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Local ISDF module (with k-sampling) for PBC mean-field calculation. #62

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121 changes: 121 additions & 0 deletions examples/isdf/00-RHF_diamond.py
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import numpy as np
from pyscf import lib
from pyscf.gto.mole import *

from pyscf.isdf import isdf_tools_cell
from pyscf.isdf import isdf_local_k
from pyscf.isdf import isdf_jk
from pyscf.isdf import isdf_local

from pyscf.lib.parameters import BOHR

MOL_STRUCTURE = '''
C 0. 0. 0.
C 0.8917 0.8917 0.8917
C 1.7834 1.7834 0.
C 2.6751 2.6751 0.8917
C 1.7834 0. 1.7834
C 2.6751 0.8917 2.6751
C 0. 1.7834 1.7834
C 0.8917 2.6751 2.6751
'''

#### NOTE: a full tests on combinations of parameters ####

C_ARRAY = [15, 15, 20, 25, 30, 30]
RELA_CUTOFF = [3e-2, 1e-2, 3e-3, 1e-3, 3e-4, 1e-4]
SuperCell_ARRAY = [
# [1, 1, 1],
[1, 1, 2],
# [1, 2, 2],
# [2, 2, 2],
# [3, 3, 3],
# [2, 4, 4],
# [3, 4, 4],
# [5, 5, 5],
# [6, 6, 6],
# [1, 1, 4],
# [1, 1, 8],
# [1, 1, 16],
# [1, 1, 32],
]


Ke_CUTOFF = [70]
boxlen = 3.5668
Basis = ['gth-dzvp']

PARTITION = [
[[0,1],[2,3],[4,5],[6,7]],
[[0,1,2,3],[4,5,6,7]],
[[0,1,2,3,4,5,6,7]],
[[0],[1],[2],[3],[4],[5],[6],[7]],
]

if __name__ == '__main__':

boxlen = 3.57371000
prim_a = np.array([[boxlen,0.0,0.0],[0.0,boxlen,0.0],[0.0,0.0,boxlen]])
atm = [
['C', (0. , 0. , 0. )],
['C', (0.8934275 , 0.8934275 , 0.8934275)],
['C', (1.786855 , 1.786855 , 0. )],
['C', (2.6802825 , 2.6802825 , 0.8934275)],
['C', (1.786855 , 0. , 1.786855)],
['C', (2.6802825 , 0.8934275 , 2.6802825)],
['C', (0. , 1.786855 , 1.786855)],
['C', (0.8934275 , 2.6802825 , 2.6802825)],
]

for supercell in SuperCell_ARRAY:
ke_cutoff = Ke_CUTOFF[0]
for partition in PARTITION: ## test different partition of atoms
for basis in Basis:
for c, rela_cutoff in zip(C_ARRAY, RELA_CUTOFF):
# for c in C_ARRAY:
print('--------------------------------------------')
print('C = %.2e, supercell = %s, kc_cutoff = %d, basis = %s, partition = %s' % (
c, str(supercell), ke_cutoff, basis, partition))

prim_cell = isdf_tools_cell.build_supercell(atm, prim_a, Ls = [1,1,1], ke_cutoff=ke_cutoff, basis=basis, pseudo="gth-pade", verbose=4)
prim_mesh = prim_cell.mesh
print("prim_mesh = ", prim_mesh)

mesh = [supercell[0] * prim_mesh[0], supercell[1] * prim_mesh[1], supercell[2] * prim_mesh[2]]
mesh = np.array(mesh, dtype=np.int32)

cell, supercell_group = isdf_tools_cell.build_supercell_with_partition(atm, prim_a, partition=partition, Ls = supercell, ke_cutoff=ke_cutoff, mesh=mesh, basis=basis, pseudo="gth-pade", verbose=4)

cell.incore_anyway = False
cell.max_memory = 200 # force to call with_df.get_jk

t1 = (lib.logger.process_clock(),lib.logger.perf_counter())

