Skip to content
GitLab
Commit bc9a0527 authored by Lauri Himanen's avatar Lauri Himanen
Browse files

Added support for parsing the D2 and D3 vdW settings.

parent 4961e40b
Expand all Hide whitespace changes
Inline Side-by-side
parser/parser-cp2k/cp2kparser/versions/cp2k262/commonparser.py
View file @ bc9a0527
......@@ -42,6 +42,7 @@ class CP2KCommonParser(CommonParser):
#=======================================================================
# Globally cached values
self.cache_service.add("simulation_cell", single=False, update=False)
self.cache_service.add("lattice_vectors", single=False, update=False)
self.cache_service.add("number_of_scf_iterations", 0)
self.cache_service.add("atom_positions", single=False, update=True)
self.cache_service.add("atom_labels", single=False, update=False)
......@@ -232,6 +233,34 @@ class CP2KCommonParser(CommonParser):
SM( " DFT\| Self-interaction correction \(SIC\)\s+(?P<self_interaction_correction_method>[^\n]+)"),
],
),
SM( " vdW POTENTIAL\|\s+",
forwardMatch=True,
sections=["x_cp2k_section_vdw_settings"],
subMatchers=[
SM( " vdW POTENTIAL\|\s+(?P<x_cp2k_vdw_type>{})".format(self.regexs.eol)),
SM( " vdW POTENTIAL\|\s+Potential Form:\s+(?P<x_cp2k_vdw_name>{})".format(self.regexs.eol)),
SM( " vdW POTENTIAL\|\s+BJ Damping:\s+(?P<x_cp2k_vdw_bj_damping_name>{})".format(self.regexs.eol)),
SM( " vdW POTENTIAL\|\s+Cutoff Radius \[Bohr\]:\s+(?P<x_cp2k_vdw_cutoff_radius>{})".format(self.regexs.float)),
SM( " vdW POTENTIAL\|\+sScaling Factor:s+(?P<x_cp2k_vdw_scaling_factor>{})".format(self.regexs.float),
sections=["x_cp2k_section_vdw_d2_settings"],
subMatchers=[
SM( " vdW POTENTIAL\|\s+Exp Prefactor for Damping:\s+(?P<x_cp2k_vdw_damping_factor>{})".format(self.regexs.float)),
SM( " vdW PARAMETER\|\s+Atom=(?P<x_cp2k_vdw_parameter_element_name>{})\s+C6\[J*nm^6*mol^-1\]=\s+(?P<x_cp2k_vdw_parameter_c6>{})\s+r\(vdW\)\[A\]=\s+(?P<x_cp2k_vdw_parameter_radius>{})".format(self.regexs.word, self.regexs.float, self.regexs.float),
sections=["x_cp2k_section_vdw_element_settings"],
repeats=True,
),
],
),
SM( " vdW POTENTIAL\|\s+s6 Scaling Factor:\s+(?P<x_cp2k_vdw_s6_scaling_factor>{})".format(self.regexs.float),
sections=["x_cp2k_section_vdw_d3_settings"],
subMatchers=[
SM( " vdW POTENTIAL\|\s+sr6 Scaling Factor:\s+(?P<x_cp2k_vdw_sr6_scaling_factor>{})".format(self.regexs.float)),
SM( " vdW POTENTIAL\|\s+s8 Scaling Factor:\s+(?P<x_cp2k_vdw_s8_scaling_factor>{})".format(self.regexs.float)),
SM( " vdW POTENTIAL\|\s+Cutoff for CN calculation:\s+(?P<x_cp2k_vdw_cn_cutoff>{})".format(self.regexs.float)),
],
)
]
),
SM( " DFT\+U\|",
adHoc=self.adHoc_dft_plus_u,
),
......@@ -427,6 +456,19 @@ class CP2KCommonParser(CommonParser):
backend.addValue("number_of_basis_sets_atom_centered", len(self.basis_set_info))
backend.closeSection("section_method_basis_set", method_basis_id)
def onClose_x_cp2k_section_vdw_settings(self, backend, gIndex, section):
"""Figures out the common metainfo for vdw from the CP2K specific
settings.
