Merge pull request #3 from AllanChain/update-with-force

Add tri feature which is needed for force calculation

DeepSolid/base_config.py

@@ -135,6 +135,7 @@ def default() -> ml_collections.ConfigDict:
                 'hidden_dims':  ((256, 32), (256, 32), (256, 32)),
                 'determinants':  8,
                 'after_determinants':  1,
+                'distance_type': 'nu',
             },
             'twist': (0.0, 0.0, 0.0), # Difine the twist of wavefunction,
                                       # twists are given in terms of fractions of supercell reciprocal vectors

DeepSolid/network.py

@@ -58,18 +58,19 @@ def enforce_pbc(latvec, epos):
 
 
 def init_solid_fermi_net_params(
-        key: jnp.ndarray,
-        data,
-        atoms: jnp.ndarray,
-        spins: Tuple[int, int],
-        envelope_type: str = 'full',
-        bias_orbitals: bool = False,
-        use_last_layer: bool = False,
-        eps: float = 0.01,
-        full_det: bool = True,
-        hidden_dims: FermiLayers = ((256, 32), (256, 32), (256, 32)),
-        determinants: int = 16,
-        after_determinants: Union[int, Tuple[int, ...]] = 1,
+    key: jnp.ndarray,
+    data,
+    atoms: jnp.ndarray,
+    spins: Tuple[int, int],
+    envelope_type: str = 'full',
+    bias_orbitals: bool = False,
+    use_last_layer: bool = False,
+    eps: float = 0.01,
+    full_det: bool = True,
+    hidden_dims: FermiLayers = ((256, 32), (256, 32), (256, 32)),
+    determinants: int = 16,
+    after_determinants: Union[int, Tuple[int, ...]] = 1,
+    distance_type='nu',
 ):
     """Initializes parameters for the Fermionic Neural Network.
 
@@ -107,7 +108,13 @@ def init_solid_fermi_net_params(
     del data
 
     natom = atoms.shape[0]
-    in_dims = (natom * 4, 4)
+    if distance_type == 'nu':
+        in_dims = (natom * 4, 4)
+    elif distance_type == 'tri':
+        in_dims = (natom * 7, 7)
+    else:
+        raise ValueError('Unrecognized distance function.')
+
     active_spin_channels = [spin for spin in spins if spin > 0]
     nchannels = len(active_spin_channels)
     # The input to layer L of the one-electron stream is from
@@ -179,38 +186,6 @@ def init_solid_fermi_net_params(
     return params
 
 
-def construct_input_features(
-        x: jnp.ndarray,
-        atoms: jnp.ndarray,
-        ndim: int = 3) -> Tuple[jnp.ndarray, jnp.ndarray, jnp.ndarray, jnp.ndarray]:
-    """Constructs inputs to Fermi Net from raw electron and atomic positions.
-      Args:
-        x: electron positions. Shape (nelectrons*ndim,).
-        atoms: atom positions. Shape (natoms, ndim).
-        ndim: dimension of system. Change only with caution.
-      Returns:
-        ae, ee, r_ae, r_ee tuple, where:
-          ae: atom-electron vector. Shape (nelectron, natom, 3).
-          ee: atom-electron vector. Shape (nelectron, nelectron, 3).
-          r_ae: atom-electron distance. Shape (nelectron, natom, 1).
-          r_ee: electron-electron distance. Shape (nelectron, nelectron, 1).
-        The diagonal terms in r_ee are masked out such that the gradients of these
-        terms are also zero.
-      """
-
-    assert atoms.shape[1] == ndim
-    ae = jnp.reshape(x, [-1, 1, ndim]) - atoms[None, ...]
-    ee = jnp.reshape(x, [1, -1, ndim]) - jnp.reshape(x, [-1, 1, ndim])
-
-    r_ae = jnp.linalg.norm(ae, axis=2, keepdims=True)
-    # Avoid computing the norm of zero, as is has undefined grad
-    n = ee.shape[0]
-    r_ee = (
-            jnp.linalg.norm(ee + jnp.eye(n)[..., None], axis=-1) * (1.0 - jnp.eye(n)))
-
-    return ae, ee, r_ae, r_ee[..., None]
-
-
 def scaled_f(w):
     """
     see Phys. Rev. B 94, 035157
@@ -229,23 +204,6 @@ def scaled_g(w):
     return w * (1 - 3. / 2. * jnp.abs(w / jnp.pi) + 1. / 2. * jnp.abs(w / jnp.pi) ** 2)
 
