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Commit fbbd0f41 authored by Lauri Himanen's avatar Lauri Himanen
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Added some part of the basis set information, added atomic kind information,... 

Added some part of the basis set information, added atomic kind information, added other misc stuff.
parent 1070a2d1
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Showing with 11830 additions and 6890 deletions
.gitignore
View file @ fbbd0f41
......@@ -69,6 +69,7 @@ parser/parser-cp2k/cp2kparser/versions/**/input_data/*.html
parser/parser-cp2k/cp2kparser/tools/input_metainfo.json
test/unittests/BASIS_SET
test/unittests/GTH_POTENTIALS
test/unittests/cp2k_2.6.2/data
# Setuptools install folder
parser/parser-cp2k/cp2kparser.egg-info/
parser/parser-cp2k/cp2kparser/generic/inputparsing.py
View file @ fbbd0f41
......@@ -76,6 +76,19 @@ class CP2KInput(object):
return None
return section
def get_section_list(self, path):
split_path = path.split("/")
last_section = split_path[-1]
split_path.pop()
section = self.root_section
for part in split_path:
section = section.get_subsection(part)
if not section:
message = "The CP2K input does not contain the section {}".format(path)
logger.warning(message)
return None
return section.get_subsection_list(last_section)
def get_keyword_and_section(self, path):
split_path = path.rsplit("/", 1)
keyword = split_path[1]
......@@ -350,6 +363,10 @@ class Section(object):
else:
logger.error("The subsection '{}' in '{}' does not exist.".format(name, self.name))
def get_subsection_list(self, name):
subsection = self.sections.get(name)
return subsection
def get_section_parameter(self):
"""Get the section parameter, or if not specified the lone keyword
value.
......
parser/parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py
View file @ fbbd0f41
......@@ -29,6 +29,8 @@ class CommonMatcher(object):
self.regex_eol = "[^\n]+" # Regex for a single alphabetical letter
self.section_method_index = None
self.section_system_index = None
self.test_electronic_structure_method = "DFT"
self.basis_to_kind_mapping = []
#=======================================================================
# Cache levels
......@@ -38,6 +40,8 @@ class CommonMatcher(object):
'self_interaction_correction_method': CachingLevel.Cache,
'x_cp2k_section_programinformation': CachingLevel.ForwardAndCache,
'x_cp2k_section_quickstep_settings': CachingLevel.ForwardAndCache,
'x_cp2k_section_atomic_kind': CachingLevel.ForwardAndCache,
'x_cp2k_section_kind_basis_set': CachingLevel.ForwardAndCache,
}
#=======================================================================
......@@ -203,6 +207,51 @@ class CommonMatcher(object):
],
otherMetaInfo=["self_interaction_correction_method"],
),
SM( " DFT\+U\|",
adHoc=self.adHoc_dft_plus_u(),
),
SM( " QS\|",
forwardMatch=True,
subMatchers=[
SM( " QS\| Method:\s+{}".format(self.regex_word)),
SM( " QS\| Density plane wave grid type\s+{}".format(self.regex_eol)),
SM( " QS\| Number of grid levels:\s+{}".format(self.regex_i)),
SM( " QS\| Density cutoff \[a\.u\.\]:\s+{}".format(self.regex_f)),
SM( " QS\| Multi grid cutoff \[a\.u\.\]: 1\) grid level\s+{}".format(self.regex_f)),
SM( " QS\| 2\) grid level\s+{}".format(self.regex_f)),
