Merge pull request #221 from amcadmus/master

Merge bug fixings to master

.github/workflows/test_import.yml

@@ -0,0 +1,18 @@
+name: test Python import
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      with:
+        python-version: '3.9'
+        architecture: 'x64'
+    - run: python -m pip install .
+    - run: python -c 'import dpdata'
+

dpdata/deepmd/comp.py

@@ -8,9 +8,12 @@ def _cond_load_data(fname) :
         tmp = np.load(fname)
     return tmp
 
-def _load_set(folder) :
-    cells = np.load(os.path.join(folder, 'box.npy'))
+def _load_set(folder, nopbc: bool) :
     coords = np.load(os.path.join(folder, 'coord.npy'))
+    if nopbc:
+        cells = np.zeros((coords.shape[0], 3,3))
+    else:
+        cells = np.load(os.path.join(folder, 'box.npy'))
     eners  = _cond_load_data(os.path.join(folder, 'energy.npy'))
     forces = _cond_load_data(os.path.join(folder, 'force.npy'))
     virs   = _cond_load_data(os.path.join(folder, 'virial.npy'))
@@ -22,14 +25,16 @@ def to_system_data(folder,
     # data is empty
     data = load_type(folder, type_map = type_map)
     data['orig'] = np.zeros([3])
+    if os.path.isfile(os.path.join(folder, "nopbc")):
+        data['nopbc'] = True
     sets = sorted(glob.glob(os.path.join(folder, 'set.*')))
     all_cells = []
     all_coords = []
     all_eners = []
     all_forces = []
     all_virs = []
     for ii in sets :
-        cells, coords, eners, forces, virs = _load_set(ii)
+        cells, coords, eners, forces, virs = _load_set(ii, data.get('nopbc', False))
         nframes = np.reshape(cells, [-1,3,3]).shape[0]
         all_cells.append(np.reshape(cells, [nframes,3,3]))
         all_coords.append(np.reshape(coords, [nframes,-1,3]))
@@ -50,8 +55,6 @@ def to_system_data(folder,
         data['forces'] = np.concatenate(all_forces, axis = 0)
     if len(all_virs) > 0:
         data['virials'] = np.concatenate(all_virs, axis = 0)
-    if os.path.isfile(os.path.join(folder, "nopbc")):
-        data['nopbc'] = True
     return data
 
 

dpdata/deepmd/raw.py

@@ -33,10 +33,13 @@ def to_system_data(folder, type_map = None, labels = True) :
     if os.path.isdir(folder) :
         data = load_type(folder, type_map = type_map)
         data['orig'] = np.zeros([3])        
-        data['cells'] = np.loadtxt(os.path.join(folder, 'box.raw'))
-        data['coords'] = np.loadtxt(os.path.join(folder, 'coord.raw'))
-        data['cells'] = np.reshape(data['cells'], [-1, 3, 3])
-        nframes = data['cells'].shape[0]
+        data['coords'] = np.loadtxt(os.path.join(folder, 'coord.raw'), ndmin=2)
+        nframes = data['coords'].shape[0]
+        if os.path.isfile(os.path.join(folder, "nopbc")):
+            data['nopbc'] = True
+            data['cells'] = np.zeros((nframes, 3,3))
+        else:
+            data['cells'] = np.loadtxt(os.path.join(folder, 'box.raw'), ndmin=2)
         data['cells'] = np.reshape(data['cells'], [nframes, 3, 3])
         data['coords'] = np.reshape(data['coords'], [nframes, -1, 3])
         if labels :

dpdata/pymatgen/molecule.py

@@ -1,5 +1,8 @@
 import numpy as np
-from pymatgen.core import Molecule
+try:
+    from pymatgen.core import Molecule
+except ImportError:
+    pass
 from collections import Counter
 import dpdata
 

tests/comp_sys.py

@@ -35,10 +35,11 @@ def test_nframs(self):
     def test_cell(self):
         self.assertEqual(self.system_1.get_nframes(),
                          self.system_2.get_nframes())        
-        np.testing.assert_almost_equal(self.system_1.data['cells'], 
-                                       self.system_2.data['cells'], 
-                                       decimal = self.places,
-                                       err_msg = 'cell failed')
+        if not self.system_1.nopbc and not self.system_2.nopbc:
+            np.testing.assert_almost_equal(self.system_1.data['cells'], 
+                                        self.system_2.data['cells'], 
+                                        decimal = self.places,
+                                        err_msg = 'cell failed')
 
     def test_coord(self): 
         self.assertEqual(self.system_1.get_nframes(),