 
-def sin_relative_distance(xea, a, b):
-    '''
-
-    :param xea:
-    :param a:
-    :param b:
-    :return: periodic relative distance [ne, na, 6]
-    '''
-    w = jnp.einsum('...ijk,lk->...ijl', xea, b)
-    mod = (w + jnp.pi) // (2 * jnp.pi)
-    w = (w - mod * 2 * jnp.pi)
-    # w = jnp.mod(w + jnp.pi, 2 * jnp.pi) - jnp.pi
-    # r1 = jnp.einsum('...i,ij->...j', scaled_f(w), a)
-    r2 = jnp.einsum('...i,ij->...j', scaled_g(w), a)
-    return r2
-
-
 def nu_distance(xea, a, b):
     """
     see Phys. Rev. B 94, 035157
@@ -265,11 +223,36 @@ def nu_distance(xea, a, b):
     sd = result ** 0.5
     return sd, rel
 
+
+def tri_distance(xea, a, b):
+    """
+    see Phys. Rev. Lett. 130, 036401 (2023).
+    :param xea: relative distance between electrons and atoms
+    :param a: lattice vectors of primitive cell divided by 2\pi.
+    :param b: reciprocal vectors of primitive cell.
+    :return: periodic generalized relative and absolute distance of xea.
+    """
+    w = jnp.einsum('...ijk,lk->...ijl', xea, b)
+    sg = jnp.sin(w)
+    cg = jnp.cos(w)
+    rel_sin = jnp.einsum('...i,ij->...j', sg, a)
+    rel_cos = jnp.einsum('...i,ij->...j', cg, a)
+    rel = jnp.concatenate([rel_sin, rel_cos], axis=-1)
+    metric = jnp.einsum('ij,kj->ik', a, a)
+    vector_sin = sg[..., :, None] * sg[..., None, :]
+    vector_cos = (1-cg[..., :, None]) * (1-cg[..., None, :])
+    vector = vector_cos + vector_sin
+    sd = jnp.einsum('...ij,ij->...', vector, metric) ** 0.5
+    return sd, rel
+
+
 def construct_periodic_input_features(
-        x: jnp.ndarray,
-        atoms: jnp.ndarray,
-        simulation_cell=None,
-        ndim: int = 3) -> Tuple[jnp.ndarray, jnp.ndarray, jnp.ndarray, jnp.ndarray]:
+    x: jnp.ndarray,
+    atoms: jnp.ndarray,
+    simulation_cell=None,
+    ndim: int = 3,
+    distance_type: str = 'nu',
+) -> Tuple[jnp.ndarray, jnp.ndarray, jnp.ndarray, jnp.ndarray]:
     """Constructs a periodic generalized inputs to Fermi Net from raw electron and atomic positions.
     see Phys. Rev. B 94, 035157
       Args:
@@ -285,14 +268,21 @@ def construct_periodic_input_features(
         The diagonal terms in r_ee are masked out such that the gradients of these
         terms are also zero.
       """
+    if distance_type == 'nu':
+        distance_func = nu_distance
+    elif distance_type == 'tri':
+        distance_func = tri_distance
+    else:
+        raise ValueError('Unrecognized distance function.')
+
     primitive_cell = simulation_cell.original_cell
     x = x.reshape(-1, ndim)
     n = x.shape[0]
     prim_x, _ = enforce_pbc(primitive_cell.a, x)
 