SM( " QS\| 3\) grid level\s+{}".format(self.regex_f)),
SM( " QS\| 4\) grid level\s+{}".format(self.regex_f)),
SM( " QS\| Grid level progression factor:\s+{}".format(self.regex_f)),
SM( " QS\| Relative density cutoff \[a\.u\.\]:".format(self.regex_f)),
SM( " QS\| Consistent realspace mapping and integration"),
SM( " QS\| Interaction thresholds: eps_pgf_orb:\s+{}".format(self.regex_f)),
SM( " QS\| eps_filter_matrix:\s+{}".format(self.regex_f)),
SM( " QS\| eps_core_charge:\s+{}".format(self.regex_f)),
SM( " QS\| eps_rho_gspace:\s+{}".format(self.regex_f)),
SM( " QS\| eps_rho_rspace:\s+{}".format(self.regex_f)),
SM( " QS\| eps_gvg_rspace:\s+{}".format(self.regex_f)),
SM( " QS\| eps_ppl:\s+{}".format(self.regex_f)),
SM( " QS\| eps_ppnl:\s+{}".format(self.regex_f)),
],
),
SM( " ATOMIC KIND INFORMATION",
sections=["x_cp2k_section_atomic_kinds", "section_method_basis_set"],
subMatchers=[
SM( "\s+(?P<x_cp2k_kind_number>{0})\. Atomic kind: (?P<x_cp2k_kind_element_symbol>{1})\s+Number of atoms:\s+(?P<x_cp2k_kind_number_of_atoms>{1})".format(self.regex_i, self.regex_word),
repeats=True,
sections=["x_cp2k_section_atomic_kind", "x_cp2k_section_kind_basis_set"],
subMatchers=[
SM( " Orbital Basis Set\s+(?P<x_cp2k_kind_basis_set_name>{})".format(self.regex_word)),
SM( " Number of orbital shell sets:\s+(?P<x_cp2k_basis_set_number_of_orbital_shell_sets>{})".format(self.regex_i)),
SM( " Number of orbital shells:\s+(?P<x_cp2k_basis_set_number_of_orbital_shells>{})".format(self.regex_i)),
SM( " Number of primitive Cartesian functions:\s+(?P<x_cp2k_basis_set_number_of_primitive_cartesian_functions>{})".format(self.regex_i)),
SM( " Number of Cartesian basis functions:\s+(?P<x_cp2k_basis_set_number_of_cartesian_basis_functions>{})".format(self.regex_i)),
SM( " Number of spherical basis functions:\s+(?P<x_cp2k_basis_set_number_of_spherical_basis_functions>{})".format(self.regex_i)),
SM( " Norm type:\s+(?P<x_cp2k_basis_set_norm_type>{})".format(self.regex_i)),
]
)
]
),
SM( " Total number of",
forwardMatch=True,
sections=["x_cp2k_section_total_numbers"],
......@@ -245,7 +294,13 @@ class CommonMatcher(object):
SM( " max_diis:\s+{}".format(self.regex_i)),
SM( " eps_scf:\s+(?P<scf_threshold_energy_change>{})".format(self.regex_f)),
]
)
),
SM( " MP2\|",
adHoc=self.adHoc_mp2()
),
SM( " RI-RPA\|",
adHoc=self.adHoc_rpa()
),
]
)
......@@ -285,7 +340,32 @@ class CommonMatcher(object):
def onClose_x_cp2k_section_quickstep_settings(self, backend, gIndex, section):
backend.addValue("program_basis_set_type", "gaussian")
# backend.addValue("electronic_structure_method", "DFT")
backend.addValue("electronic_structure_method", self.test_electronic_structure_method)
def onClose_section_method_basis_set(self, backend, gIndex, section):
backend.addValue("method_basis_set_kind", "wavefunction")
backend.addValue("number_of_basis_sets_atom_centered", len(self.basis_to_kind_mapping))
backend.addArrayValues("mapping_section_method_basis_set_atom_centered", np.array(self.basis_to_kind_mapping))
def onClose_x_cp2k_section_atomic_kind(self, backend, gIndex, section):
kindID = backend.openSection("section_method_atom_kind")
basisID = backend.openSection("section_basis_set_atom_centered")
element_symbol = section.get_latest_value("x_cp2k_kind_element_symbol")
