[BUG] Reading data error for ABACUS 3.2 #449
Description
Summary
dpdata/abacus/md.py could not extract data from init_bulk module in dpgen.
The version of dpdata is 0.2.14 installed by deepmd-kit offline installation package.
The dpdata is run by init_bulk module in dpgen. The fp data is from ABACUS 3.2. In the stage of collecting data within init_bulk, it turns errors in screen output:
path_work = scale-1.000/000003
scale-1.000/000003
path_work = scale-1.000/000004
scale-1.000/000004
path_work = scale-1.000/000005
scale-1.000/000005
Traceback (most recent call last):
File "/home/user/deepmd-kit/bin/dpgen", line 8, in
sys.exit(main())
File "/home/user/deepmd-kit/lib/python3.10/site-packages/dpgen/main.py", line 233, in main
args.func(args)
File "/home/user/deepmd-kit/lib/python3.10/site-packages/dpgen/data/gen.py", line 1598, in gen_init_bulk
coll_abacus_md(jdata)
File "/home/user/deepmd-kit/lib/python3.10/site-packages/dpgen/data/gen.py", line 1247, in coll_abacus_md
_sys = dpdata.LabeledSystem(oo, type_map=type_map, fmt="abacus/md")
File "/home/user/deepmd-kit/lib/python3.10/site-packages/dpdata/system.py", line 283, in init
self.from_fmt(
File "/home/user/deepmd-kit/lib/python3.10/site-packages/dpdata/system.py", line 320, in from_fmt
return self.from_fmt_obj(load_format(fmt), file_name, **kwargs)
File "/home/user/deepmd-kit/lib/python3.10/site-packages/dpdata/system.py", line 1183, in from_fmt_obj
data = fmtobj.from_labeled_system(file_name, **kwargs)
File "/home/user/deepmd-kit/lib/python3.10/site-packages/dpdata/plugins/abacus.py", line 64, in from_labeled_system
return dpdata.abacus.md.get_frame(file_name)
File "/home/user/deepmd-kit/lib/python3.10/site-packages/dpdata/abacus/md.py", line 187, in get_frame
coords, cells, force, stress = get_coords_from_dump(dumplines, natoms)
File "/home/user/deepmd-kit/lib/python3.10/site-packages/dpdata/abacus/md.py", line 75, in get_coords_from_dump
celldm = float(dumplines[iline + 1].split(" ")[-1])
ValueError: could not convert string to float: 'Angstrom'
In addition, No deepmd folder generated in STRU.01x01x01/02.md/sys-0002-0001. If the data is from ABACUS 3.1.4 (<3.2), screen output of dpgen is:
path_work = scale-1.000/000003
scale-1.000/000003
path_work = scale-1.000/000004
scale-1.000/000004
path_work = scale-1.000/000005
scale-1.000/000005
/home/user/deepmd-kit/lib/python3.10/site-packages/dpdata/abacus/md.py:204: UserWarning: Structure 7 are unconverged and not collected!
warnings.warn(f"Structure %s are unconverged and not collected!" % unconv_stru)
131
It seems to be running normally now.