support nopbc

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 +103,10 @@ 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])
-
+    try:
+        os.remove(os.path.join(folder, "nopbc"))
+    except OSError:
+        pass
+    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 +69,10 @@ 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]))
-
+    try:
+        os.remove(os.path.join(folder, "nopbc"))
+    except OSError:
+        pass
+    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

@@ -284,6 +284,7 @@ def sub_system(self, f_idx) :
             tmp.data[ii] = self.data[ii]
         tmp.data['cells'] = self.data['cells'][f_idx].reshape(-1, 3, 3)
         tmp.data['coords'] = self.data['coords'][f_idx].reshape(-1, self.data['coords'].shape[1], 3)
+        tmp.data['nopbc'] = self.nopbc
         return tmp
 
 
@@ -319,6 +320,9 @@ 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 +730,12 @@ 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')
@@ -1018,6 +1028,7 @@ def from_gaussian_log(self, file_name, md=False):
             self.data = dpdata.gaussian.log.to_system_data(file_name, md=md)
         except AssertionError:
             self.data['energies'], self.data['forces']= [], []
+            self.data['nopbc'] = True
 
 
     def from_cp2k_output(self, file_name) :
@@ -1245,7 +1256,7 @@ def to_deepmd_npy(self, folder, set_size = 5000, prec=np.float32) :
 def check_System(data):
     keys={'atom_names','atom_numbs','cells','coords','orig','atom_types'}
     assert( isinstance(data,dict) )
-    assert( set(data.keys())==keys )
+    assert( keys.issubset(set(data.keys())) )
     if len(data['coords']) > 0 :
         assert( len(data['coords'][0])==len(data['atom_types'])==sum(data['atom_numbs']) )
     else :

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) :
@@ -97,4 +100,12 @@ def test_virial(self) :
                                            places = self.v_places,
                                            msg = 'virials[%d][%d][%d] failed' % (ff,ii,jj))
 
-
+class IsPBC:                    
+    def test_is_pbc(self):
+        self.assertFalse(self.system_1.nopbc)
+        self.assertFalse(self.system_2.nopbc)
+
+class IsNoPBC:                    
+    def test_is_nopbc(self):
+        self.assertTrue(self.system_1.nopbc)
+        self.assertTrue(self.system_2.nopbc)

tests/test_deepmd_comp.py

@@ -2,9 +2,9 @@
 import numpy as np
 import unittest
 from context import dpdata
-from comp_sys import CompLabeledSys, CompSys
+from comp_sys import CompLabeledSys, CompSys, IsPBC
 
-class TestDeepmdLoadDumpComp(unittest.TestCase, CompLabeledSys):
+class TestDeepmdLoadDumpComp(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp (self) :
         self.system_1 = dpdata.LabeledSystem('poscars/OUTCAR.h2o.md', 
                                              fmt = 'vasp/outcar')
@@ -25,7 +25,7 @@ def tearDown(self) :
             shutil.rmtree('tmp.deepmd.npy')
 
 
-class TestDeepmdCompNoLabels(unittest.TestCase, CompSys) :
+class TestDeepmdCompNoLabels(unittest.TestCase, CompSys, IsPBC) :
     def setUp (self) :
         self.system_1 = dpdata.System('poscars/POSCAR.h2o.md',
                                       fmt = 'vasp/poscar')
@@ -45,7 +45,7 @@ def tearDown(self) :
             shutil.rmtree('tmp.deepmd.npy')
 
 
-class TestDeepmdCompNoLabels(unittest.TestCase, CompSys) :
+class TestDeepmdCompNoLabels(unittest.TestCase, CompSys, IsPBC) :
     def setUp(self) :
         self.dir_name = 'tmp.deepmd.npy.nol'
         natoms = 3

tests/test_deepmd_raw.py

@@ -2,9 +2,9 @@
 import numpy as np
 import unittest
 from context import dpdata
-from comp_sys import CompLabeledSys, CompSys
+from comp_sys import CompLabeledSys, CompSys, IsPBC
 
-class TestDeepmdLoadRaw(unittest.TestCase, CompLabeledSys):
+class TestDeepmdLoadRaw(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp (self) :
         self.system_1 = dpdata.LabeledSystem('poscars/OUTCAR.h2o.md', 
                                              fmt = 'vasp/outcar')
@@ -17,7 +17,7 @@ def setUp (self) :
         self.v_places = 6
 
 
-class TestDeepmdDumpRaw(unittest.TestCase, CompLabeledSys):
+class TestDeepmdDumpRaw(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp (self) :
         self.system_1 = dpdata.LabeledSystem('poscars/OUTCAR.h2o.md', 
                                              fmt = 'vasp/outcar')
@@ -131,7 +131,7 @@ def test_npy_type_map_enforce (self) :
 
 
 
-class TestDeepmdRawNoLabels(unittest.TestCase, CompSys) :
+class TestDeepmdRawNoLabels(unittest.TestCase, CompSys, IsPBC) :
     def setUp (self) :
         self.system_1 = dpdata.System('poscars/POSCAR.h2o.md',
                                       fmt = 'vasp/poscar')
@@ -149,7 +149,7 @@ def tearDown(self) :
             shutil.rmtree('tmp.deepmd')
 