     # prim_xea = minimal_imag.dist_i(atoms.ravel(), prim_x.ravel())
     prim_xea = prim_x[..., None, :] - atoms
-    prim_periodic_sea, prim_periodic_xea = nu_distance(prim_xea,
+    prim_periodic_sea, prim_periodic_xea = distance_func(prim_xea,
                                                        primitive_cell.AV,
                                                        primitive_cell.BV)
     prim_periodic_sea = prim_periodic_sea[..., None]
@@ -301,7 +291,7 @@ def construct_periodic_input_features(
     # sim_xee = sim_minimal_imag.dist_matrix(sim_x.ravel())
     sim_xee = sim_x[:, None, :] - sim_x[None, :, :]
 
-    sim_periodic_see, sim_periodic_xee = nu_distance(sim_xee + jnp.eye(n)[..., None],
+    sim_periodic_see, sim_periodic_xee = distance_func(sim_xee + jnp.eye(n)[..., None],
                                                      simulation_cell.AV,
                                                      simulation_cell.BV)
     sim_periodic_see = sim_periodic_see * (1.0 - jnp.eye(n))
@@ -474,7 +464,8 @@ def solid_fermi_net_orbitals(params, x,
                              atoms=None,
                              spins=(None, None),
                              envelope_type=None,
-                             full_det=False):
+                             full_det=False,
+                             distance_type='nu'):
     """Forward evaluation of the Solid Neural Network up to the orbitals.
      Args:
        params: A dictionary of parameters, containing fields:
@@ -506,9 +497,9 @@ def solid_fermi_net_orbitals(params, x,
        envelope, depending on the envelope type.
      """
 
-    ae_, ee_, r_ae, r_ee = construct_periodic_input_features(x, atoms,
-                                                             simulation_cell=simulation_cell,
-                                                             )
+    ae_, ee_, r_ae, r_ee = construct_periodic_input_features(
+        x, atoms, simulation_cell=simulation_cell, distance_type=distance_type
+    )
     ae = jnp.concatenate((r_ae, ae_), axis=2)
     ae = jnp.reshape(ae, [jnp.shape(ae)[0], -1])
     ee = jnp.concatenate((r_ee, ee_), axis=2)
@@ -576,6 +567,7 @@ def eval_func(params, x,
               spins=(None, None),
               envelope_type='full',
               full_det=False,
+              distance_type='nu',
               method_name='eval_slogdet'):
     '''
     generates the wavefunction of simulation cell.
@@ -597,6 +589,7 @@ def eval_func(params, x,
                                                 atoms=atoms,
                                                 spins=spins,
                                                 envelope_type=envelope_type,
+                                                distance_type=distance_type,
                                                 full_det=full_det)
     if method_name == 'eval_slogdet':
         _, result = logdet_matmul(orbitals)
@@ -623,6 +616,7 @@ def make_solid_fermi_net(
     hidden_dims: FermiLayers = ((256, 32), (256, 32), (256, 32)),
     determinants: int = 16,
     after_determinants: Union[int, Tuple[int, ...]] = 1,
+    distance_type='nu',
     method_name='eval_logdet',
 ):
     '''
@@ -655,6 +649,7 @@ def make_solid_fermi_net(
         hidden_dims=hidden_dims,
         determinants=determinants,
         after_determinants=after_determinants,
+        distance_type=distance_type,
     )
     network = functools.partial(
         eval_func,
@@ -664,6 +659,7 @@ def make_solid_fermi_net(
         spins=simulation_cell.nelec,
         envelope_type=envelope_type,
         full_det=full_det,
+        distance_type=distance_type,
         method_name=method_name,
     )
     method.init = init

bin/deepsolid

@@ -8,7 +8,6 @@
 # modified from FermiNet:https://github.com/deepmind/ferminet
 
 import sys
-import os
 
 from absl import app
 from absl import flags