pbc_isdf_info = isdf_local.PBC_ISDF_Info_Quad(cell, with_robust_fitting=True, direct=False, rela_cutoff_QRCP=rela_cutoff)
pbc_isdf_info.build_IP_local(c=c, group=supercell_group, Ls=[supercell[0]*4, supercell[1]*4, supercell[2]*4])
print("pbc_isdf_info.naux = ", pbc_isdf_info.naux)
print("effective c = ", float(pbc_isdf_info.naux) / pbc_isdf_info.nao)
pbc_isdf_info.build_auxiliary_Coulomb()

t2 = (lib.logger.process_clock(), lib.logger.perf_counter())

print(isdf_jk._benchmark_time(t1, t2, 'build_isdf', pbc_isdf_info))

# for bunch_size in BUNCHSIZE_IO:
### perform scf ###

from pyscf.pbc import scf

t1 = (lib.logger.process_clock(), lib.logger.perf_counter())
mf = scf.RHF(cell)
mf.with_df = pbc_isdf_info
mf.max_cycle = 32
mf.conv_tol = 1e-7
pbc_isdf_info.direct_scf = mf.direct_scf
mf.kernel()
t2 = (lib.logger.process_clock(), lib.logger.perf_counter())
print(isdf_jk._benchmark_time(t1, t2, 'scf_isdf', pbc_isdf_info))

del mf
del pbc_isdf_info
exit(1)
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Is there a reason why you exit(1) in all of the examples? This signifies an error has occurred which should not be the case if it reaches the end of the code.

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Thanks for pointing out this issue. It is added just because I do not want run all the for-loops when I am testing the code. It should not appear here and I will comment this out.

115 changes: 115 additions & 0 deletions examples/isdf/01-KRHF_TiO2.py
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from functools import reduce
import numpy as np
from pyscf import lib
import pyscf.pbc.gto as pbcgto
from pyscf.pbc.gto import Cell
from pyscf.pbc import tools
from pyscf.pbc.lib.kpts import KPoints
from pyscf.pbc.lib.kpts_helper import is_zero, gamma_point, member
from pyscf.gto.mole import *

from pyscf.isdf import isdf_tools_cell
from pyscf.isdf import isdf_local_k
from pyscf.isdf import isdf_jk

MOL_STRUCTURE = '''
Ti 2.3246330643 2.3246330643 1.4853414945
Ti 0.0000000000 0.0000000000 -0.0000000000
O 0.9065353261 3.7427308025 1.4853414945
O 3.7427308025 0.9065353261 1.4853414945
O 1.4180977382 1.4180977382 0.0000000000
O 3.2311683903 3.2311683903 0.0000000000
'''

atm = [
['Ti',(2.3246330643,2.3246330643, 1.4853414945)],
['Ti',(0.0000000000,0.0000000000, 0.0000000000)],
['O ',(0.9065353261,3.7427308025, 1.4853414945)],
['O ',(3.7427308025,0.9065353261, 1.4853414945)],
['O ',(1.4180977382,1.4180977382, 0.0000000000)],
['O ',(3.2311683903,3.2311683903, 0.0000000000)],
]
boxlen = [4.6492659759,4.6492659759,2.9706828877]

C_ARRAY = [15,20,25,30] ## if rela_cutoff_QRCP is set, then c is used to when performing random projection, which can be relative large.
RELA_QR = [1e-2,1e-3,2e-4,1e-4]
SuperCell_ARRAY = [
# [1,1,1],
[2,2,2],
[3,3,3],
[4,4,4],
[5,5,5],
[6,6,6],
]
Ke_CUTOFF = [128, 192]

Basis = ['gth-cc-tzvp-Ye']

prim_partition = [[0],[1],[2],[3],[4],[5]]

if __name__ == '__main__':

prim_a = np.array([[boxlen[0],0.0,0.0],[0.0,boxlen[1],0.0],[0.0,0.0,boxlen[2]]])
pseudo = 'gth-hf-rev'

for supercell in SuperCell_ARRAY:
for basis in Basis:
for ke_cutoff in Ke_CUTOFF:

