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Merge pull request #2 from molssi-seamm/dev
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Improved citation handling
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@seamm
seamm authored Oct 20, 2024
2 parents 6e7a404 + 9239145 commit 12f34e2
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Showing 2 changed files with 76 additions and 73 deletions.
2 changes: 2 additions & 0 deletions HISTORY.rst
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
=======
History
=======
2024.10.20 -- Improved citation handling

2024.10.15 -- Added various convergence metrics to results
* Added maximum force, gradient, etc. to results.
* Improved control over when to calculate the Hessian matrix.
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147 changes: 74 additions & 73 deletions seamm_geometric/seamm_geometric.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@
import math
import os
from pathlib import Path
import pprint
import re
import shutil
import string
Expand Down Expand Up @@ -39,7 +38,7 @@

logger = logging.getLogger(__name__)
job = printing.getPrinter()
printer = printing.getPrinter("goemeTRIC")
printer = printing.getPrinter("geomeTRIC")

# Regexp to remove ansi escape sequences
ansi_escape = re.compile(r"\x1B(?:[@-Z\\-_]|\[[0-?]*[ -/]*[@-~])")
Expand Down Expand Up @@ -96,38 +95,22 @@ def calc_new(self, coords, dirname):
"""
xyz = coords.reshape(-1, 3) * Q_(1.0, "a_0").m_as("angstrom")

energy, gradient = self.step.calculate_gradients(xyz)
energy, gradient = self.step.geometric_calculate_gradients(xyz)

return {"energy": energy, "gradient": gradient.ravel()}


class geomeTRIC_mixin:
"""A mixin class for running a geomeTRIC optimization."""

def read_bibliography(self):
"""Read the bibliography from a file and add to the local bibliography"""
if "geomeTRIC" not in self._bibliography:
try:
data = (
files("seamm_geometric.data").joinpath("references.bib").read_text()
)
tmp = bibtexparser.loads(data).entries_dict
writer = bibtexparser.bwriter.BibTexWriter()
for key, data in tmp.items():
self.logger.info(f" {key}")
self._bibliography[key] = writer._entry_to_bibtex(data)
self.logger.debug("Bibliography\n" + pprint.pformat(self._bibliography))
except Exception:
pass

def calculate_gradients(self, coordinates):
def geometric_calculate_gradients(self, coordinates):
"""Given the new coordinates, calculate the energy and gradients.
Parameters
----------
coordinates : [3, n_atoms] array of coordinates
"""
self.step = self.step + 1
self._step = self._step + 1
fmt = "05d"

# Make the geometric output readable by removing the ANSI escape sequences
Expand Down Expand Up @@ -181,7 +164,7 @@ def calculate_gradients(self, coordinates):
self.subflowchart.executor = self.flowchart.executor

# Direct most output to iteration.out
step_id = f"step_{self.step:{fmt}}"
step_id = f"step_{self._step:{fmt}}"
step_dir = Path(self._working_directory) / step_id
step_dir.mkdir(parents=True, exist_ok=True)

Expand Down Expand Up @@ -212,12 +195,12 @@ def calculate_gradients(self, coordinates):
traceback.print_exc(file=sys.stderr)
traceback.print_exc(file=sys.stdout)
except Exception as e:
printer.job(f"Caught exception in step {self.step}: {str(e)}")
printer.job(f"Caught exception in step {self._step}: {str(e)}")
traceback.print_exc(file=sys.stdout)
with open(step_dir / "stderr.out", "a") as fd:
traceback.print_exc(file=fd)
raise
self.logger.debug(f"End of step {self.step}")
self.logger.debug(f"End of step {self._step}")

# Remove any redirection of printing.
if self._file_handler is not None:
Expand All @@ -235,7 +218,7 @@ def calculate_gradients(self, coordinates):
if len(paths) == 0:
raise RuntimeError(
"There are no energy and gradients in properties.json for step "
f"{self.step} in {step_dir}."
f"{self._step} in {step_dir}."
)
else:
# Find the most recent and assume that is the one wanted
Expand Down Expand Up @@ -295,6 +278,17 @@ def calculate_gradients(self, coordinates):
# Units!
gradients = np.array(gradients) * Q_(1.0, funits).to("E_h/a_0").magnitude

