support nopbc

Author: njzjz

dpdata/deepmd/comp.py

@@ -48,6 +48,8 @@ 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
 
 
@@ -101,5 +103,6 @@ def dump(folder,
             np.save(os.path.join(set_folder, 'virial'), virials[set_stt:set_end])
         if 'atom_pref' in data:
             np.save(os.path.join(set_folder, "atom_pref"), atom_pref[set_stt:set_end])
-        
+    if data.get("nopbc", False):
+        os.mknod(os.path.join(folder, "nopbc"))
 

dpdata/deepmd/raw.py

@@ -49,6 +49,8 @@ def to_system_data(folder, type_map = None, labels = True) :
             if os.path.exists(os.path.join(folder, 'virial.raw')) :
                 data['virials'] = np.loadtxt(os.path.join(folder, 'virial.raw'))
                 data['virials'] = np.reshape(data['virials'], [nframes, 3, 3])
+        if os.path.isfile(os.path.join(folder, "nopbc")):
+            data['nopbc'] = True
         return data
     else :        
         raise RuntimeError('not dir ' + folder)
@@ -67,5 +69,6 @@ def dump (folder, data) :
         np.savetxt(os.path.join(folder, 'force.raw'),   np.reshape(data['forces'],   [nframes, -1]))
     if 'virials' in data :
         np.savetxt(os.path.join(folder, 'virial.raw'), np.reshape(data['virials'], [nframes, 9]))
-    
+    if data.get("nopbc", False):
+        os.mknod(os.path.join(folder, "nopbc"))
 

dpdata/gaussian/log.py

@@ -69,4 +69,5 @@ def to_system_data(file_name, md=False):
     data['coords'] = np.array(coords_t)
     data['orig'] = np.array([0, 0, 0])
     data['cells'] = np.array([[[100., 0., 0.], [0., 100., 0.], [0., 0., 100.]] for _ in energy_t])
+    data['nopbc'] = True
     return data

dpdata/system.py

@@ -319,6 +319,9 @@ def append(self, system) :
             assert(all(eq))
         for ii in ['coords', 'cells'] :
             self.data[ii] = np.concatenate((self.data[ii], system[ii]), axis = 0)
+        if self.nopbc and not system.nopbc:
+            # appended system uses PBC, cancel nopbc 
+            self.data['nopbc'] = False
         return True
 
     def sort_atom_names(self, type_map=None):
@@ -726,6 +729,12 @@ def perturb(self,
                 perturbed_system.append(tmp_system)
         return perturbed_system
 
+    @property
+    def nopbc(self):
+        if self.data.get("nopbc", False):
+            return True
+        return False
+
 def get_cell_perturb_matrix(cell_pert_fraction):
     if cell_pert_fraction<0:
         raise RuntimeError('cell_pert_fraction can not be negative')

tests/comp_sys.py

@@ -58,6 +58,9 @@ def test_coord(self):
                                            places = self.places,
                                            msg = 'coord[%d][%d][%d] failed' % (ff,ii,jj))
 
+    def test_nopbc(self):
+        self.assertEqual(self.system_1.nopbc, self.system_2.nopbc)
+
 
 class CompLabeledSys (CompSys) :
     def test_energy(self) :

tests/test_gaussian_log.py

@@ -18,6 +18,9 @@ def test_atom_types(self) :
         for ii in range(len(self.atom_types)) :
             self.assertEqual(self.system.data['atom_types'][ii], self.atom_types[ii])
 
+    def test_nopbc(self):
+        self.assertEqual(self.nopbc, True)
+
 class TestGaussianLoadLog(unittest.TestCase, TestGaussianLog):
     def setUp (self) :
         self.system = dpdata.LabeledSystem('gaussian/methane.gaussianlog',