"""
vdw_name = section["x_cp2k_vdw_name"][0]
name_map = {
"S. Grimme, JCC 27: 1787 (2006)": "G06",
"S. Grimme et al, JCP 132: 154104 (2010)": "G10",
}
nomad_vdw_name = name_map.get(vdw_name)
if nomad_vdw_name is not None:
backend.addValue("van_der_Waals_method", nomad_vdw_name)
def onClose_x_cp2k_section_atomic_kind(self, backend, gIndex, section):
# basisID = backend.openSection("section_basis_set_atom_centered")
......@@ -541,6 +583,7 @@ class CP2KCommonParser(CommonParser):
# Push the results to cache
self.cache_service["simulation_cell"] = cell
self.cache_service["lattice_vectors"] = cell
def adHoc_atom_forces(self, parser):
"""Used to extract the final atomic forces printed at the end of a
......
parser/parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py
View file @ bc9a0527
......@@ -249,6 +249,7 @@ class CP2KGeoOptParser(MainHierarchicalParser):
def onClose_section_system(self, backend, gIndex, section):
self.cache_service.addArrayValues("simulation_cell", unit="angstrom")
self.cache_service.addArrayValues("lattice_vectors", unit="angstrom")
def onClose_section_method(self, backend, gIndex, section):
traj_file = self.file_service.get_file_by_id("trajectory")
......
parser/parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py
View file @ bc9a0527
......@@ -298,10 +298,12 @@ class CP2KMDParser(MainHierarchicalParser):
# simulation cel only on the first step to section_system
if i_step == 0 and self.ensemble == "NPT" and self.cell_iterator is None:
self.cache_service.addArrayValues("simulation_cell", unit="angstrom")
self.cache_service.addArrayValues("lattice_vectors", unit="angstrom")
# Unchanging cell
if self.ensemble != "NPT":
self.cache_service.addArrayValues("simulation_cell", unit="angstrom")
self.cache_service.addArrayValues("lattice_vectors", unit="angstrom")
# Trajectory
if freqs["trajectory"][1] and self.traj_iterator is not None:
......@@ -352,6 +354,7 @@ class CP2KMDParser(MainHierarchicalParser):
line = next(self.cell_iterator)
cell = np.reshape(line, (3, 3))
self.backend.addArrayValues("simulation_cell", cell, unit="angstrom")
self.backend.addArrayValues("lattice_vectors", cell, unit="angstrom")
# Output file
if md_steps:
......
parser/parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py
View file @ bc9a0527
......@@ -92,6 +92,7 @@ class CP2KSinglePointParser(MainHierarchicalParser):
"""
self.cache_service.addArrayValues("atom_positions", unit="angstrom")
self.cache_service.addArrayValues("simulation_cell", unit="angstrom")
self.cache_service.addArrayValues("lattice_vectors", unit="angstrom")
#===========================================================================
# adHoc functions
regtests/cp2k_2.6.2/GTH_BASIS_SETS 0 → 100644
View file @ bc9a0527
This diff is collapsed.
regtests/cp2k_2.6.2/POTENTIAL 0 → 100644
View file @ bc9a0527
This diff is collapsed.
regtests/cp2k_2.6.2/dftd3.dat 0 → 100644
View file @ bc9a0527
This diff is collapsed.