 
-class TestDeepmdCompNoLabels(unittest.TestCase, CompSys) :
+class TestDeepmdCompNoLabels(unittest.TestCase, CompSys, IsPBC) :
     def setUp(self) :
         self.dir_name = 'tmp.deepmd.nol'
         natoms = 3

tests/test_gaussian_log.py

@@ -2,7 +2,6 @@
 import numpy as np
 import unittest
 from context import dpdata
-from comp_sys import CompLabeledSys
 
 class TestGaussianLog :
     def test_atom_names(self) :
@@ -18,6 +17,9 @@ 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.system.nopbc, True)
+
 class TestGaussianLoadLog(unittest.TestCase, TestGaussianLog):
     def setUp (self) :
         self.system = dpdata.LabeledSystem('gaussian/methane.gaussianlog', 

tests/test_json.py

@@ -2,9 +2,9 @@
 import numpy as np
 import unittest
 from context import dpdata
-from comp_sys import CompLabeledSys
+from comp_sys import CompLabeledSys, IsPBC
 
-class TestJsonLoad(unittest.TestCase, CompLabeledSys):
+class TestJsonLoad(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp (self) :
         self.system_1 = dpdata.LabeledSystem('poscars/OUTCAR.h2o.md',
                                              fmt = 'vasp/outcar')
@@ -14,7 +14,7 @@ def setUp (self) :
         self.f_places = 6
         self.v_places = 4
 
-class TestAsDict(unittest.TestCase, CompLabeledSys):
+class TestAsDict(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp (self) :
         self.system_1 = dpdata.LabeledSystem('poscars/OUTCAR.h2o.md',
                                              fmt = 'vasp/outcar')

tests/test_lammps_dump_skipload.py

@@ -2,9 +2,9 @@
 import numpy as np
 import unittest
 from context import dpdata
-from comp_sys import CompSys
+from comp_sys import CompSys, IsPBC
 
-class TestLmpDumpSkip(unittest.TestCase, CompSys):
+class TestLmpDumpSkip(unittest.TestCase, CompSys, IsPBC):
 
     def setUp(self): 
         self.system_1 = dpdata.System(os.path.join('poscars', 'conf.5.dump'), 

tests/test_multisystems.py

@@ -4,6 +4,7 @@
 from context import dpdata
 from comp_sys import CompSys
 from comp_sys import CompLabeledSys
+from comp_sys import IsNoPBC
 from itertools import permutations
 
 class MultiSystems:
@@ -17,7 +18,7 @@ def test_systems_size(self):
     def test_atom_names(self):
         self.assertEqual(self.atom_names, self.systems.atom_names)
 
-class TestMultiSystems(unittest.TestCase, CompLabeledSys, MultiSystems):
+class TestMultiSystems(unittest.TestCase, CompLabeledSys, MultiSystems, IsNoPBC):
     def setUp(self):
         self.places = 6
         self.e_places = 6
@@ -39,7 +40,7 @@ def setUp(self):
         self.atom_names = ['C', 'H']
 
 
-class TestMultiSystemsAdd(unittest.TestCase, CompLabeledSys, MultiSystems):
+class TestMultiSystemsAdd(unittest.TestCase, CompLabeledSys, MultiSystems, IsNoPBC):
     def setUp(self):
         self.places = 6
         self.e_places = 6
@@ -76,7 +77,7 @@ def setUp(self):
         self.system_sizes = {'C1H4O0':1, 'C0H0O2':1}
         self.atom_names = ['C', 'H', 'O']
 
-class TestMultiDeepmdDumpRaw(unittest.TestCase, CompLabeledSys):
+class TestMultiDeepmdDumpRaw(unittest.TestCase, CompLabeledSys, IsNoPBC):
     def setUp (self) :
         self.places = 6
         self.e_places = 6
@@ -94,7 +95,7 @@ def setUp (self) :
         self.system_1 = dpdata.LabeledSystem(os.path.join(path, 'C1H3'), fmt='deepmd/raw', type_map = ['C', 'H'])
         self.system_2 = system_3
 
-class TestMultiDeepmdDumpComp(unittest.TestCase, CompLabeledSys):
+class TestMultiDeepmdDumpComp(unittest.TestCase, CompLabeledSys, IsNoPBC):
     def setUp (self) :
         self.places = 6
         self.e_places = 4

tests/test_perturb.py

@@ -2,7 +2,7 @@
 import numpy as np
 import unittest
 from context import dpdata
-from comp_sys import CompSys
+from comp_sys import CompSys, IsPBC
 
 from unittest.mock import Mock
 from unittest.mock import patch, MagicMock 
@@ -103,7 +103,7 @@ def get_rand_generator():
         yield np.asarray([0.01525907, 0.68387374, 0.39768541, 0.55596047, 0.26557088, 0.60883073])
 
