fix_bug simplify.py (#1114)

to fix the break of dpgen simplify with "labeled true", when the last
iter picked all candidate frames but still have non-zero failed frames

output files of the last iter：
```
ls iter.000002/01.model_devi/data.rest/*
...
iter.000002/01.model_devi/data.rest/my_elements:
box.raw  coord.raw  energy.raw  force.raw  type_map.raw  type.raw  virial.raw
...
```
no `set.000` within,

then model_devi of iter.000003 breaks, due to no labeld systems can be
loaded, where `iter.000003/01.model_devi/data.rest.old` is the symlink
of `iter.000002/01.model_devi/data.rest`
https://github.com/deepmodeling/dpgen/blob/355f8eda0c212fe3a072f0865d1ac0d0d7c753b1/dpgen/simplify/simplify.py#L171

**tracking clues**
rest_idx only contains not-picked candidates_idx of this iter

https://github.com/deepmodeling/dpgen/blob/355f8eda0c212fe3a072f0865d1ac0d0d7c753b1/dpgen/simplify/simplify.py#L292
```
/dpgen/simplify/simplify.py

def post_model_devi(iter_index, jdata, mdata):
    ...
    counter = {"candidate": sys_candinate.get_nframes(), "accurate": sys_accurate.get_nframes(), "failed": sys_failed.get_nframes()} <<-------
    ....
    # candinate: pick up randomly
    iter_pick_number = jdata['iter_pick_number']
    idx = np.arange(counter['candidate'])   <<----
    assert(len(idx) == len(labels))
    np.random.shuffle(idx)
    pick_idx = idx[:iter_pick_number]
    rest_idx = idx[iter_pick_number:]    <<--
```

but "rest_systems" for next iter should contain both "not-picked
candidates" and "sys_failed" of this iter:

https://github.com/deepmodeling/dpgen/blob/355f8eda0c212fe3a072f0865d1ac0d0d7c753b1/dpgen/simplify/simplify.py#L314
```
/dpgen/simplify/simplify.py

def post_model_devi(iter_index, jdata, mdata):
    ...
    for j in rest_idx:       <<------
        sys_name, sys_id = labels[j]
        rest_systems.append(sys_candinate[sys_name][sys_id])  <<----
    rest_systems += sys_failed  <<--
```

thus, 
the size passed to `set_size` should be `rest_systems.get_nframes()`,
didn't find the necessity of the size_check of the deleted "if line",
thought it only the insurance in case of set_zise =0 when passing the
size of rest_idx

**when breaked, err would be like**:
std output of dpgen:
```
INFO:dpgen:-------------------------iter.000003 task 05--------------------------
Traceback (most recent call last):
  File "/opt/anaconda3/bin/dpgen", line 8, in <module>
    sys.exit(main())
  File "/opt/anaconda3/lib/python3.8/site-packages/dpgen/main.py", line 185, in main
    args.func(args)
  File "/opt/anaconda3/lib/python3.8/site-packages/dpgen/simplify/simplify.py", line 535, in gen_simplify
    run_iter(args.PARAM, args.MACHINE)
  File "/opt/anaconda3/lib/python3.8/site-packages/dpgen/simplify/simplify.py", line 508, in run_iter
    post_model_devi(ii, jdata, mdata)
  File "/opt/anaconda3/lib/python3.8/site-packages/dpgen/simplify/simplify.py", line 250, in post_model_devi
    sys_entire = dpdata.MultiSystems(type_map = type_map).from_deepmd_npy(os.path.join(work_path, rest_data_name + ".old"), labeled=labeled)
  File "/opt/anaconda3/lib/python3.8/site-packages/dpdata/system.py", line 1465, in from_format
    return self.from_fmt_obj(ff(), file_name, **kwargs)
  File "/opt/anaconda3/lib/python3.8/site-packages/dpdata/system.py", line 1188, in from_fmt_obj
    system = LabeledSystem().from_fmt_obj(fmtobj, dd, **kwargs)
  File "/opt/anaconda3/lib/python3.8/site-packages/dpdata/system.py", line 1078, in from_fmt_obj
    data = fmtobj.from_labeled_system(file_name, **kwargs)
  File "/opt/anaconda3/lib/python3.8/site-packages/dpdata/plugins/deepmd.py", line 60, in from_labeled_system
    return dpdata.deepmd.comp.to_system_data(file_name, type_map=type_map, labels=True)
  File "/opt/anaconda3/lib/python3.8/site-packages/dpdata/deepmd/comp.py", line 50, in to_system_data
    data['cells'] = np.concatenate(all_cells, axis = 0)
  File "<__array_function__ internals>", line 5, in concatenate
ValueError: need at least one array to concatenate
```
iter.000003/01.model_devi/model_devi.log:
```
WARNING:tensorflow:From /opt/deepmd-kit-2.1.5/lib/python3.10/site-packages/tensorflow/python/compat/v2_compat.py:107: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.
Instructions for updating:
non-resource variables are not supported in the long term
WARNING:root:To get the best performance, it is recommended to adjust the number of threads by setting the environment variables OMP_NUM_THREADS, TF_INTRA_OP_PARALLELISM_THREADS, and TF_INTER_OP_PARALLELISM_THREADS.
WARNING:root:Environment variable KMP_BLOCKTIME is empty. Use the default value 0
WARNING:root:Environment variable KMP_AFFINITY is empty. Use the default value granularity=fine,verbose,compact,1,0
/opt/deepmd-kit-2.1.5/lib/python3.10/importlib/__init__.py:169: UserWarning: The NumPy module was reloaded (imported a second time). This can in some cases result in small but subtle issues and is discouraged.
  _bootstrap._exec(spec, module)
Traceback (most recent call last):
  File "/opt/deepmd-kit-2.1.5/bin/dp", line 10, in <module>
    sys.exit(main())
  File "/opt/deepmd-kit-2.1.5/lib/python3.10/site-packages/deepmd/entrypoints/main.py", line 576, in main
    make_model_devi(**dict_args)
  File "/opt/deepmd-kit-2.1.5/lib/python3.10/site-packages/deepmd/infer/model_devi.py", line 199, in make_model_devi
    dp_data = DeepmdData(system, set_prefix, shuffle_test=False, type_map=tmap)
  File "/opt/deepmd-kit-2.1.5/lib/python3.10/site-packages/deepmd/utils/data.py", line 51, in __init__
    self.mixed_type = self._check_mode(self.dirs[0])  # mixed_type format only has one set
IndexError: list index out of range
```



Signed-off-by: Wanrun Jiang
<58099845+Vibsteamer@users.noreply.github.com>

Signed-off-by: Wanrun Jiang <58099845+Vibsteamer@users.noreply.github.com>

Author: Vibsteamer

dpgen/simplify/simplify.py

@@ -299,8 +299,7 @@ def post_model_devi(iter_index, jdata, mdata):
     rest_systems += sys_failed
     sys_data_path = os.path.join(work_path, rest_data_name)
     rest_systems.to_deepmd_raw(sys_data_path)
-    if rest_idx.size:
-        rest_systems.to_deepmd_npy(sys_data_path, set_size=rest_idx.size)
+    rest_systems.to_deepmd_npy(sys_data_path, set_size=rest_systems.get_nframes())
 
 
     # dump the accurate data -- to another directory