kind_number = section.get_latest_value("x_cp2k_kind_number")
basis_set_name = section.get_latest_value(["x_cp2k_section_kind_basis_set", "x_cp2k_kind_basis_set_name"])
atom_number = self.get_atomic_number(element_symbol)
kind_label = element_symbol + str(kind_number)
backend.addValue("method_atom_kind_atom_number", atom_number)
backend.addValue("method_atom_kind_label", kind_label)
backend.addValue("basis_set_atom_number", atom_number)
backend.addValue("basis_set_atom_centered_short_name", basis_set_name)
# Add the reference based mapping between basis and atomic kind
self.basis_to_kind_mapping.append([basisID, kindID])
backend.closeSection("section_basis_set_atom_centered", basisID)
backend.closeSection("section_method_atom_kind", kindID)
def onClose_x_cp2k_section_programinformation(self, backend, gIndex, section):
input_file = section.get_latest_value("x_cp2k_input_filename")
......@@ -401,12 +481,12 @@ class CommonMatcher(object):
"""
def wrapper(parser):
parser.fIn.readline()
eigenvalues = np.array([float(x) for x in parser.fIn.readline().split()][::-1])
eigenvalues = np.array([float(x) for x in parser.fIn.readline().split()])
parser.fIn.readline()
row1 = [float(x) for x in parser.fIn.readline().split()]
row2 = [float(x) for x in parser.fIn.readline().split()]
row3 = [float(x) for x in parser.fIn.readline().split()]
eigenvectors = np.fliplr(np.array([row1, row2, row3]))
eigenvectors = np.array([row1, row2, row3])
parser.backend.addArrayValues("x_cp2k_stress_tensor_eigenvalues", eigenvalues, unit="GPa")
parser.backend.addArrayValues("x_cp2k_stress_tensor_eigenvectors", eigenvectors)
return wrapper
......@@ -432,7 +512,7 @@ class CommonMatcher(object):
def wrapper(parser):
# Define the regex that extracts the information
regex_string = r"\s+\d+\s+\d+\s+(\w+)\s+\d+\s+({0})\s+({0})\s+({0})".format(self.regex_f)
regex_string = r"\s+\d+\s+(\d+)\s+(\w+)\s+\d+\s+({0})\s+({0})\s+({0})".format(self.regex_f)
regex_compiled = re.compile(regex_string)
match = True
......@@ -450,9 +530,9 @@ class CommonMatcher(object):
if result:
match = True
label = result.groups()[0]
label = result.groups()[1] + result.groups()[0]
labels.append(label)
coordinate = [float(x) for x in result.groups()[1:]]
coordinate = [float(x) for x in result.groups()[2:]]
coordinates.append(coordinate)
else:
match = False
......@@ -487,12 +567,28 @@ class CommonMatcher(object):
return wrapper
def adHoc_dft_plus_u(self):
def wrapper(parser):
self.test_electronic_structure_method = "DFT+U"
return wrapper
def adHoc_mp2(self):
def wrapper(parser):
self.test_electronic_structure_method = "MP2"
return wrapper
def adHoc_rpa(self):
def wrapper(parser):
self.test_electronic_structure_method = "RPA"
return wrapper
def debug(self):
def wrapper(parser):
print "FOUND"
print("FOUND")
return wrapper
#===========================================================================
# MISC functions
def getOnCloseTriggers(self):
"""
Returns:
......@@ -503,3 +599,42 @@ class CommonMatcher(object):
for attr, callback in extractOnCloseTriggers(self).items():
onClose[attr] = [callback]
return onClose
def get_atomic_number(self, symbol):
""" Returns the atomic number when given the atomic symbol.
Args:
symbol: atomic symbol as string
Returns:
The atomic number (number of protons) for the given symbol.
