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Code style standardization
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@lint-action
lint-action committed Jun 12, 2023
1 parent 95b8b77 commit 6eaed47
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Showing 4 changed files with 89 additions and 81 deletions.
37 changes: 20 additions & 17 deletions ccinput/calculation.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -447,25 +447,28 @@ def to_xtb(self):
t = "dihedral"

return f"{t}: {ids_str}\n"

def to_nwchem(self):
ids_str = " ".join([str(i) for i in self.ids])
converstion_factor = 1.00
type = len(self.ids)
if type == 1:
t = "fix atom"
elif type == 2:
t = "spring bond"
converstion_factor = 1.8897259886
elif type == 3:
raise UnimplementedError("Constraints on angles are not implemented in nwchem")
elif type == 4:
t = "spring dihedral"
ids_str = " ".join([str(i) for i in self.ids])
converstion_factor = 1.00
type = len(self.ids)
if type == 1:
t = "fix atom"
elif type == 2:
t = "spring bond"
converstion_factor = 1.8897259886
elif type == 3:
raise UnimplementedError(
"Constraints on angles are not implemented in nwchem"
)
elif type == 4:
t = "spring dihedral"

if self.scan:
pass # TO DO
else:
return f"{t} {ids_str} 200.0 {self.start_d*converstion_factor :.8f} \n"

if self.scan:
pass # TO DO
else:
return f"{t} {ids_str} 200.0 {self.start_d*converstion_factor :.8f} \n"

def parse_freeze_constraints(arr, xyz_str, software=""):
if len(arr) == 0:
Expand Down
82 changes: 45 additions & 37 deletions ccinput/packages/nwchem.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,11 +76,15 @@ def __init__(self, calc):
self.has_scan = False
self.appendix = []
self.command_line = ""
if self.calc.parameters.theory_level == 'hf' or self.calc.parameters.method == 'uhf' or self.calc.parameters.method == 'rhf' : # Name of the block for HF is scf
self.calc.parameters.theory_level = 'scf'
self.method_block=f"{self.calc.parameters.theory_level}"
self.calculation_block=""
self.additional_block=""
if (
self.calc.parameters.theory_level == "hf"
or self.calc.parameters.method == "uhf"
or self.calc.parameters.method == "rhf"
): # Name of the block for HF is scf
self.calc.parameters.theory_level = "scf"
self.method_block = f"{self.calc.parameters.theory_level}"
self.calculation_block = ""
self.additional_block = ""
self.method_block = f"{self.calc.parameters.theory_level}"
self.calculation_block = ""
self.additional_block = ""
Expand Down Expand Up @@ -108,27 +112,27 @@ def clean(self, s):
)
return "".join([c for c in s if c in WHITELIST])

def separate_lines(self,text):
lines = text.split(';')
def separate_lines(self, text):
lines = text.split(";")
clean = []
for line in lines :
if line != '':
for line in lines:
if line != "":
clean.append(self.clean(line.lower()).strip())
else :
else:
pass
return "\n".join(clean)

def handle_tasks(self):
for word in self.KEYWORDS[self.calc.type]:
self.tasks += f'task {self.calc.parameters.theory_level} {word} \n'
#handle levels of theory
if(self.calc.parameters.theory_level == 'scf') :
self.tasks += f"task {self.calc.parameters.theory_level} {word} \n"
# handle levels of theory
if self.calc.parameters.theory_level == "scf":
scf_block = "\n"
if self.calc.parameters.method != 'hf':
if self.calc.parameters.method != "hf":
scf_block += f"{self.calc.parameters.method} \n"
scf_block += f"{SOFTWARE_MULTIPLICITY['nwchem'][self.calc.multiplicity]} \n"
self.method_block+= scf_block
if(self.calc.parameters.theory_level == 'dft') :
self.method_block += scf_block
if self.calc.parameters.theory_level == "dft":
dft_block = f"""
xc {self.calc.parameters.method}
mult {self.calc.multiplicity}
Expand All @@ -147,33 +151,38 @@ def handle_basis_sets(self):
self.basis_set = f"* library {basis_set}"

def handle_specifications(self):
if self.calc.parameters.specifications != '':
temp = "\n" # Here we will store frequency related specifiations in case of FREQOPT calculations
if self.calc.parameters.specifications != "":
temp = "\n" # Here we will store frequency related specifiations in case of FREQOPT calculations
s = self.separate_lines(self.calc.parameters.specifications)
for spec in s.split('\n'):
for spec in s.split("\n"):
# format of the specifications is BLOCK_NAME1(command1);BLOCK_NAME2(command2);...
matched = re.search(r".*\((.*)\)",spec)
if matched == None :
matched = re.search(r".*\((.*)\)", spec)
if matched == None:
self.additional_block += f"{spec} \n"
else :
else:
command = matched.group(1)
block_name = spec[:matched.span(1)[0]-1]
if block_name == 'scf' or block_name == 'dft' or block_name == 'hf' :
self.method_block += f"{command} \n"
elif (block_name == 'opt' or block_name == 'ts') and (self.calc.type == CalcType.CONSTR_OPT or self.calc.type == CalcType.OPT or self.calc.type == CalcType.TS or self.calc.type == CalcType.OPTFREQ) :
if self.calculation_block == '':
block_name = spec[: matched.span(1)[0] - 1]
if block_name == "scf" or block_name == "dft" or block_name == "hf":
self.method_block += f"{command} \n"
elif (block_name == "opt" or block_name == "ts") and (
self.calc.type == CalcType.CONSTR_OPT
or self.calc.type == CalcType.OPT
or self.calc.type == CalcType.TS
or self.calc.type == CalcType.OPTFREQ
):
if self.calculation_block == "":
self.calculation_block += f"\n driver \n"
self.calculation_block += f"{command} \n"
elif block_name == 'nmr' and self.calc.type == CalcType.NMR :
elif block_name == "nmr" and self.calc.type == CalcType.NMR:
self.calculation_block += f"{command} \n"
elif block_name == 'freq' and self.calc.type == CalcType.FREQ :
if self.calculation_block == '':
elif block_name == "freq" and self.calc.type == CalcType.FREQ:
if self.calculation_block == "":
self.calculation_block += f"\n freq \n"
self.calculation_block += f"{command} \n"
elif block_name == 'freq' and self.calc.type == CalcType.OPTFREQ :
elif block_name == "freq" and self.calc.type == CalcType.OPTFREQ:
temp += f"{command} \n"
if temp != '\n':
self.additional_block += f'freq {temp} end \n'
if temp != "\n":
self.additional_block += f"freq {temp} end \n"

