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[pull] main from cyllab:main #43

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Aug 30, 2024
Merged

[pull] main from cyllab:main #43

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f6112fa
Switched ORCA specifications to a more modular approach
RaphaelRobidas Aug 29, 2024
2806dcd
Changed how ORCA specifications work
RaphaelRobidas Aug 29, 2024
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18 changes: 13 additions & 5 deletions ccinput/drivers/pysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@

class PysisDriver:
SUPPORTED_PACKAGES = ["xtb", "orca"]
IGNORED_ORCA_BLOCKS = ["%MaxCore"]
IGNORED_ORCA_BLOCKS = ["MaxCore", "pal"]

SUPPORTED_KEYWORDS = {
CalcType.TS: "tsopt",
Expand Down Expand Up @@ -187,11 +187,19 @@ def handle_main_parameters(self):
).replace("SP ", ""),
)

BLOCK_TEMPLATE = """%{}
{}
end"""

cleaned_blocks = []
for block in orca_inp.blocks:
block_name = block.split("\n")[0].split()[0]
if block_name not in self.IGNORED_ORCA_BLOCKS:
cleaned_blocks.append(block.replace('"', '\\"'))
for block, content in orca_inp.blocks.items():
if block not in self.IGNORED_ORCA_BLOCKS:
cleaned_blocks.append(
BLOCK_TEMPLATE.format(
block,
"\n".join([l.replace('"', '\\"') for l in content]).strip(),
)
)

cleaned_blocks_lines = "\n".join(cleaned_blocks)
if cleaned_blocks_lines.strip() != "":
Expand Down
35 changes: 2 additions & 33 deletions ccinput/packages/gaussian.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
get_npxyz,
check_fragments,
add_fragments_xyz,
parse_specifications,
)
from ccinput.constants import CalcType, ATOMIC_NUMBER, LOWERCASE_ATOMIC_SYMBOLS
from ccinput.exceptions import InvalidParameter, ImpossibleCalculation
Expand Down Expand Up @@ -104,39 +105,7 @@ def add_commands(self, commands):
def handle_specifications(self):
s = self.clean(self.calc.parameters.specifications.lower())

# Could be more sophisticated to catch other incorrect specifications
if s.count("(") != s.count(")"):
raise InvalidParameter("Invalid specifications: parenthesis not matching")

_specifications = ""
remove = False
for c in s:
if c == " " and remove:
continue
_specifications += c
if c == "(":
remove = True
elif c == ")":
remove = False

for spec in _specifications.split(" "):
if spec.strip() == "":
continue
if spec.find("(") != -1:
key, options = spec.split("(")
options = options.replace(")", "")
for option in options.split(","):
if option.strip() != "":
self.add_option(key, option)
elif spec.find("=") != -1:
try:
key, option = spec.split("=")
except ValueError:
raise InvalidParameter(f"Invalid specification: {spec}")
self.add_option(key, option)
else:
self.add_option(spec, "")

parse_specifications(s, self.add_option)
if self.calc.parameters.d3:
self.add_option("EmpiricalDispersion", "GD3")
elif self.calc.parameters.d3bj:
Expand Down
142 changes: 79 additions & 63 deletions ccinput/packages/orca.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
get_abs_basis_set,
clean_xyz,
warn,
parse_specifications,
)
from ccinput.exceptions import (
InvalidParameter,
Expand Down Expand Up @@ -61,15 +62,15 @@ def __init__(self, calc):
self.calc = calc
self.has_scan = False
self.pal = 0
self.blocks = []
self.blocks = {}
self.command_line = ""
self.additional_commands = ""
self.xyz_structure = ""
self.block_lines = ""
self.input_file = ""
self.specifications = {}
self.solvation_radii = {}
self.aux_basis_sets = {}
self.specifications_list = []

if self.calc.type not in self.CALC_TYPES:
raise ImpossibleCalculation(
Expand Down Expand Up @@ -99,26 +100,44 @@ def confirmed_specifications(self):

def clean(self, s):
WHITELIST = set(
"0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ/()=-,. "
"0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ/()=-,. {}_[]"
)
return "".join([c for c in s if c in WHITELIST])

