From db75d97be563364383e0ca09654bba1332d39f47 Mon Sep 17 00:00:00 2001 From: shigetomo <mr525@icloud.com> Date: Sat, 2 Dec 2023 23:22:45 +0900 Subject: [PATCH] Delete some comments --- dpdata/openmx/omx.py | 26 ++++---------------------- 1 file changed, 4 insertions(+), 22 deletions(-) diff --git a/dpdata/openmx/omx.py b/dpdata/openmx/omx.py index 5fdbcfce..54f8ead4 100644 --- a/dpdata/openmx/omx.py +++ b/dpdata/openmx/omx.py @@ -19,30 +19,19 @@ from collections import OrderedDict -# | key | type | dimension | are labels | description -# | --- | --- | --- | --- | --- -# | 'atom_names' | list of str | ntypes | False | The name of each atom type -# | 'atom_numbs' | list of int | ntypes | False | The number of atoms of each atom type -# | 'atom_types' | np.ndarray | natoms | False | Array assigning type to each atom -# | 'cells' | np.ndarray | nframes x 3 x 3 | False | The cell tensor of each frame -# | 'coords' | np.ndarray | nframes x natoms x 3 | False | The atom coordinates -# | 'energies' | np.ndarray | nframes | True | The frame energies -# | 'forces' | np.ndarray | nframes x natoms x 3 | True | The atom forces -# | 'virials' | np.ndarray | nframes x 3 x 3 | True | The virial tensor of each frame - -# // iterout.c from OpenMX soure code +### iterout.c from OpenMX soure code: column numbers and physical quantities ### # /* 1: */ -# /* 5,6,7: force */ +# /* 2,3,4: */ +# /* 5,6,7: force * # /* 8: x-component of velocity */ # /* 9: y-component of velocity */ # /* 10: z-component of velocity */ # /* 11: Net charge, electron charge is defined to be negative. */ # /* 12: magnetic moment (muB) */ -# /* 13,14: angles of spin */ +# /* 13,14: angles of spin */ # load atom_names, atom_numbs, atom_types, cells def load_param_file(fname, mdname): - ### future request: read from .md not .dat ### with open(fname) as dat_file: lines = dat_file.readlines() atom_names = [] @@ -172,14 +161,7 @@ def to_system_label(fname, mdname, data): print(atom_names) print(atom_numbs) print(atom_types) - # print(cells) # print(cells.shape) # print(coords.shape) - # print(data["coords"].shape) - # print(data["cells"]) - # print(data["cells"].shape) - # print(csteps) - # print(energy) # print(len(energy)) - # print(force) # print(force.shape) \ No newline at end of file