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Make charge and spin properties of a Geometry #43

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merged 5 commits into from
Nov 24, 2024
Merged

Make charge and spin properties of a Geometry #43

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89844cc
Add charge and spin for Geometry
matterhorn103 Nov 22, 2024
039c872
Delegate charge and spin to Geometry
matterhorn103 Nov 23, 2024
be4a1bf
Don't override chrg and uhf explicitly set in list of commands
matterhorn103 Nov 23, 2024
7e7bf41
Adjust plugin scripts to create Geometry from CJSON and not pass char…
matterhorn103 Nov 23, 2024
0d9cc2b
Fix Geometry creation from CJSON
matterhorn103 Nov 23, 2024
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4 changes: 1 addition & 3 deletions conformers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -133,7 +133,7 @@
# Read input from Avogadro
avo_input = json.loads(sys.stdin.read())
# Extract the coords
geom = easyxtb.Geometry.from_xyz(avo_input["xyz"].split("\n"))
geom = easyxtb.Geometry.from_cjson(avo_input["cjson"])

# If provided crest path different to that stored, use it and save it
if Path(avo_input["crest_bin"]) != easyxtb.CREST_BIN:
Expand All @@ -157,8 +157,6 @@
# Run calculation; returns set of conformers as well as Calculation object
conformers, calc = easyxtb.calc.conformers(
geom,
charge=avo_input["charge"],
multiplicity=avo_input["spin"],
solvation=solvation,
method=2,
ewin=ewin_kcal,
Expand Down
4 changes: 1 addition & 3 deletions deprotonate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,13 +39,11 @@
# Read input from Avogadro
avo_input = json.loads(sys.stdin.read())
# Extract the coords
geom = easyxtb.Geometry.from_xyz(avo_input["xyz"].split("\n"))
geom = easyxtb.Geometry.from_cjson(avo_input["cjson"])

# Run calculation; returns set of tautomers as well as Calculation object
tautomers, calc = easyxtb.calc.deprotonate(
geom,
charge=avo_input["charge"],
multiplicity=avo_input["spin"],
solvation=easyxtb.config["solvent"],
method=2,
return_calc=True,
Expand Down
62 changes: 21 additions & 41 deletions easyxtb/src/easyxtb/calc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -172,6 +172,10 @@ def run(self):
*self.runtype_args,
"--",
]
if "chrg" not in self.options and self.input_geometry.charge != 0:
command.extend(["--chrg", str(self.input_geometry.charge)])
if "uhf" not in self.options and self.input_geometry.multiplicity != 1:
command.extend(["--uhf", str(self.input_geometry.multiplicity - 1)])
for flag, value in self.options.items():
# Add appropriate number of minuses to flags
if len(flag) == 1:
Expand Down Expand Up @@ -216,7 +220,11 @@ def process_xtb(self):
# If there's an output geometry, read it
if self.output_file.with_name("xtbopt.xyz").exists():
logger.debug(f"Output geometry found at {self.output_file.with_name('xtbopt.xyz')}")
self.output_geometry = Geometry.from_file(self.output_file.with_name("xtbopt.xyz"))
self.output_geometry = Geometry.from_file(
self.output_file.with_name("xtbopt.xyz"),
charge=self.input_geometry.charge,
multiplicity=self.input_geometry.multiplicity,
)
logger.debug("Read output geometry")
else:
# Assume geom was the same at end of calc as at beginning
Expand Down Expand Up @@ -248,7 +256,11 @@ def process_crest(self):
# Conformer search
logger.debug("A conformer search was requested, so checking for files")
# Get energy and geom of lowest conformer
best = Geometry.from_file(self.output_file.with_name("crest_best.xyz"))
best = Geometry.from_file(
self.output_file.with_name("crest_best.xyz"),
charge=self.input_geometry.charge,
multiplicity=self.input_geometry.multiplicity,
)
logger.debug(f"Geometry of lowest energy conformer read from {self.output_file.with_name('crest_best.xyz')}")
self.output_geometry = best
self.energy = float(best._comment)
Expand All @@ -257,6 +269,8 @@ def process_crest(self):
conformer_geoms = Geometry.from_file(
self.output_file.with_name("crest_conformers.xyz"),
multi=True,
charge=self.input_geometry.charge,
multiplicity=self.input_geometry.multiplicity,
)
logger.debug(f"Geometries of conformers read from {self.output_file.with_name('crest_conformers.xyz')}")
self.conformers = [
Expand All @@ -273,6 +287,8 @@ def process_crest(self):
tautomer_geoms = Geometry.from_file(
self.output_file.with_name("protonated.xyz"),
multi=True,
charge=self.input_geometry.charge + 1,
multiplicity=self.input_geometry.multiplicity,
)
logger.debug(f"Geometries of tautomers read from {self.output_file.with_name('protonated.xyz')}")
self.tautomers = [
Expand All @@ -294,6 +310,8 @@ def process_crest(self):
tautomer_geoms = Geometry.from_file(
self.output_file.with_name("deprotonated.xyz"),
multi=True,
charge=self.input_geometry.charge - 1,
multiplicity=self.input_geometry.multiplicity,
)
logger.debug(f"Geometries of tautomers read from {self.output_file.with_name('deprotonated.xyz')}")
self.tautomers = [
Expand All @@ -314,8 +332,6 @@ def process_crest(self):