def add_to_block(self, block, lines):
if block in self.blocks:
self.blocks[block] += lines
else:
self.blocks[block] = lines

def add_option(self, key, option):
if option == "":
if key[-2:] == "/c":
self.aux_basis_sets["C"] = get_basis_set(key[:-2], "orca")
elif key[-3:] == "/jk":
self.aux_basis_sets["JK"] = get_basis_set(key[:-3], "orca")
elif key[-2:] == "/j":
self.aux_basis_sets["J"] = get_basis_set(key[:-2], "orca")
elif key not in self.specifications_list:
self.specifications_list.append(key)
else:
self.add_to_block(key, [option.replace("=", " ")])

def handle_specifications(self):
_specifications = (
self.clean(self.calc.parameters.specifications).lower().strip()
)

specifications_list = []
parse_specifications(_specifications, self.add_option, condense=False)

"""
if _specifications != "":
sspecs = _specifications.split()
ind = 0
while ind < len(sspecs):
spec = sspecs[ind]
if spec == "--phirshfeld":
HIRSHFELD_BLOCK = """%output
Print[ P_Hirshfeld] 1
end"""
self.blocks.append(HIRSHFELD_BLOCK)
self.add_to_block("output", ["Print[ P_Hirshfeld] 1"])
elif spec == "--nimages":
nimages = sspecs[ind + 1]
try:
Expand All @@ -127,24 +146,15 @@ def handle_specifications(self):
raise InvalidParameter("Invalid specifications")
self.specifications["nimages"] = nimages
ind += 1
elif spec[-2:] == "/c":
self.aux_basis_sets["C"] = get_basis_set(spec[:-2], "orca")
elif spec[-3:] == "/jk":
self.aux_basis_sets["JK"] = get_basis_set(spec[:-3], "orca")
elif spec[-2:] == "/j":
self.aux_basis_sets["J"] = get_basis_set(spec[:-2], "orca")
elif spec not in specifications_list:
specifications_list.append(spec)


ind += 1
"""

if self.calc.parameters.d3:
specifications_list.append("d3zero")
self.specifications_list.append("d3zero")
elif self.calc.parameters.d3bj:
specifications_list.append("d3bj")

if len(specifications_list) > 0:
self.additional_commands = " ".join(specifications_list)
self.specifications_list.append("d3bj")

def handle_command(self):
if self.calc.type == CalcType.NMR:
Expand All @@ -156,7 +166,7 @@ def handle_command(self):
elif self.calc.type == CalcType.TS:
self.command_line = "OPTTS "
if self.calc.parameters.theory_level != "xtb":
self.blocks.append("%geom\nCalc_Hess true\nend")
self.add_to_block("geom", ["Calc_Hess true"])
elif self.calc.type == CalcType.MO:
self.command_line = "SP "
struct = clean_xyz(self.calc.xyz)
Expand Down Expand Up @@ -184,8 +194,9 @@ def handle_command(self):
else:
raise InvalidParameter("Unimplemented multiplicity")

mo_block = f"""%plots
dim1 45
self.add_to_block(
"plots",
f"""dim1 45
dim2 45
dim3 45
min1 0
Expand All @@ -199,9 +210,10 @@ def handle_command(self):
MO("in-LUMO.cube",{n_LUMO},0);
MO("in-LUMOA.cube",{n_LUMO1},0);
MO("in-LUMOB.cube",{n_LUMO2},0);
end
"""
self.blocks.append(mo_block)
""".split(
"\n"
),
)
elif self.calc.type == CalcType.FREQ:
self.command_line = "FREQ "
elif self.calc.type == CalcType.CONSTR_OPT:
Expand All @@ -220,31 +232,35 @@ def handle_command(self):
freeze.append(constr.to_orca())

if len(scans) > 0:
scan_block = """%geom Scan
scan_block = """Scan
{}
end
end"""
self.blocks.append(scan_block.format("".join(scans).strip()))
"""
self.add_to_block(
"geom", scan_block.format("".join(scans).strip()).split("\n")
)

