Add PBC interface

pyscf · Aug 9, 2024 · f9cf5b2 · f9cf5b2
1 parent 8f92bb3
commit f9cf5b2
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Showing 4 changed files with 30 additions and 8 deletions.
diff --git a/pyscf/dispersion/dftd3.py b/pyscf/dispersion/dftd3.py
@@ -64,17 +64,21 @@ def __init__(self, mol, xc, version='d3bj', atm=False):
                      for ia in range(mol.natm)]
         nuc_types = np.asarray(nuc_types, dtype=np.int32)
         self.natm = mol.natm
-        self._lattice = lib.c_null_ptr()
-        self._periodic = lib.c_null_ptr()
+        if isinstance(mol, gto.Mole):
+            lattice = lib.c_null_ptr()
+            periodic = lib.c_null_ptr()
+        else: # pbc.gto.Cell
+            a = mol.lattice_vectors()
+            lattice = a.ctypes
+            periodic = ctypes.byref(ctypes.c_bool(True))
 
         err = libdftd3.dftd3_new_error()
         self._mol = libdftd3.dftd3_new_structure(
             err,
             ctypes.c_int(mol.natm),
             nuc_types.ctypes.data_as(ctypes.c_void_p),
             coords.ctypes.data_as(ctypes.c_void_p),
-            self._lattice,
-            self._periodic,
+            lattice, periodic,
         )
         error_check(err)
 

diff --git a/pyscf/dispersion/dftd4.py b/pyscf/dispersion/dftd4.py
@@ -50,8 +50,13 @@ def __init__(self, mol, xc, atm=False):
                      for ia in range(mol.natm)]
         nuc_types = np.asarray(nuc_types, dtype=np.int32)
         self.natm = mol.natm
-        self._lattice = lib.c_null_ptr()
-        self._periodic = lib.c_null_ptr()
+        if isinstance(mol, gto.Mole):
+            lattice = lib.c_null_ptr()
+            periodic = lib.c_null_ptr()
+        else: # pbc.gto.Cell
+            a = mol.lattice_vectors()
+            lattice = a.ctypes
+            periodic = ctypes.byref(ctypes.c_bool(True))
 
         err = libdftd4.dftd4_new_error()
         self._mol = libdftd4.dftd4_new_structure(
@@ -60,8 +65,7 @@ def __init__(self, mol, xc, atm=False):
             nuc_types.ctypes.data_as(ctypes.c_void_p),
             coords.ctypes.data_as(ctypes.c_void_p),
             charge.ctypes.data_as(ctypes.c_void_p),
-            self._lattice,
-            self._periodic,
+            lattice, periodic,
         )
         error_check(err)
 

diff --git a/pyscf/dispersion/tests/test_d3.py b/pyscf/dispersion/tests/test_d3.py
@@ -1,3 +1,4 @@
+import numpy as np
 import pytest
 import pyscf
 from pyscf.dispersion.dftd3 import DFTD3Dispersion
@@ -20,3 +21,9 @@ def test_d3_gradients():
     assert abs(out['energy'] - -0.002682864283734) < 1e-10
     assert abs(out['gradient'][0, 2] - 0.0004553384490128) < 1e-10
     assert abs(out['virial'][2, 2] - -0.000860464962618) < 1e-10
+
+def test_d3_with_pbc():
+    mol = pyscf.M(atom='H 0 0 0; H 0 0 1', a=np.eye(3)*2)
+    model = DFTD3Dispersion(mol, xc='WB97X')
+    out = model.get_dispersion()
+    assert abs(out['energy'] - -0.0014506963767424985) < 1e-10
diff --git a/pyscf/dispersion/tests/test_d4.py b/pyscf/dispersion/tests/test_d4.py
@@ -1,3 +1,4 @@
+import numpy as np
 import pytest
 import pyscf
 from pyscf.dispersion.dftd4 import DFTD4Dispersion
@@ -20,3 +21,9 @@ def test_d4_gradients():
     assert abs(out['energy'] - -0.000967454204722) < 1e-10
     assert abs(out['gradient'][0,2] - 9.31972590827e-06) < 1e-10
     assert abs(out['virial'][2,2] - -1.76117295226e-05) < 1e-10
+
+def test_d4_with_pbc():
+    mol = pyscf.M(atom='H 0 0 0; H 0 0 1', a=np.eye(3)*2)
+    model = DFTD4Dispersion(mol, xc='WB97X')
+    out = model.get_dispersion()
+    assert abs(out['energy'] - -0.002715970438476524) < 1e-10