# Handle contraints
if self.calc.type == CalcType.CONSTR_OPT:
Expand All @@ -184,9 +193,8 @@ def handle_specifications(self):
self.additional_block += constraint.to_nwchem()
self.additional_block += "end \n"

if self.additional_block.strip() != '':
self.additional_block = '\n' + self.additional_block

if self.additional_block.strip() != "":
self.additional_block = "\n" + self.additional_block

def handle_xyz(self):
lines = [i + "\n" for i in clean_xyz(self.calc.xyz).split("\n") if i != ""]
Expand Down
47 changes: 23 additions & 24 deletions ccinput/tests/test_nwchem.py
View file
Original file line number Diff line number Diff line change
@@ -1,9 +1,12 @@
from ccinput.tests.testing_utilities import InputTests
from ccinput.exceptions import InvalidParameter, ImpossibleCalculation, UnimplementedError
from ccinput.exceptions import (
InvalidParameter,
ImpossibleCalculation,
UnimplementedError,
)


class NwchemTests(InputTests):

def test_sp_HF(self):
params = {
"nproc": 8,
Expand Down Expand Up @@ -40,7 +43,7 @@ def test_sp_HF(self):
"""

self.assertTrue(self.is_equivalent(REF, inp.input_file))

def test_sp_DFT(self):
params = {
"nproc": 8,
Expand Down Expand Up @@ -120,21 +123,21 @@ def test_sp_DFT_specifications(self):
self.assertTrue(self.is_equivalent(REF, inp.input_file))

def test_sp_DFT_specifications2(self):
params = {
"nproc": 8,
"mem": "10000MB",
"type": "Single-Point Energy",
"file": "Cl.xyz",
"software": "nwchem",
"method": "M06-2X",
"basis_set": "Def2-SVP",
"charge": "-1",
"specifications": "dft(grid coarse)",
}

inp = self.generate_calculation(**params)

REF = """
params = {
"nproc": 8,
"mem": "10000MB",
"type": "Single-Point Energy",
"file": "Cl.xyz",
"software": "nwchem",
"method": "M06-2X",
"basis_set": "Def2-SVP",
"charge": "-1",
"specifications": "dft(grid coarse)",
}

inp = self.generate_calculation(**params)

REF = """
TITLE "File created by ccinput"
start Cl
memory total 10000 mb
Expand All @@ -157,7 +160,7 @@ def test_sp_DFT_specifications2(self):
task dft energy
"""

self.assertTrue(self.is_equivalent(REF, inp.input_file))
self.assertTrue(self.is_equivalent(REF, inp.input_file))

def test_superfluous_specifications(self):
params = {
Expand Down Expand Up @@ -313,7 +316,7 @@ def test_opt_DFT(self):
"""

self.assertTrue(self.is_equivalent(REF, inp.input_file))

def test_freq_HF(self):
params = {
"nproc": 8,
Expand Down Expand Up @@ -908,7 +911,6 @@ def test_specifications_mixed(self):

self.assertTrue(self.is_equivalent(REF, inp.input_file))


def test_special_char(self):
params = {
"nproc": 8,
Expand Down Expand Up @@ -1251,7 +1253,6 @@ def test_opt_freq2(self):

self.assertTrue(self.is_equivalent(REF, inp.input_file))


def test_opt_freq_spec(self):
params = {
"nproc": 8,
Expand Down Expand Up @@ -1392,7 +1393,6 @@ def test_d3_d3bj_crash(self):
with self.assertRaises(InvalidParameter):
self.generate_calculation(**params)


def test_unavailable_calc_type(self):
params = {
"nproc": 8,
Expand All @@ -1407,4 +1407,3 @@ def test_unavailable_calc_type(self):

with self.assertRaises(ImpossibleCalculation):
self.generate_calculation(**params)

4 changes: 1 addition & 3 deletions ccinput/utilities.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -292,9 +292,7 @@ def get_method(method, software):
pass
else:
if abs_method in SOFTWARE_METHODS[software]:
return (
method[0] + SOFTWARE_METHODS[software][abs_method]
)
return method[0] + SOFTWARE_METHODS[software][abs_method]
# nwchem also supports combination of functionals
if len(method.split()) == 2:
xc_check = is_exchange_correlation_combination(
Expand Down

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