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Implemented PBC for Gamma point (real wavefunction) #85

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Merged
merged 11 commits into from
Dec 6, 2024
Merged

Implemented PBC for Gamma point (real wavefunction) #85

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163c2e5
Implemented ECPs
kousuke-nakano Sep 19, 2024
63c677b
Implemented the ECP part and added several missing factors in the TRE…
kousuke-nakano Nov 12, 2024
3556fd5
make mol.atom_charge(i) a list also for an atom.
kousuke-nakano Nov 12, 2024
6949296
Implemented PBC for Gamma point (real wavefunction).
kousuke-nakano Nov 13, 2024
7408933
Merge branch 'pyscf:master' into master
kousuke-nakano Nov 13, 2024
db9cde9
Revert "Implemented PBC for Gamma point (real wavefunction)."
kousuke-nakano Nov 13, 2024
bbdda7f
Merge branch 'master' into master
kousuke-nakano Nov 14, 2024
65ee739
Merge branch 'pyscf:master' into master
kousuke-nakano Nov 16, 2024
b17a73b
Implemented PBC for Gamma point (real wavefunction).
kousuke-nakano Nov 18, 2024
52ba8d7
mol.a is replaced with mol.lattice_vectors() in pyscf/tools/trexio.py
kousuke-nakano Dec 1, 2024
c222ad9
Remove the unreachable error handling code
sunqm Dec 6, 2024
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38 changes: 29 additions & 9 deletions pyscf/tools/trexio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
from pyscf import lib
from pyscf import gto
from pyscf import scf
from pyscf import pbc
from pyscf import fci

import trexio
Expand Down Expand Up @@ -49,15 +50,20 @@ def _mol_to_trexio(mol, trexio_file):
trexio.write_nucleus_point_group(trexio_file, mol.groupname)

# 2.3 Periodic boundary calculations
try:
mol.a
periodic = True
raise NotImplementedError('PBC is not supported yet.')
if isinstance(mol, pbc.gto.Cell):
# 2.3 Periodic boundary calculations (pbc group)
trexio.write_pbc_periodic(trexio_file, True)
# 2.2 Cell

except AttributeError:
periodic = False
trexio.write_pbc_periodic(trexio_file, periodic)
lattice = mol.lattice_vectors()
a = lattice[0] # unit is Bohr
b = lattice[1] # unit is Bohr
c = lattice[2] # unit is Bohr
trexio.write_cell_a(trexio_file, a)
trexio.write_cell_b(trexio_file, b)
trexio.write_cell_c(trexio_file, c)
else:
# 2.3 Periodic boundary calculations (pbc group)
trexio.write_pbc_periodic(trexio_file, False)

# 2.4 Electron (electron group)
electron_up_num, electron_dn_num = mol.nelec
Expand Down Expand Up @@ -200,9 +206,23 @@ def _mol_to_trexio(mol, trexio_file):


def _scf_to_trexio(mf, trexio_file):
# 4.2 Molecular orbitals (mo group)
mol = mf.mol
_mol_to_trexio(mol, trexio_file)

# 2.3 Periodic boundary calculations (pbc group)
if isinstance(mol, pbc.gto.Cell):
kpt = mf.kpt
kpt = mol.get_scaled_kpts(kpt)
if np.all(np.array(kpt) == 0.0):
# gamma point PBC. Real wavefunction
trexio.write_pbc_k_point_num(trexio_file, 1)
trexio.write_pbc_k_point(trexio_file, [kpt])
trexio.write_pbc_k_point_weight(trexio_file, [1.0])
else:
# general point PBC. Complex wavefunction
raise NotImplementedError("Complex WF is not yet implemented.")

# 4.2 Molecular orbitals (mo group)
if isinstance(mf, scf.uhf.UHF):
mo_energy = np.ravel(mf.mo_energy)
mo = np.hstack(*mf.mo_coeff)
Expand Down