"""
chemical_symbols = [
'X', 'H', 'He', 'Li', 'Be',
'B', 'C', 'N', 'O', 'F',
'Ne', 'Na', 'Mg', 'Al', 'Si',
'P', 'S', 'Cl', 'Ar', 'K',
'Ca', 'Sc', 'Ti', 'V', 'Cr',
'Mn', 'Fe', 'Co', 'Ni', 'Cu',
'Zn', 'Ga', 'Ge', 'As', 'Se',
'Br', 'Kr', 'Rb', 'Sr', 'Y',
'Zr', 'Nb', 'Mo', 'Tc', 'Ru',
'Rh', 'Pd', 'Ag', 'Cd', 'In',
'Sn', 'Sb', 'Te', 'I', 'Xe',
'Cs', 'Ba', 'La', 'Ce', 'Pr',
'Nd', 'Pm', 'Sm', 'Eu', 'Gd',
'Tb', 'Dy', 'Ho', 'Er', 'Tm',
'Yb', 'Lu', 'Hf', 'Ta', 'W',
'Re', 'Os', 'Ir', 'Pt', 'Au',
'Hg', 'Tl', 'Pb', 'Bi', 'Po',
'At', 'Rn', 'Fr', 'Ra', 'Ac',
'Th', 'Pa', 'U', 'Np', 'Pu',
'Am', 'Cm', 'Bk', 'Cf', 'Es',
'Fm', 'Md', 'No', 'Lr'
]
atomic_numbers = {}
for Z, name in enumerate(chemical_symbols):
atomic_numbers[name] = Z
return atomic_numbers[symbol]
parser/parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py
View file @ fbbd0f41
......@@ -64,7 +64,7 @@ class CP2KInputParser(BasicParser):
self.cache_service.add("vel_add_last")
self.cache_service.add("each_geo_opt")
self.cache_service.add("traj_add_last")
self.cache_service.add("electronic_structure_method")
# self.cache_service.add("electronic_structure_method")
def parse(self):
......@@ -219,6 +219,23 @@ class CP2KInputParser(BasicParser):
#=======================================================================
# See if some more exotic calculation is requested (e.g. MP2, DFT+U, GW, RPA)
# Search for a WF_CORRELATION section
# correlation = self.input_tree.get_section("FORCE_EVAL/DFT/XC/WF_CORRELATION")
# method = "DFT"
# if correlation.accessed:
# method = correlation.get_keyword_value_raw("METHOD")
# if method != "NONE":
# # Can't really decide which method used (MP2, RPA, GW)
# method = None
# # Search for DFT+U settings
# kinds = self.input_tree.get_section_list("FORCE_EVAL/SUBSYS/KIND")
# for kind in kinds:
# dft_u = kind.get_subsection("DFT_PLUS_U")
# if dft_u.accessed:
# method = "DFT+U"
# self.cache_service["electronic_structure_method"] = method
#=======================================================================
# Stress tensor calculation method
......
test/unittests/cp2k_2.6.2/electronic_structure_method/dft_plus_u/H2O-rks-diag-pos-1.xyz 0 → 100644
View file @ fbbd0f41
3
i = 1, E = -17.1638827717
O 0.0000004141 0.0000001855 -0.1099295744
H 0.0000000178 -0.7406066558 0.4944715801
H 0.0000000190 0.7406068464 0.4944717369
3
i = 2, E = -17.1638839665
O 0.0000000169 0.0000001909 -0.1091323465
H 0.0000000562 -0.7415786058 0.4930021571
H 0.0000000591 0.7415788439 0.4930023132
test/unittests/cp2k_2.6.2/electronic_structure_method/dft_plus_u/H2O-rks-diag.inp 0 → 100644
View file @ fbbd0f41
&GLOBAL
PROJECT H2O-rks-diag
PRINT_LEVEL low
RUN_TYPE GEO_OPT
&END GLOBAL
&MOTION
&GEO_OPT
OPTIMIZER BFGS
MAX_ITER 2
&END GEO_OPT
&END MOTION
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME ../../data/GTH_BASIS_SETS
POTENTIAL_FILE_NAME ../../data/GTH_POTENTIALS
PLUS_U_METHOD mulliken_charges
&MGRID
CUTOFF 200
&END MGRID
&PRINT