DM_CACHED = None

from pyscf.gto.basis import parse_nwchem
fbas="basis.dat"
atms = ['O', 'Ti']
basis = {atm:parse_nwchem.load(fbas, atm) for atm in atms}
print("basis = ", basis)


prim_cell = isdf_tools_cell.build_supercell(atm, prim_a, Ls = [1,1,1], ke_cutoff=ke_cutoff, basis=basis, pseudo=pseudo, spin=0, verbose=10)
cell = prim_cell

### perform scf ###

from pyscf.pbc import scf, dft
from pyscf.pbc.dft import multigrid

nk = supercell
kpts = cell.make_kpts(nk)

for c,rela_qr in list(zip(C_ARRAY,RELA_QR)):

print('--------------------------------------------')
print('C = %d, QR=%f, supercell = %s, kc_cutoff = %d, basis = %s' % (c, rela_qr, str(supercell), ke_cutoff, basis))

### create the isdf object ###

t1 = (lib.logger.process_clock(), lib.logger.perf_counter())
pbc_isdf_info = isdf_local_k.PBC_ISDF_Info_Quad_K(cell,
kmesh=nk,
with_robust_fitting=True,
rela_cutoff_QRCP=rela_qr,
direct=True,
limited_memory=True,
build_K_bunchsize=128, ## NOTE:control the memory cost in building K
# use_occ_RI_K=False
)
pbc_isdf_info.verbose = 10
pbc_isdf_info.build_IP_local(c=c, m=5, group=prim_partition)
print("effective c = ", float(pbc_isdf_info.naux) / pbc_isdf_info.nao)
t2 = (lib.logger.process_clock(), lib.logger.perf_counter())
print(isdf_jk._benchmark_time(t1, t2, 'build ISDF', pbc_isdf_info))

t1 = (lib.logger.process_clock(), lib.logger.perf_counter())
mf = scf.KRHF(cell, kpts)
mf.with_df = pbc_isdf_info
mf.max_cycle = 100
mf.conv_tol = 1e-8
mf.conv_tol_grad = 1e-3
if DM_CACHED is not None:
mf.kernel(DM_CACHED)
else:
mf.kernel()
t2 = (lib.logger.process_clock(), lib.logger.perf_counter())

print(isdf_jk._benchmark_time(t1, t2, 'RHF_bench', mf))
DM_CACHED = mf.make_rdm1()
139 changes: 139 additions & 0 deletions examples/isdf/02-UHF_CCO.py
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import numpy as np
from pyscf import lib
from pyscf.gto.mole import *

from pyscf.isdf import isdf_tools_cell
from pyscf.isdf import isdf_local_k
from pyscf.isdf import isdf_jk
from pyscf.isdf import isdf_local

from pyscf.lib.parameters import BOHR

#### NOTE: a full tests on combinations of parameters ####

prim_a = np.array(
[[14.572056092, 0.000000000, 0.000000000],
[0.000000000, 14.572056092, 0.000000000],
[0.000000000, 0.000000000, 6.010273939],]) * BOHR
atm = [
['Cu', (1.927800, 1.927800, 1.590250)],
['Cu', (5.783400, 5.783400, 1.590250)],
['Cu', (1.927800, 5.783400, 1.590250)],
['Cu', (5.783400, 1.927800, 1.590250)],
['O', (1.927800, 3.855600, 1.590250)],
['O', (3.855600, 5.783400, 1.590250)],
['O', (5.783400, 3.855600, 1.590250)],
['O', (3.855600, 1.927800, 1.590250)],
['O', (0.000000, 1.927800, 1.590250)],
['O', (1.927800, 7.711200, 1.590250)],
['O', (7.711200, 5.783400, 1.590250)],
['O', (5.783400, 0.000000, 1.590250)],
['Ca', (0.000000, 0.000000, 0.000000)],
['Ca', (3.855600, 3.855600, 0.000000)],
['Ca', (7.711200, 3.855600, 0.000000)],
['Ca', (3.855600, 7.711200, 0.000000)],
]

