Python dump_pyscf 예제들

예제 #1

파일: test_water.py 프로젝트: adc-connect/adcc-testdata

    def run_scf(self):
        fn = "water_sto3g.hdf5"
        if os.path.isfile(fn):
            return fn

        mol = gto.M(
            atom="""
            O 0 0 0
            H 0 0 1.795239827225189
            H 1.693194615993441 0 -0.599043184453037
            """,
            basis='sto-3g',
            unit="Bohr"
        )
        mf = scf.RHF(mol)
        mf.conv_tol = 1e-11
        mf.conv_tol_grad = 1e-10
        mf.kernel()
        return atd.dump_pyscf(mf, fn)

예제 #2

파일: test_cn.py 프로젝트: adc-connect/adcc-testdata

    def run_scf(self):
        fn = "cn_sto3g.hdf5"
        if os.path.isfile(fn):
            return fn

        mol = gto.M(
            atom="""
            C 0 0 0
            N 0 0 2.2143810738114829
            """,
            spin=1,
            basis='sto-3g',
            unit="Bohr",
        )
        mf = scf.UHF(mol)
        mf.conv_tol = 1e-11
        mf.conv_tol_grad = 1e-10
        mf.diis = scf.EDIIS()
        mf.diis_space = 5
        mf.max_cycle = 500
        mf.kernel()
        return atd.dump_pyscf(mf, fn)

예제 #3

파일: generate_hfdata_h2o_def2tzvp.py 프로젝트: yychuang/adcc

## ---------------------------------------------------------------------
import sys

from pyscf import gto, scf
from static_data import xyz
from os.path import dirname, join

sys.path.insert(0, join(dirname(__file__), "adcc-testdata"))

import adcctestdata as atd  # noqa: E402

# Run SCF in pyscf and converge super-tight using an EDIIS
mol = gto.M(atom=xyz["h2o"], basis='def2-tzvp', unit="Bohr")
mf = scf.RHF(mol)
mf.conv_tol = 1e-13
mf.conv_tol_grad = 1e-12
mf.diis = scf.EDIIS()
mf.diis_space = 3
mf.max_cycle = 500
mf.kernel()
h5f = atd.dump_pyscf(mf, "h2o_def2tzvp_hfdata.hdf5")

# Store configuration parameters for interesting cases to generate
# reference data for. The data is stored as a stringified dict.
h5f["reference_cases"] = str({
    "gen": {},
    "cvs": {
        "core_orbitals": 1
    },
})

예제 #4

파일: generate_hfdata_cn_ccpvdz.py 프로젝트: yychuang/adcc

sys.path.insert(0, join(dirname(__file__), "adcc-testdata"))

import adcctestdata as atd  # noqa: E402

# Run SCF in pyscf and converge super-tight using an EDIIS
mol = gto.M(atom=xyz["cn"], basis='cc-pvdz', unit="Bohr", spin=1, verbose=4)
mf = scf.UHF(mol)
mf.conv_tol = 1e-12
mf.conv_tol_grad = 1e-12
mf.diis = scf.EDIIS()
mf.diis_space = 3
mf.max_cycle = 600
mf = scf.addons.frac_occ(mf)
mf.kernel()
h5f = atd.dump_pyscf(mf, "cn_ccpvdz_hfdata.hdf5")

h5f["reference_cases"] = str({
    "gen": {},
    "cvs": {
        "core_orbitals": 1
    },
    "fc": {
        "frozen_core": 1
    },
    "fv": {
        "frozen_virtual": 3
    },
})

# Since CN has some symmetry some energy levels are degenerate,

예제 #5

파일: generate_hfdata_ch2nh2_sto3g.py 프로젝트: chrinide/adcc

from geometry import xyz
from os.path import dirname, join

sys.path.insert(0, join(dirname(__file__), "adcc-testdata"))

import adcctestdata as atd  # noqa: E402

# Run SCF in pyscf and converge super-tight using an EDIIS
mol = gto.M(
    atom=xyz["ch2nh2"],
    basis='sto-3g',
    unit="Bohr",
    spin=1,  # =2S, ergo doublet
    verbose=4)
mf = scf.UHF(mol)
mf.diis = scf.EDIIS()
mf.conv_tol = 1e-14
mf.conv_tol_grad = 1e-12
mf.diis_space = 6
mf.max_cycle = 500
mf = scf.addons.frac_occ(mf)
mf.kernel()
h5f = atd.dump_pyscf(mf, "ch2nh2_sto3g_hfdata.hdf5")

h5f["reference_cases"] = str({
    "gen": {},
    "cvs": {
        "core_orbitals": 2
    },
})