regtests/cp2k_2.6.2/vdw/d2/dftd2_t1.inp 0 → 100644
View file @ bc9a0527
&GLOBAL
PROJECT dftd2_t1
PRINT_LEVEL MEDIUM
RUN_TYPE ENERGY
&END GLOBAL
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME ../../GTH_BASIS_SETS
POTENTIAL_FILE_NAME ../../POTENTIAL
&MGRID
NGRIDS 1
CUTOFF 100
&END MGRID
&QS
METHOD GPW
&END QS
&SCF
SCF_GUESS ATOMIC
MAX_SCF 1
EPS_SCF 1.0e-0
&END SCF
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&vdW_POTENTIAL
DISPERSION_FUNCTIONAL PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD2
REFERENCE_FUNCTIONAL PBE
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC 6.0 6.0 6.0
PERIODIC NONE
&END
&COORD
C 7.499969 9.250001 7.500000
C 7.499969 5.750001 7.500000
H 8.205969 8.887002 6.753000
H 6.499969 8.887002 7.262000
H 7.793968 8.887002 8.485001
H 7.499969 10.340001 7.500000
H 7.199968 6.113001 6.517000
H 8.501968 6.113001 7.731000
H 6.798969 6.113001 8.252001
H 7.499969 4.660001 7.500000
&END COORD
&KIND H
BASIS_SET DZV-GTH
POTENTIAL GTH-PBE-q1
&END
&KIND C
BASIS_SET DZVP-GTH
POTENTIAL GTH-PBE-q4
&END
&END SUBSYS
&END
regtests/cp2k_2.6.2/vdw/d2/unittest.out 0 → 100644
View file @ bc9a0527
This diff is collapsed.
regtests/cp2k_2.6.2/vdw/d3/dftd3_t1-1_0.dftd 0 → 100644
View file @ bc9a0527
Pair potential vdW calculation
Dispersion potential type: DFT-D3
Scaling parameter (s6) 1.0000000000000000
Scaling parameter (s8) 0.72199999999999998
Zero Damping parameter (sr6) 1.2170000000000001
Zero Damping parameter (sr8) 1.0000000000000000
Cutoff coordination numbers 9.9999999999999995E-007
Total vdW energy [au] : -1.4768519876345225E-003
Total vdW energy [kcal] : -0.92673860612936865
regtests/cp2k_2.6.2/vdw/d3/dftd3_t1.inp 0 → 100644
View file @ bc9a0527
&GLOBAL
PROJECT dftd3_t1
PRINT_LEVEL MEDIUM
RUN_TYPE ENERGY
&END GLOBAL
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME ../../GTH_BASIS_SETS
POTENTIAL_FILE_NAME ../../POTENTIAL
&MGRID
NGRIDS 1
CUTOFF 100
&END MGRID
&QS
METHOD GPW
&END QS
&SCF
SCF_GUESS ATOMIC
MAX_SCF 1
EPS_SCF 1.0e-0
&END SCF
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&vdW_POTENTIAL
DISPERSION_FUNCTIONAL PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD3
PARAMETER_FILE_NAME ../../dftd3.dat
REFERENCE_FUNCTIONAL PBE
&PRINT_DFTD
&END
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC 6.0 6.0 6.0
PERIODIC NONE
&END
&COORD
C 7.499969 9.250001 7.500000
C 7.499969 5.750001 7.500000
H 8.205969 8.887002 6.753000
H 6.499969 8.887002 7.262000
H 7.793968 8.887002 8.485001
H 7.499969 10.340001 7.500000
H 7.199968 6.113001 6.517000
H 8.501968 6.113001 7.731000
H 6.798969 6.113001 8.252001
H 7.499969 4.660001 7.500000
&END COORD
&KIND H
BASIS_SET DZV-GTH
POTENTIAL GTH-PBE-q1
&END
&KIND C
BASIS_SET DZVP-GTH
POTENTIAL GTH-PBE-q4
&END
&END SUBSYS
&END
regtests/cp2k_2.6.2/vdw/d3/unittest.out 0 → 100644
View file @ bc9a0527
This diff is collapsed.