def energy(
input_geometry: Geometry,
charge: int = 0,
multiplicity: int = 1,
solvation: str | None = None,
method: int = 2,
n_proc: int | None = None,
Expand All @@ -326,8 +342,6 @@ def energy(
calc = Calculation(
input_geometry=input_geometry,
options={
"chrg": charge,
"uhf": multiplicity - 1,
"gfn": method,
"alpb": solvation,
"p": n_proc if n_proc else config["n_proc"],
Expand All @@ -342,8 +356,6 @@ def energy(

def optimize(
input_geometry: Geometry,
charge: int = 0,
multiplicity: int = 1,
solvation: str | None = None,
method: int = 2,
level: str = "normal",
Expand All @@ -358,8 +370,6 @@ def optimize(
runtype="opt",
runtype_args=[level],
options={
"chrg": charge,
"uhf": multiplicity - 1,
"gfn": method,
"alpb": solvation,
"p": n_proc if n_proc else config["n_proc"],
Expand All @@ -377,8 +387,6 @@ def optimize(

def frequencies(
input_geometry: Geometry,
charge: int = 0,
multiplicity: int = 1,
solvation: str | None = None,
method: int = 2,
n_proc: int | None = None,
Expand All @@ -390,8 +398,6 @@ def frequencies(
input_geometry=input_geometry,
runtype="hess",
options={
"chrg": charge,
"uhf": multiplicity - 1,
"gfn": method,
"alpb": solvation,
"p": n_proc if n_proc else config["n_proc"],
Expand All @@ -406,8 +412,6 @@ def frequencies(

def opt_freq(
input_geometry: Geometry,
charge: int = 0,
multiplicity: int = 1,
solvation: str | None = None,
method: int = 2,
level: str = "normal",
Expand All @@ -426,8 +430,6 @@ def opt_freq(
runtype="ohess",
runtype_args=[level],
options={
"chrg": charge,
"uhf": multiplicity - 1,
"gfn": method,
"alpb": solvation,
"p": n_proc if n_proc else config["n_proc"],
Expand All @@ -441,12 +443,10 @@ def opt_freq(
distorted_geom_file = calc.output_file.with_name("xtbhess.xyz")
while distorted_geom_file.exists():
calc = Calculation(
input_geometry=Geometry.from_file(distorted_geom_file),
input_geometry=Geometry.from_file(distorted_geom_file, charge=input_geometry.charge, multiplicity=input_geometry.multiplicity),
runtype="ohess",
runtype_args=[level],
options={
"chrg": charge,
"uhf": multiplicity - 1,
"gfn": method,
"alpb": solvation,
"p": n_proc if n_proc else config["n_proc"],
Expand All @@ -462,8 +462,6 @@ def opt_freq(

def orbitals(
input_geometry: Geometry,
charge: int = 0,
multiplicity: int = 1,
solvation: str | None = None,
method: int = 2,
n_proc: int | None = None,
Expand All @@ -479,8 +477,6 @@ def orbitals(
input_geometry=input_geometry,
options={
"molden": True,
"chrg": charge,
"uhf": multiplicity - 1,
"gfn": method,
"alpb": solvation,
"p": n_proc if n_proc else config["n_proc"],
Expand All @@ -495,8 +491,6 @@ def orbitals(

def conformers(
input_geometry: Geometry,
charge: int = 0,
multiplicity: int = 1,
solvation: str | None = None,
method: int = 2,
ewin: int | float = 6,
Expand All @@ -519,8 +513,6 @@ def conformers(
options={
"xnam": XTB_BIN,
method_flag: True,
"chrg": charge,
"uhf": multiplicity - 1,
"alpb": solvation,
"ewin": ewin,
"T": n_proc if n_proc else config["n_proc"],
Expand All @@ -537,8 +529,6 @@ def conformers(

def protonate(
input_geometry: Geometry,
charge: int = 0,
multiplicity: int = 1,
solvation: str | None = None,
method: int = 2,
n_proc: int | None = None,
Expand All @@ -547,8 +537,6 @@ def protonate(
"""Screen possible protonation sites and return set of tautomer Geometries and energies.

The returned tautomers are ordered from lowest to highest energy.

Note that `charge` should be the charge on the molecule before protonation.
"""
method_flag = f"gfn{method}"
calc = Calculation(
Expand All @@ -558,8 +546,6 @@ def protonate(
options={
"xnam": XTB_BIN,
method_flag: True,
"chrg": charge,
"uhf": multiplicity - 1,
"alpb": solvation,
"T": n_proc if n_proc else config["n_proc"],
},
Expand All @@ -573,8 +559,6 @@ def protonate(

def deprotonate(
input_geometry: Geometry,
charge: int = 0,
multiplicity: int = 1,
solvation: str | None = None,
method: int = 2,
n_proc: int | None = None,
Expand All @@ -583,8 +567,6 @@ def deprotonate(
"""Screen possible deprotonation sites and return set of tautomer Geometries and energies.

The returned tautomers are ordered from lowest to highest energy.

Note that `charge` should be the charge on the molecule before deprotonation.
"""
method_flag = f"gfn{method}"
calc = Calculation(
Expand All @@ -594,8 +576,6 @@ def deprotonate(
options={
"xnam": XTB_BIN,
method_flag: True,
"chrg": charge,
"uhf": multiplicity - 1,
"alpb": solvation,
"T": n_proc if n_proc else config["n_proc"],
},
Expand Down
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