fix fhi-aims bug

.gitignore

@@ -20,3 +20,4 @@ dist
 dpdata.egg-info
 _version.py
 !tests/cp2k/aimd/cp2k.log
+__pycache__

README.md

@@ -71,6 +71,8 @@ The `System` or `LabeledSystem` can be constructed from the following file forma
 | QE      | log    | False        | True    | LabeledSystem | 'qe/pw/scf'   |
 | QE      | log    | True         | False   | System        | 'qe/cp/traj'  |
 | QE      | log    | True         | True    | LabeledSystem | 'qe/cp/traj'  |
+| Fhi-aims| output | True         | True    | LabeledSystem | 'fhi_aims/md'  |
+| Fhi-aims| output | False        | True    | LabeledSystem | 'fhi_aims/scf'  |
 |quip/gap|xyz|True|True|MultiSystems|'quip/gap/xyz'|
 | PWmat   | atom.config | False        | False   | System        | 'pwmat/atom.config'  |
 | PWmat   | movement    | True         | True    | LabeledSystem | 'pwmat/movement'     |
@@ -112,6 +114,27 @@ xyz_multi_systems.systems['B1C9'].to_deepmd_raw('./my_work_dir/B1C9_raw')
 xyz_multi_systems.to_deepmd_raw('./my_deepmd_data/')
 ```
 
+You may also use the following code to parse muti-system:
+```
+from dpdata import LabeledSystem,MultiSystems
+from glob import glob
+"""
+process multi systems
+"""
+fs=glob('./*/OUTCAR')  # remeber to change here !!!
+ms=MultiSystems()
+for f in fs:
+    try:
+        ls=LabeledSystem(f)
+    except:
+        print(f)
+    if len(ls)>0:
+        ms.append(ls)
+
+ms.to_deepmd_raw('deepmd')
+ms.to_deepmd_npy('deepmd')
+```
+
 ## Access data
 These properties stored in `System` and `LabeledSystem` can be accessed by operator `[]` with the key of the property supplied, for example
 ```python

dpdata/fhi_aims/output.py

@@ -8,6 +8,7 @@
 eng_patt="Total energy uncorrected.*([-]?[0-9]{1,}[.][0-9]*[E][+-][0-9]{1,})\s+eV"
 #atom_numb_patt="Number of atoms.*([0-9]{1,})"
 
+debug = False
 def get_info (lines, type_idx_zero = False) :
 
     atom_types = []
@@ -31,26 +32,23 @@ def get_info (lines, type_idx_zero = False) :
         v_str=ii.split('|')[1].split()
         vect=[float(kk) for kk in v_str]
         cell.append(vect)
-   # print(cell)
-    #atom name
+
     _tmp=re.findall(pos_patt_first,contents)
     for ii in _tmp:
         _atom_names.append(ii[0])
     atom_names=[]
     for ii in _atom_names:
         if not ii in atom_names:
            atom_names.append(ii)
-    #atom number
-    #_atom_numb_patt=re.compile(atom_numb_patt)
+
     atom_numbs =[_atom_names.count(ii) for ii in atom_names] 
+    if type_idx_zero :
+       type_map=dict(zip(atom_names,range(len(atom_names)))) 
+    else:
+       type_map=dict(zip(atom_names,range(1,len(atom_names)+1))) 
+    atom_types=list(map(lambda  k: type_map[k], _atom_names)) 
     assert(atom_numbs is not None), "cannot find ion type info in aims output"
-
-    for idx,ii in enumerate(atom_numbs) :
-        for jj in range(ii) :
-            if type_idx_zero :
-                atom_types.append(idx)
-            else :
-                atom_types.append(idx+1)
+
 
     return [cell, atom_numbs, atom_names, atom_types ]
 
@@ -81,8 +79,9 @@ def get_frames (fname, md=True, begin = 0, step = 1) :
 
     cc = 0
     while len(blk) > 0 :
-     #   with open(str(cc),'w') as f:
-     #        f.write('\n'.join(blk))
+        if debug:
+           with open(str(cc),'w') as f:
+                f.write('\n'.join(blk))
         if cc >= begin and (cc - begin) % step == 0 :
             if cc==0:
                 coord, _cell, energy, force, virial, is_converge = analyze_block(blk, first_blk=True, md=md)