C_ARRAY = [25, 30, 35]
RELA_CUTOFF = [1e-3, 3e-4, 1e-4]
SuperCell_ARRAY = [
[1, 1, 1],
]
Ke_CUTOFF = [256]
Basis = ['gth-dzvp']

PARTITION = [
[[0], [1], [2], [3],
[4], [5], [6], [7],
[8], [9], [10], [11],
[12], [13], [14], [15]]
]

if __name__ == '__main__':

for supercell in SuperCell_ARRAY:
ke_cutoff = Ke_CUTOFF[0]
for partition in PARTITION: ## test different partition of atoms
for _basis_ in Basis:

DM_CACHED = None

from pyscf.gto.basis import parse_nwchem
fbas="basis2.dat"
atms = ['O', 'Cu', "Ca"]
basis = {atm:parse_nwchem.load(fbas, atm) for atm in atms}
# print("basis = ", basis)

pseudo = {'Cu': 'gth-pbe-q19', 'O': 'gth-pbe', 'Ca': 'gth-pbe'}

prim_cell = isdf_tools_cell.build_supercell(atm, prim_a, Ls = [1,1,1], ke_cutoff=ke_cutoff, basis=basis, pseudo=pseudo, verbose=4)
prim_mesh = prim_cell.mesh
# print("prim_mesh = ", prim_mesh)

mesh = [supercell[0] * prim_mesh[0], supercell[1] * prim_mesh[1], supercell[2] * prim_mesh[2]]
mesh = np.array(mesh, dtype=np.int32)

cell, supercell_group = isdf_tools_cell.build_supercell_with_partition(atm, prim_a,
partition = partition,
Ls = supercell,
ke_cutoff = ke_cutoff,
mesh = mesh,
basis = basis,
pseudo = pseudo,
verbose = 4)

cell.incore_anyway = False
cell.max_memory = 200 # force to call with_df.get_jk

for c, rela_cutoff in zip(C_ARRAY, RELA_CUTOFF):

print('--------------------------------------------')
print('C = %.2e, supercell = %s, kc_cutoff = %d, basis = %s, partition = %s' % (
c, str(supercell), ke_cutoff, basis, partition))

t1 = (lib.logger.process_clock(),lib.logger.perf_counter())

pbc_isdf_info = isdf_local.PBC_ISDF_Info_Quad(cell, with_robust_fitting=True,
direct=True,
rela_cutoff_QRCP=rela_cutoff,
limited_memory=True, build_K_bunchsize=56
)
pbc_isdf_info.build_IP_local(c=c, group=supercell_group)
print("pbc_isdf_info.naux = ", pbc_isdf_info.naux)
print("effective c = ", float(pbc_isdf_info.naux) / pbc_isdf_info.nao)
pbc_isdf_info.build_auxiliary_Coulomb()

t2 = (lib.logger.process_clock(), lib.logger.perf_counter())

print(isdf_jk._benchmark_time(t1, t2, 'build_isdf', pbc_isdf_info))

# for bunch_size in BUNCHSIZE_IO:
### perform scf ###

from pyscf.pbc import scf

t1 = (lib.logger.process_clock(), lib.logger.perf_counter())
mf = scf.UHF(cell)
mf.with_df = pbc_isdf_info
mf.max_cycle = 64
mf.conv_tol = 1e-7
pbc_isdf_info.direct_scf = mf.direct_scf
if DM_CACHED is not None:
mf.kernel(DM_CACHED)
else:
mf.kernel()
t2 = (lib.logger.process_clock(), lib.logger.perf_counter())
print(isdf_jk._benchmark_time(t1, t2, 'scf_isdf', pbc_isdf_info))

del mf
del pbc_isdf_info

### GDF benchmark ###

mf = scf.UHF(cell).density_fit()
mf.max_cycle = 64
mf.conv_tol = 1e-7
# pbc_isdf_info.direct_scf = mf.direct_scf
mf.kernel(DM_CACHED)

exit(1)
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