 # %%
-class TestPerturbNormal(unittest.TestCase, CompSys):
+class TestPerturbNormal(unittest.TestCase, CompSys, IsPBC):
     @patch('numpy.random')
     def setUp (self, random_mock):
         random_mock.rand = NormalGenerator().rand
@@ -113,7 +113,7 @@ def setUp (self, random_mock):
         self.system_2 = dpdata.System('poscars/POSCAR.SiC.normal',fmt='vasp/poscar')
         self.places = 6
 
-class TestPerturbUniform(unittest.TestCase, CompSys):
+class TestPerturbUniform(unittest.TestCase, CompSys, IsPBC):
     @patch('numpy.random')
     def setUp (self, random_mock) :
         random_mock.rand = UniformGenerator().rand
@@ -123,7 +123,7 @@ def setUp (self, random_mock) :
         self.system_2 = dpdata.System('poscars/POSCAR.SiC.uniform',fmt='vasp/poscar')
         self.places = 6
 
-class TestPerturbConst(unittest.TestCase, CompSys):
+class TestPerturbConst(unittest.TestCase, CompSys, IsPBC):
     @patch('numpy.random')
     def setUp (self, random_mock) :
         random_mock.rand = ConstGenerator().rand

tests/test_qe_cp_traj_skipload.py

@@ -4,8 +4,9 @@
 from context import dpdata
 from comp_sys import CompSys
 from comp_sys import CompLabeledSys
+from comp_sys import IsPBC
 
-class TestPWSCFTrajSkip(unittest.TestCase, CompSys):
+class TestPWSCFTrajSkip(unittest.TestCase, CompSys, IsPBC):
     def setUp(self): 
         self.system_1 = dpdata.System(os.path.join('qe.traj', 'traj6'), 
                                       fmt = 'qe/cp/traj',
@@ -21,7 +22,7 @@ def setUp(self):
         self.f_places = 6
         self.v_places = 4
 
-class TestPWSCFLabeledTrajSkip(unittest.TestCase, CompLabeledSys):
+class TestPWSCFLabeledTrajSkip(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp(self): 
         self.system_1 = dpdata.LabeledSystem(os.path.join('qe.traj', 'traj6'), 
                                              fmt = 'qe/cp/traj',

tests/test_quip_gap_xyz.py

@@ -2,9 +2,9 @@
 import numpy as np
 import unittest
 from context import dpdata
-from comp_sys import CompLabeledSys
+from comp_sys import CompLabeledSys, IsPBC
 
-class TestQuipGapxyz1(unittest.TestCase, CompLabeledSys):
+class TestQuipGapxyz1(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp (self) :
         self.multi_systems = dpdata.MultiSystems.from_file('xyz/xyz_unittest.xyz','quip/gap/xyz')
         self.system_1 = self.multi_systems.systems['B1C9']
@@ -14,7 +14,7 @@ def setUp (self) :
         self.f_places = 6
         self.v_places = 4
 
-class TestQuipGapxyz2(unittest.TestCase, CompLabeledSys):
+class TestQuipGapxyz2(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp (self) :
         self.system_temp0 = dpdata.MultiSystems.from_file(file_name='xyz/xyz_unittest.xyz', fmt='quip/gap/xyz')
         self.system_1 = self.system_temp0.systems['B5C7'] # .sort_atom_types()
@@ -27,7 +27,7 @@ def setUp (self) :
         self.f_places = 6
         self.v_places = 4
 
-class TestQuipGapxyzsort1(unittest.TestCase, CompLabeledSys):
+class TestQuipGapxyzsort1(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp (self) :
         self.multi_systems_1 = dpdata.MultiSystems.from_file('xyz/xyz_unittest.sort.xyz','quip/gap/xyz')
         self.system_1 = self.multi_systems_1.systems['B5C7']
@@ -39,7 +39,7 @@ def setUp (self) :
         self.f_places = 6
         self.v_places = 4
 
-class TestQuipGapxyzsort2(unittest.TestCase, CompLabeledSys):
+class TestQuipGapxyzsort2(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp (self) :
         self.multi_systems_1 = dpdata.MultiSystems.from_file('xyz/xyz_unittest.sort.xyz','quip/gap/xyz')
         self.system_1 = self.multi_systems_1.systems['B1C9']
@@ -51,7 +51,7 @@ def setUp (self) :
         self.f_places = 6
         self.v_places = 4
 
-class TestQuipGapxyzfield(unittest.TestCase, CompLabeledSys):
+class TestQuipGapxyzfield(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp (self) :
         self.multi_systems_1 = dpdata.MultiSystems.from_file('xyz/xyz_unittest.field.xyz','quip/gap/xyz')
         self.system_1 = self.multi_systems_1.systems['B1C9']
@@ -63,7 +63,7 @@ def setUp (self) :
         self.f_places = 6
         self.v_places = 4
 
-class TestQuipGapxyzfield2(unittest.TestCase, CompLabeledSys):
+class TestQuipGapxyzfield2(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp (self) :
         self.multi_systems_1 = dpdata.MultiSystems.from_file('xyz/xyz_unittest.field.xyz','quip/gap/xyz')
         self.system_1 = self.multi_systems_1.systems['B5C7']