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Switched ORCA specifications to a more modular approach
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@RaphaelRobidas
RaphaelRobidas committed Aug 29, 2024
1 parent 17c1411 commit f6112fa
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Showing 3 changed files with 180 additions and 166 deletions.
18 changes: 13 additions & 5 deletions ccinput/drivers/pysis.py
View file
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
92 changes: 47 additions & 45 deletions ccinput/packages/orca.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -61,11 +61,10 @@ 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 = {}
Expand Down Expand Up @@ -103,6 +102,12 @@ def clean(self, s):
)
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 handle_specifications(self):
_specifications = (
self.clean(self.calc.parameters.specifications).lower().strip()
Expand All @@ -115,10 +120,7 @@ def handle_specifications(self):
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 Down Expand Up @@ -156,7 +158,7 @@ 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 +186,9 @@ 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 +202,10 @@ 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 +224,33 @@ 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"]
else:
nimages = 8
self.blocks.append(neb_block.format(self.calc.aux_name, nimages))
self.add_to_block(
"neb", [f'product "{self.calc.aux_name}.xyz"', f"nimages {nimages}"]
)

method = get_method(self.calc.parameters.method, "orca")
if self.calc.parameters.theory_level not in [
Expand Down Expand Up @@ -279,10 +285,6 @@ 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 +342,7 @@ 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 +356,7 @@ 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 +401,6 @@ 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 +414,15 @@ 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 @@ -443,7 +435,17 @@ 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}"""

cmd = f"{self.command_line} {self.additional_commands}".replace(" ", " ")
raw = self.TEMPLATE.format(
cmd,
Expand Down
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