예제 #6

파일: hf3.py 프로젝트: adc-connect/adcc-testdata

## adcc-testdata is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with adcc-testdata. If not, see <http://www.gnu.org/licenses/>.
##
## ---------------------------------------------------------------------
import os
import adcctestdata as atd

from pyscf import gto, scf

if not os.path.isfile("hf3.hdf5"):
    mol = gto.M(
        atom='H 0 0 0;'
             'F 0 0 2.5',
        basis='6-31G',
        unit="Bohr",
        spin=2  # =2S, ergo triplet
    )
    mf = scf.UHF(mol)
    mf.conv_tol = 1e-14
    mf.grad_conv_tol = 1e-10
    mf.kernel()
    atd.dump_pyscf(mf, "hf3.hdf5")

atd.dump_reference("hf3.hdf5", "adc2", "hf3_sf_adc2.hdf5", n_states_full=2,
                   n_spin_flip=5, print_level=100)

예제 #7

파일: water_fc.py 프로젝트: adc-connect/adcc-testdata

import adcctestdata as atd

from pyscf import gto, scf

if not os.path.isfile("water.hdf5"):
    mol = gto.M(atom="""
        O 0 0 0
        H 0 0 1.795239827225189
        H 1.693194615993441 0 -0.599043184453037
        """,
                basis='def2-tzvp',
                unit="Bohr")
    mf = scf.RHF(mol)
    mf.conv_tol = 1e-13
    mf.conv_tol_grad = 1e-12
    mf.diis = scf.EDIIS()
    mf.diis_space = 3
    mf.max_cycle = 500
    mf.kernel()

    atd.dump_pyscf(mf, "water.hdf5")

atd.dump_reference("water.hdf5",
                   "adc2",
                   "water_fc_adc2.hdf5",
                   n_states_full=2,
                   n_singlets=5,
                   n_triplets=3,
                   print_level=100,
                   frozen_core=[0, 43])

예제 #8

from os.path import dirname, join

from static_data import xyz

sys.path.insert(0, join(dirname(__file__), "adcc-testdata"))

import adcctestdata as atd  # noqa: E402

# Run SCF in pyscf and converge super-tight using an EDIIS
mol = gto.M(
    atom=xyz["hf"],
    basis='6-31G',
    unit="Bohr",
    spin=2,  # =2S, ergo triplet
    verbose=4
)
mf = scf.UHF(mol)
mf.diis = scf.EDIIS()
mf.conv_tol = 1e-14
mf.conv_tol_grad = 1e-12
mf.diis_space = 3
mf.max_cycle = 500
mf.kernel()
h5f = atd.dump_pyscf(mf, "hf3_631g_hfdata.hdf5")

h5f["reference_cases"] = str({
    "gen":   {},
    "fc":    {"frozen_core":    1},
    "fv":    {"frozen_virtual": 3},
})

예제 #9

파일: generate_hfdata_h2o_sto3g.py 프로젝트: yychuang/adcc

sys.path.insert(0, join(dirname(__file__), "adcc-testdata"))

import adcctestdata as atd  # noqa: E402

# Run SCF in pyscf and converge super-tight using an EDIIS
mol = gto.M(
    atom=xyz["h2o"],
    basis='sto-3g',
    unit="Bohr"
)
mf = scf.RHF(mol)
mf.conv_tol = 1e-13
mf.conv_tol_grad = 1e-12
mf.diis = scf.EDIIS()
mf.diis_space = 3
mf.max_cycle = 500
mf.kernel()
h5f = atd.dump_pyscf(mf, "h2o_sto3g_hfdata.hdf5")

# Store configuration parameters for interesting cases to generate
# reference data for. The data is stored as a stringified dict.
h5f["reference_cases"] = str({
    "gen":    {},
    "cvs":    {"core_orbitals":  1},
    "fc":     {"frozen_core":    1},
    "fv":     {"frozen_virtual": 1},
    "fv-cvs": {"core_orbitals":  1, "frozen_virtual": 1},
    "fc-fv":  {"frozen_core":    1, "frozen_virtual": 1},
})