&DFT_CONTROL_PARAMETERS
&END DFT_CONTROL_PARAMETERS
&END PRINT
&QS
EPS_DEFAULT 1.0E-8
MAP_CONSISTENT
&END QS
&SCF
EPS_SCF 1.0E-5
MAX_SCF 30
&OT OFF
MINIMIZER cg
&END OT
&OUTER_SCF OFF
EPS_SCF 1.0E-5
MAX_SCF 10
&END OUTER_SCF
&PRINT
&RESTART
&EACH
MD 1
QS_SCF 30
&END
ADD_LAST NUMERIC
FILENAME =RESTART-rks-diag
BACKUP_COPIES 0
&END RESTART
&END PRINT
SCF_GUESS atomic
&END SCF
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC 4.0 4.0 4.0
&END CELL
&COORD
O 0.000 0.000 -0.111
H 0.000 -0.744 0.495
H 0.000 0.744 0.495
&END COORD
&KIND H
BASIS_SET DZVP-GTH
POTENTIAL GTH-PBE-q1
&END KIND
&KIND O
BASIS_SET DZVP-GTH
POTENTIAL GTH-PBE-q6
&DFT_PLUS_U
L 1
U_MINUS_J [eV] 2.0
&END DFT_PLUS_U
&END KIND
&PRINT
&KINDS
&END KINDS
&END PRINT
&END SUBSYS
&END FORCE_EVAL
test/unittests/cp2k_2.6.2/electronic_structure_method/mp2/H2O-01.inp 0 → 100644
View file @ fbbd0f41
&GLOBAL
PROJECT H2O-01
PRINT_LEVEL MEDIUM
RUN_TYPE ENERGY
&END GLOBAL
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME ../../data/EMSL_BASIS_SETS
POTENTIAL_FILE_NAME ../../data/POTENTIAL
&MGRID
CUTOFF 300
REL_CUTOFF 40
&END MGRID
&POISSON
PERIODIC NONE
POISSON_SOLVER MT
&END POISSON
&QS
METHOD GAPW
EPS_DEFAULT 1.0E-12
&END QS
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-5
MAX_SCF 1000
ADDED_MOS 1000 1000
&END SCF
&XC
&XC_FUNCTIONAL NONE
&END XC_FUNCTIONAL
&HF
FRACTION 1.0000000
&SCREENING
EPS_SCHWARZ 1.0E-7
&END SCREENING
&END HF
&WF_CORRELATION
METHOD DIRECT_CANONICAL
MEMORY 100.
&END
&END XC
! UKS
&END DFT
&SUBSYS
&CELL
ABC 7.0 7.0 7.0
PERIODIC NONE
&END CELL
&COORD
O 0.000000 0.000000 -0.111000
H 0.000000 -0.744000 0.495000
H 0.000000 0.744000 0.495000
&END COORD
&KIND H
BASIS_SET aug-cc-pVDZ
POTENTIAL ALL
&END KIND
&KIND O
BASIS_SET aug-cc-pVDZ
POTENTIAL ALL
&END KIND
&TOPOLOGY
&CENTER_COORDINATES
&END
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL
test/unittests/cp2k_2.6.2/electronic_structure_method/rpa/H2O_gas.xyz 0 → 100644
View file @ fbbd0f41
3
O 0.000000 0.000000 -0.111000
H 0.000000 -0.744000 0.495000
H 0.000000 0.744000 0.495000
test/unittests/cp2k_2.6.2/electronic_structure_method/rpa/RI_RPA_H2O.inp 0 → 100644
View file @ fbbd0f41
&GLOBAL
PROJECT RI_RPA_H2O
PRINT_LEVEL MEDIUM
RUN_TYPE ENERGY
&TIMINGS
THRESHOLD 0.01
&END
&END GLOBAL
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME ../../data/HFX_BASIS
POTENTIAL_FILE_NAME ../../data/GTH_POTENTIALS
&MGRID
CUTOFF 100
REL_CUTOFF 20
&END MGRID
&POISSON
PERIODIC NONE
POISSON_SOLVER WAVELET
&END POISSON
&QS
METHOD GPW
EPS_DEFAULT 1.0E-15
EPS_PGF_ORB 1.0E-30
&END QS
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-7
MAX_SCF 100
&PRINT
&RESTART OFF
&END
&END
&END SCF
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&WF_CORRELATION
METHOD RI_RPA_GPW
&WFC_GPW
CUTOFF 100
REL_CUTOFF 20
&END
&RI_RPA
RPA_NUM_QUAD_POINTS 40
&HF
FRACTION 1.0000000
&SCREENING
EPS_SCHWARZ 1.0E-8
SCREEN_ON_INITIAL_P FALSE
&END SCREENING
&END HF
&END RI_RPA
MEMORY 200.