# Citation!
self.geometric_read_bibliography()
if "seamm_geometric" in self._bibliography:
self.references.cite(
raw=self._bibliography["seamm_geometric"],
alias="seamm_geometric",
module="seamm_geometric",
level=2,
note="Main reference for the geomeTRIC connector for SEAMM.",
)

return energy, gradients

def describe_geomeTRIC_optimizer(self, P=None, short=False, natoms=None):
Expand Down Expand Up @@ -379,7 +373,7 @@ def describe_geomeTRIC_optimizer(self, P=None, short=False, natoms=None):
tmp_text.append(line.center(70))
criteria = formula["criteria"]

result = str(__(text, dedent=False, indent=3 * " ", **P))
result = str(__(text, dedent=False, indent=4 * " ", **P))
result += "\n".join(tmp_text)

table = {
Expand All @@ -401,6 +395,49 @@ def describe_geomeTRIC_optimizer(self, P=None, short=False, natoms=None):

return result

def geometric_read_bibliography(self):
"""Read the bibliography from a file and add to the local bibliography"""
self.logger.debug("Reading the seamm_geometric bibliography")
if "seamm-geometric" not in self._bibliography:
try:
data = (
files("seamm_geometric.data").joinpath("references.bib").read_text()
)
tmp = bibtexparser.loads(data).entries_dict
writer = bibtexparser.bwriter.BibTexWriter()
for key, data in tmp.items():
self.logger.debug(f" {key}")
self._bibliography[key] = writer._entry_to_bibtex(data)
except Exception as e:
self.logger.info(
f"Exception in reading seamm_geometric bibliography: {e}"
)
if "seamm_geometric" in self._bibliography:
try:
template = string.Template(self._bibliography["seamm_geometric"])

if "untagged" in __version__ or "unknown" in __version__:
# Development version
year = datetime.now().year
month = datetime.now().month
else:
year, month = __version__.split(".")[0:2]
try:
month = calendar.month_abbr[int(month)].lower()
except Exception:
year = datetime.now().year
month = datetime.now().month
month = calendar.month_abbr[int(month)].lower()

citation = template.substitute(
month=month, version=__version__, year=str(year)
)

self._bibliography["seamm_geometric"] = citation
except Exception as e:
printer.important(f"Exception in citation {type(e)}: {e}")
printer.important(traceback.format_exc())

def run_geomeTRIC_optimizer(self, P, PP):
"""Run an optimization using geomeTRIC.
Expand Down Expand Up @@ -473,7 +510,7 @@ def run_geomeTRIC_optimizer(self, P, PP):
else:
max_steps = P["max steps"]

self.step = 0
self._step = 0
logPath = self._working_directory / "geomeTRIC.out"
logIni = self._working_directory / "log.ini"
logIni.write_text(
Expand Down Expand Up @@ -594,8 +631,6 @@ def run_geomeTRIC_optimizer(self, P, PP):
step = coordinates - m.xyzs[-2].reshape(-1, 3)
self._results["maximum_step"] = np.max(np.linalg.norm(step, axis=1))

self.analyze()

if self.logger.isEnabledFor(logging.DEBUG):
logger.debug("optimized coordinates")
for i in range(n_atoms):
Expand Down Expand Up @@ -650,47 +685,13 @@ def run_geomeTRIC_optimizer(self, P, PP):
for subdirectory in subdirectories[:-1]:
shutil.rmtree(subdirectory)

# Citation!
self.read_bibliography()
self.references.cite(
raw=self._bibliography["geomeTRIC"],
alias="geomeTRIC",
module="seamm_geometric",
level=1,
note="Main reference for geomeTRIC.",
)

if "seamm_geometric" in self._bibliography:
try:
template = string.Template(self._bibliography["seamm_geometric"])

if "untagged" in __version__ or "unknown" in __version__:
# Development version
year = datetime.now().year
month = datetime.now().month
else:
year, month = __version__.split(".")[0:2]
try:
month = calendar.month_abbr[int(month)].lower()
except Exception:
year = datetime.now().year
month = datetime.now().month
month = calendar.month_abbr[int(month)].lower()

citation = template.substitute(
month=month, version=__version__, year=str(year)
)

title = "seamm_geometric".split("_")
title = " ".join([s.capitalize() for s in title[0:-2]])
self.references.cite(
raw=citation,
alias="seamm_geometric",
module="seamm_geometric",
level=self.citation_level,
note=(f"The principle citation for the {title} step in " "SEAMM."),
)

except Exception as e:
printer.important(f"Exception in citation {type(e)}: {e}")
printer.important(traceback.format_exc())
# Citation
self.geometric_read_bibliography()
if "geomeTRIC" in self._bibliography:
self.references.cite(
raw=self._bibliography["geomeTRIC"],
alias="geomeTRIC",
module="seamm_geometric",
level=1,
note="Main reference for geomeTRIC.",
)

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