예제 #10

## along with adcc-testdata. If not, see <http://www.gnu.org/licenses/>.
##
## ---------------------------------------------------------------------
import os
import adcctestdata as atd

from pyscf import gto, scf

if not os.path.isfile("water_uhf.hdf5"):
    mol = gto.M(
        atom="""
        O 0 0 0
        H 0 0 1.795239827225189
        H 1.693194615993441 0 -0.599043184453037
        """,
        basis='cc-pvdz',
        unit="Bohr"
    )
    mf = scf.UHF(mol)
    mf.conv_tol = 1e-13
    mf.conv_tol_grad = 1e-12
    mf.diis = scf.EDIIS()
    mf.diis_space = 3
    mf.max_cycle = 500
    mf.kernel()

    atd.dump_pyscf(mf, "water_uhf.hdf5")

atd.dump_reference("water_uhf.hdf5", "adc2", "water_uhf_adc2.hdf5",
                   n_states_full=2, n_states=8, print_level=100)

예제 #11

from os.path import dirname, join

sys.path.insert(0, join(dirname(__file__), "adcc-testdata"))

import adcctestdata as atd  # noqa: E402

# Run SCF in pyscf and converge super-tight using an EDIIS
mol = gto.M(atom=xyz["h2s"], basis='6311+g**', unit="Bohr", verbose=4)
mf = scf.RHF(mol)
mf.conv_tol = 1e-12
mf.conv_tol_grad = 1e-12
mf.diis = scf.EDIIS()
mf.diis_space = 3
mf.max_cycle = 100
mf.kernel()
h5f = atd.dump_pyscf(mf, "h2s_6311g_hfdata.hdf5")

core = "core_orbitals"
fc = "frozen_core"
fv = "frozen_virtual"
h5f["reference_cases"] = str({
    "gen": {},  # noqa: E201, E202
    "cvs": {
        core: 1,
    },  # noqa: E201, E202
    "fc": {
        fc: 1,
    },  # noqa: E201, E202
    "fv": {
        fv: 3
    },  # noqa: E201, E202

예제 #12

파일: generate_hfdata_methox_sto3g.py 프로젝트: yychuang/adcc

from pyscf import gto, scf
from os.path import dirname, join

from static_data import xyz

sys.path.insert(0, join(dirname(__file__), "adcc-testdata"))

import adcctestdata as atd  # noqa: E402

# Run SCF in pyscf and converge super-tight using an EDIIS
mol = gto.M(atom=xyz["r2methyloxirane"],
            basis='sto-3g',
            unit="Bohr",
            verbose=4)
mf = scf.RHF(mol)
mf.diis = scf.EDIIS()
mf.conv_tol = 1e-13
mf.conv_tol_grad = 1e-12
mf.diis_space = 3
mf.max_cycle = 500
mf.kernel()
h5f = atd.dump_pyscf(mf, "methox_sto3g_hfdata.hdf5")

h5f["reference_cases"] = str({
    "gen": {},
    "cvs": {
        "core_orbitals": 1
    },
})

예제 #13

파일: cn.py 프로젝트: adc-connect/adcc-testdata

##
## ---------------------------------------------------------------------
import os
import adcctestdata as atd

from pyscf import gto, scf

if not os.path.isfile("cn.hdf5"):
    mol = gto.M(
        atom="""
        C 0 0 0
        N 0 0 2.2143810738114829
        """,
        basis='cc-pvdz',
        unit="Bohr",
        spin=1,
        verbose=4,
    )
    mf = scf.UHF(mol)
    mf.conv_tol = 1e-11
    mf.conv_tol_grad = 1e-10
    mf.diis = scf.EDIIS()
    mf.diis_space = 3
    mf.max_cycle = 500
    mf.kernel()

    atd.dump_pyscf(mf, "cn.hdf5")

atd.dump_reference("cn.hdf5", "adc2", "cn_adc2.hdf5", n_states_full=3,
                   n_states=5, print_level=100)

예제 #14

## along with adcc-testdata. If not, see <http://www.gnu.org/licenses/>.
##
## ---------------------------------------------------------------------
import os
import adcctestdata as atd

from pyscf import gto, scf

if not os.path.isfile("water_small.hdf5"):
    mol = gto.M(
        atom="""
        O 0 0 0
        H 0 0 1.795239827225189
        H 1.693194615993441 0 -0.599043184453037
        """,
        basis='3-21g',
        unit="Bohr"
    )
    mf = scf.RHF(mol)
    mf.conv_tol = 1e-13
    mf.conv_tol_grad = 1e-12
    mf.diis = scf.EDIIS()
    mf.diis_space = 3
    mf.max_cycle = 500
    mf.kernel()

    atd.dump_pyscf(mf, "water_small.hdf5")

atd.dump_reference("water_small.hdf5", "adc2", "water_small_adc2.hdf5",
                   n_states_full=2, n_singlets=5, n_triplets=3, print_level=100)