in file, whose syntax is

boolean_cg boolean_at
step
x boolean_user lower_b upper_b
y boolean_user lower_b upper_b
z boolean_user lower_b upper_b

• boolean_cg, boolean_at, boolean_user = t or f

• x, y, z = p or s

• lower_b, upper_b = real number

For example,

t t
34
p t 0. 100.
s f
p f -50. 150.

boolean_cg and boolean_at decide whether the files cac_cg_#.vtk and cac_atom_#.vtk are involved in the conversion, respectively. For example, if boolean_cg = t and boolean_at = f, only cac_cg_#.vtk is converted.

In the example, step = 34, meaning that files cac_cg_34.vtk and/or cac_atom_34.vtk should be prepared, and the output file is dump.34.

x, y, and z set the boundary conditions along the x, y, and z directions, respectively.

If boolean_user = t, it should be followed by lower_b and upper_b, in units of Angstrom, which provide user-defined lower and upper bounds of the simulation cell along the corresponding direction. If boolean_user = f, lower_b and upper_b, e.g., -50. and 150. in the last line of the example, become irrelevant; in this case, the two bounds along a certain direction are calculated using the nodal and atomic positions in the two *.vtk files.