NUMBER_PROC 1
&END
&END XC
&END DFT
&SUBSYS
&CELL
ABC [angstrom] 8.000 8.000 8.000
PERIODIC NONE
&END CELL
&KIND H
BASIS_SET DZVP-GTH
RI_AUX_BASIS_SET RI_DZVP-GTH
POTENTIAL GTH-PBE-q1
&END KIND
&KIND O
BASIS_SET DZVP-GTH
RI_AUX_BASIS_SET RI_DZVP-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&TOPOLOGY
COORD_FILE_NAME H2O_gas.xyz
COORD_FILE_FORMAT xyz
&CENTER_COORDINATES
&END
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL
test/unittests/cp2k_2.6.2/energy_force/Si_bulk8-nonbonded_nl_p1-1.out 0 → 100644
View file @ fbbd0f41
NONBONDED NEIGHBOR LISTS IN angstrom (PROCESS 1)
Atom-A X Y Z Atom-B X Y Z Cell(i,j,k) Distance ONFO VDW-scale EI-scale
7 1.357674 -1.357674 -1.357674 1 0.000000 0.000000 0.000000 0 0 0 2.3516
5 -1.357674 1.357674 -1.357674 1 0.000000 0.000000 0.000000 0 0 0 2.3516
8 -1.357674 -1.357674 1.357674 1 0.000000 0.000000 0.000000 0 0 0 2.3516
6 1.357674 1.357674 1.357674 1 0.000000 0.000000 0.000000 0 0 0 2.3516
6 1.357674 1.357674 1.357674 2 0.000000 2.715349 2.715349 0 0 0 2.3516
6 1.357674 1.357674 1.357674 3 2.715349 2.715349 0.000000 0 0 0 2.3516
6 1.357674 1.357674 1.357674 4 2.715349 0.000000 2.715349 0 0 0 2.3516
7 1.357674 -1.357674 -1.357674 3 2.715349 2.715349 0.000000 0 -1 0 2.3516
5 -1.357674 1.357674 -1.357674 3 2.715349 2.715349 0.000000 -1 0 0 2.3516
8 -1.357674 -1.357674 1.357674 4 2.715349 0.000000 2.715349 -1 0 0 2.3516
2 0.000000 2.715349 2.715349 8 -1.357674 -1.357674 1.357674 0 1 0 2.3516
3 2.715349 2.715349 0.000000 8 -1.357674 -1.357674 1.357674 1 1 0 2.3516
4 2.715349 0.000000 2.715349 7 1.357674 -1.357674 -1.357674 0 0 1 2.3516
2 0.000000 2.715349 2.715349 5 -1.357674 1.357674 -1.357674 0 0 1 2.3516
4 2.715349 0.000000 2.715349 5 -1.357674 1.357674 -1.357674 1 0 1 2.3516
2 0.000000 2.715349 2.715349 7 1.357674 -1.357674 -1.357674 0 1 1 2.3516
Total number of neighbor interactions for process 1: 16