Adding a function that could deal with the magnetic_force and spin when using the ABACUS's deltaspin module #657
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WalkthroughThe recent update focuses on code quality improvements, reorganization, and minor functional enhancements across multiple files. Key changes include fixing import statements, reformatting code, and adding new functions to handle specific data in the Changes
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Actionable comments posted: 5
Out of diff range and nitpick comments (1)
dpdata/abacus/scf.py (1)
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370-401: Remove commented-out print statements.Commented-out code should be removed to maintain code cleanliness.
- # print(force_deltaspin) - # print(coords_deltaspin) - # print(spin) - # print(mag_forces) - # print(force) - # print(coords) - # print("atom_names = ", data['atom_names']) - # print("natoms = ", data['atom_numbs']) - # print("types = ", data['atom_types']) - # print("cells = ", data['cells']) - # print("coords = ", data['coords']) - # print("energy = ", data['energies']) - # print("force = ", data['forces']) - # print("virial = ", data['virials']) - # print("spin = ", data['spin']) - # print("mag_forces = ", data['mag_forces']) - # print("force_deltaspin = ", data['force_deltaspin']) - # print("coords_deltaspin = ", data['coords_deltaspin'])
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Actionable comments posted: 3
Out of diff range and nitpick comments (7)
dpdata/abacus/scf.py (7)
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26-26: Use format specifiers instead of percent format for better readability and consistency.- print("Can not find file %s" % ifile) + print("Can not find file {}".format(ifile))
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94-94: Use format specifiers instead of percent format for better readability and consistency.- print("coord_type = %s" % coord_type) + print("coord_type = {}".format(coord_type))
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134-134: Use format specifiers instead of percent format for better readability and consistency.- print("Input coordination type is invalid.\n Only direct and cartesian are accepted.") + print("Input coordination type is invalid.\n Only direct and cartesian are accepted.")
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527-527: Use format specifiers instead of percent format for better readability and consistency.- out += "%.3f " % mass[iele] + out += "{:.3f} ".format(mass[iele])
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531-531: Use format specifiers instead of percent format for better readability and consistency.- out += "%s\n" % pp_file[iele] + out += "{}\n".format(pp_file[iele])
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540-540: Use format specifiers instead of percent format for better readability and consistency.- out += "%s\n" % numerical_orbital[iele] + out += "{}\n".format(numerical_orbital[iele])
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545-545: Use format specifiers instead of percent format for better readability and consistency.- out += "NUMERICAL_DESCRIPTOR\n%s\n" % numerical_descriptor + out += "NUMERICAL_DESCRIPTOR\n{}\n".format(numerical_descriptor)
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Actionable comments posted: 3
Out of diff range and nitpick comments (7)
dpdata/abacus/scf.py (7)
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26-26: Use format specifiers instead of percent format for better readability and consistency.- print("Can not find file %s" % ifile) + print("Can not find file {}".format(ifile))
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94-94: Use format specifiers instead of percent format for better readability and consistency.- print("coord_type = %s" % coord_type) + print("coord_type = {}".format(coord_type))
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134-134: Use format specifiers instead of percent format for better readability and consistency.- path_out = os.path.join(fname, "OUT.%s/running_scf.log" % suffix) + path_out = os.path.join(fname, "OUT.{}/running_scf.log".format(suffix))
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530-530: Use format specifiers instead of percent format for better readability and consistency.- inlines = ["ntype %d" % nele] + inlines = ["ntype {}".format(nele)]
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534-534: Use format specifiers instead of percent format for better readability and consistency.- out += "%.3f " % mass[iele] + out += "{:.3f} ".format(mass[iele])
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543-543: Use format specifiers instead of percent format for better readability and consistency.- out += "%s\n" % pp_file[iele] + out += "{}\n".format(pp_file[iele])
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548-548: Use format specifiers instead of percent format for better readability and consistency.- out += "%s\n" % numerical_orbital[iele] + out += "{}\n".format(numerical_orbital[iele])
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@amcadmus @chazeon I cloned the original dpdata code into my local space. But failed to pip install with these codes. Now, I add some function into the dpdata to deal with the deltaspin_scf abacus calculation results. And now, it failed with the PR process. I checked my code. It should be workable. Could you please help me with it? |
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
I don't know in what step led me to make this mistake. I will change the format and resubmit again. |
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| data["mag_forces"] = mag_forces[np.newaxis, :, :] | ||
| data["spin"] = spin[np.newaxis, :, :] | ||
| data["coords_deltaspin"] = coords_deltaspin[np.newaxis, :, :] | ||
| data["force_deltaspin"] = force_deltaspin[np.newaxis, :, :] | ||
| data["deltaspin"] = deltaspin |
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Still, these data types should be added to DTYPES, otherwise I don't think indexing, slicing, or appending will work.
Lines 1193 to 1198 in 1d87e82
| # print("spin = ", data['spin']) | ||
| # print("mag_forces = ", data['mag_forces']) | ||
| # print("force_deltaspin = ", data['force_deltaspin']) | ||
| # print("coords_deltaspin = ", data['coords_deltaspin']) |
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commented codes should be removed
Adding a new function, two files were changed.
I add three parameters in the data when reading data from the OUT.ABACUS/running_scf.log.
When we use the deltaspin module during the scf calculation, the dpdata could grep the magnetic force and spin to the system and print the modified coords.npy and forces.npy.
Summary by CodeRabbit
Bug Fixes
py3Dmolto ensure proper functionality.Refactor
Chores
.pre-commit-config.yamlwith new URLs and revisions for repositories..gitattributesto enforce line endings for Python test files.