if len(freeze) > 0:
freeze_block = """%geom Constraints
freeze_block = """Constraints
{}
end
end"""
self.blocks.append(freeze_block.format("".join(freeze).strip()))
"""
self.add_to_block(
"geom", freeze_block.format("".join(freeze).strip()).split("\n")
)
elif self.calc.type == CalcType.SP:
self.command_line = "SP "
elif self.calc.type == CalcType.MEP: #### Second structure to handle
self.command_line = "NEB "
neb_block = """%neb
product "{}.xyz"
nimages {}
end"""
if "nimages" in self.specifications:
nimages = self.specifications["nimages"]
self.add_to_block("neb", [f'product "{self.calc.aux_name}.xyz"'])
if "neb" in self.blocks:
for entry in self.blocks["neb"]:
if entry.find("nimages") != -1:
break
else:
self.add_to_block("neb", ["nimages 8"])
else:
nimages = 8
self.blocks.append(neb_block.format(self.calc.aux_name, nimages))
self.add_to_block("neb", ["nimages 8"])

method = get_method(self.calc.parameters.method, "orca")
if self.calc.parameters.theory_level not in [
Expand Down Expand Up @@ -279,10 +295,6 @@ def handle_custom_basis_sets(self):
if a not in unique_atoms:
unique_atoms.append(a)

BS_TEMPLATE = """%basis
{}
end"""

custom_bs = ""
for el, bs_keyword in self.calc.parameters.custom_basis_sets.items():
if el not in unique_atoms:
Expand Down Expand Up @@ -340,7 +352,7 @@ def handle_custom_basis_sets(self):
custom_bs += "end"

if custom_bs != "":
self.blocks.append(BS_TEMPLATE.format(custom_bs.strip()))
self.add_to_block("basis", custom_bs.split("\n"))

def handle_xyz(self):
lines = [i + "\n" for i in clean_xyz(self.calc.xyz).split("\n") if i != ""]
Expand All @@ -354,12 +366,7 @@ def handle_pal_mem(self):
self.pal = self.calc.nproc
self.mem_per_core = int(self.calc.mem / self.calc.nproc)

pal_mem_block = f"""%MaxCore {self.mem_per_core}
%pal
nprocs {self.pal}
end"""

self.blocks.append(pal_mem_block)
self.add_to_block("pal", [f"nprocs {self.pal}"])

def parse_custom_solvation_radii(self):
for radius in self.calc.parameters.custom_solvation_radii.split(";"):
Expand Down Expand Up @@ -404,8 +411,6 @@ def handle_solvation(self):
radii_set = self.calc.parameters.solvation_radii
custom_radii = self.calc.parameters.custom_solvation_radii

solv_block = ""

if self.calc.parameters.method[:3].lower() == "xtb":
self.command_line += f" ALPB({solvent_keyword})"
elif model == "smd":
Expand All @@ -419,18 +424,15 @@ def handle_solvation(self):
self.solvation_radii[35] = 2.60

radii_specs = self.get_radii_specs()
solv_block = f"""%cpcm
smd true
SMDsolvent "{solvent_keyword}"
{radii_specs}end"""
self.blocks.append(solv_block)

self.add_to_block(
"cpcm", ["smd true", f'SMDsolvent "{solvent_keyword}"', radii_specs]
)
elif model == "cpcm":
self.command_line += f"CPCM({solvent_keyword}) "
radii_specs = self.get_radii_specs()
if radii_specs != "":
solv_block = f"""%cpcm
{radii_specs}end"""
self.blocks.append(solv_block)
self.add_to_block("cpcm", [radii_specs])
if radii_set not in ["", "default", "bondi"]:
raise UnimplementedError(
"As of now, ccinput does not know how to request "
Expand All @@ -443,8 +445,22 @@ def handle_solvation(self):
)

def create_input_file(self):
self.block_lines = "\n".join(self.blocks)
self.block_lines = ""
for name, content in sorted(self.blocks.items(), key=lambda i: i[0]):
self.block_lines += """%{}
{}
end
""".format(
name, "\n".join(content).strip()
)

self.block_lines += f"""%MaxCore {self.mem_per_core}"""

if len(self.specifications_list) > 0:
self.additional_commands = " ".join(self.specifications_list)

cmd = f"{self.command_line} {self.additional_commands}".replace(" ", " ")

raw = self.TEMPLATE.format(
cmd,
self.calc.charge,
Expand Down
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