regtests/cp2k_2.6.2/vdw/d3_bj/dftd3_t1-1_0.dftd 0 → 100644
View file @ bc9a0527
Pair potential vdW calculation
Dispersion potential type: DFT-D3(BJ)
Scaling parameter (s6) 1.0000000000000000
Scaling parameter (s8) 0.78749999999999998
BJ Damping parameter (a1) 0.42890000000000000
BJ Damping parameter (a2) 4.4406999999999996
Cutoff coordination numbers 9.9999999999999995E-007
Total vdW energy [au] : -3.5512378384574906E-003
Total vdW energy [kcal] : -2.2284353692865868
regtests/cp2k_2.6.2/vdw/d3_bj/dftd3bj_t1.inp 0 → 100644
View file @ bc9a0527
&GLOBAL
PROJECT dftd3_t1
PRINT_LEVEL MEDIUM
RUN_TYPE ENERGY
&END GLOBAL
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME ../../GTH_BASIS_SETS
POTENTIAL_FILE_NAME ../../POTENTIAL
&MGRID
NGRIDS 1
CUTOFF 100
&END MGRID
&QS
METHOD GPW
&END QS
&SCF
SCF_GUESS ATOMIC
MAX_SCF 1
EPS_SCF 1.0e-0
&END SCF
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&vdW_POTENTIAL
DISPERSION_FUNCTIONAL PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD3(BJ)
PARAMETER_FILE_NAME ../../dftd3.dat
REFERENCE_FUNCTIONAL PBE
&PRINT_DFTD
&END
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC 6.0 6.0 6.0
PERIODIC NONE
&END
&COORD
C 7.499969 9.250001 7.500000
C 7.499969 5.750001 7.500000
H 8.205969 8.887002 6.753000
H 6.499969 8.887002 7.262000
H 7.793968 8.887002 8.485001
H 7.499969 10.340001 7.500000
H 7.199968 6.113001 6.517000
H 8.501968 6.113001 7.731000
H 6.798969 6.113001 8.252001
H 7.499969 4.660001 7.500000
&END COORD
&KIND H
BASIS_SET DZV-GTH
POTENTIAL GTH-PBE-q1
&END
&KIND C
BASIS_SET DZVP-GTH
POTENTIAL GTH-PBE-q4
&END
&END SUBSYS
&END
regtests/cp2k_2.6.2/vdw/d3_bj/unittest.out 0 → 100644
View file @ bc9a0527
This diff is collapsed.
regtests/regtests.py
View file @ bc9a0527
......@@ -348,12 +348,16 @@ class TestEnergyForce(unittest.TestCase):
def test_simulation_cell(self):
cell = self.results["simulation_cell"]
vectors = self.results["lattice_vectors"]
n_vectors = cell.shape[0]
n_dim = cell.shape[1]
self.assertEqual(n_vectors, 3)
self.assertEqual(n_dim, 3)
expected_cell = convert_unit(np.array([[5.431, 0, 0], [0, 5.431, 0], [0, 0, 5.431]]), "angstrom")
self.assertTrue(np.array_equal(cell, expected_cell))
self.assertTrue(np.array_equal(vectors, expected_cell))
def test_number_of_atoms(self):
n_atoms = self.results["number_of_atoms"]
......@@ -1100,6 +1104,25 @@ class TestMDEnsembles(unittest.TestCase):
self.assertTrue(np.array_equal(expected_cell_end, simulation_cell[-1, :, :]))
class TestVDWMethod(unittest.TestCase):
"""Tests that different van der Waals methods are recognized correctly.
"""
def test_d2(self):
results = get_result("vdw/d2")
result = results["van_der_Waals_method"]
self.assertEqual(result, "G06")
def test_d3(self):
results = get_result("vdw/d3")
result = results["van_der_Waals_method"]
self.assertEqual(result, "G10")
def test_d3_bj(self):
results = get_result("vdw/d3_bj")
result = results["van_der_Waals_method"]
self.assertEqual(result, "G10")
class TestElectronicStructureMethod(unittest.TestCase):
"""Tests that different methods are recognized correctly.
"""
......@@ -1146,6 +1169,8 @@ if __name__ == '__main__':
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMD))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDPrintSettings))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDEnsembles))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMDEnsembles))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestVDWMethod))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestElectronicStructureMethod))
alltests = unittest.TestSuite(suites)
unittest.TextTestRunner(verbosity=0).run(alltests)
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment