# -*- coding: utf-8 -*-
"""Non-graphical part of the Thermochemistry step in a Psi4 flowchart
"""
import json
import logging
from pathlib import Path
import pkg_resources
from tabulate import tabulate
import psi4_step
import molsystem
import seamm
from seamm_util import Q_, units_class
import seamm_util.printing as printing
from seamm_util.printing import FormattedText as __
# In addition to the normal logger, two logger-like printing facilities are
# defined: "job" and "printer". "job" send output to the main job.out file for
# the job, and should be used very sparingly, typically to echo what this step
# will do in the initial summary of the job.
#
# "printer" sends output to the file "step.out" in this steps working
# directory, and is used for all normal output from this step.
logger = logging.getLogger(__name__)
job = printing.getPrinter()
printer = printing.getPrinter("Psi4")
# Add this module's properties to the standard properties
path = Path(pkg_resources.resource_filename(__name__, "data/"))
csv_file = path / "properties.csv"
if path.exists():
molsystem.add_properties_from_file(csv_file)
[docs]
class Thermochemistry(psi4_step.Energy):
"""
The non-graphical part of a Thermochemistry step in a flowchart.
Attributes
----------
parser : configargparse.ArgParser
The parser object.
options : tuple
It contains a two item tuple containing the populated namespace and the
list of remaining argument strings.
subflowchart : seamm.Flowchart
A SEAMM Flowchart object that represents a subflowchart, if needed.
parameters : ThermochemistryParameters
The control parameters for Thermochemistry.
See Also
--------
TkThermochemistry,
Thermochemistry, ThermochemistryParameters
"""
def __init__(
self,
flowchart=None,
title="Thermochemistry",
extension=None,
logger=logger,
):
"""A substep for Thermochemistry in a subflowchart for Psi4.
You may wish to change the title above, which is the string displayed
in the box representing the step in the flowchart.
Parameters
----------
flowchart: seamm.Flowchart
The non-graphical flowchart that contains this step.
title: str
The name displayed in the flowchart.
extension: None
Not yet implemented
logger : Logger = logger
The logger to use and pass to parent classes
Returns
-------
None
"""
logger.debug(f"Creating Thermochemistry {self}")
super().__init__(
flowchart=flowchart,
title=title,
extension=extension,
logger=logger,
)
self._calculation = "thermochemistry"
self._model = None
self._metadata = psi4_step.metadata
self.parameters = psi4_step.ThermochemistryParameters()
@property
def header(self):
"""A printable header for this section of output"""
return "Step {}: {}".format(".".join(str(e) for e in self._id), self.title)
@property
def version(self):
"""The semantic version of this module."""
return psi4_step.__version__
@property
def git_revision(self):
"""The git version of this module."""
return psi4_step.__git_revision__
[docs]
def description_text(self, P=None, configuration=None):
"""Create the text description of what this step will do.
The dictionary of control values is passed in as P so that
the code can test values, etc.
Parameters
----------
P: dict
An optional dictionary of the current values of the control
parameters.
Returns
-------
str
A description of the current step.
"""
if not P:
P = self.parameters.values_to_dict()
text = super().description_text(
P=P, calculation_type="Thermochemistry", configuration=configuration
)
added = (
"\nThe thermodynamic functions will be calculated at temperature {T} and "
"pressure {P}."
)
return text + "\n" + __(added, **P, indent=4 * " ").__str__()
[docs]
def analyze(self, indent="", **kwargs):
"""Do any analysis of the output from this step.
Also print important results to the local step.out file using
"printer".
Parameters
----------
indent: str
An extra indentation for the output
"""
# Read in the results from json
directory = Path(self.directory)
json_file = directory / "thermochemistry.json"
if json_file.exists():
with json_file.open() as fd:
tmp = json.load(fd)
# Process the data, changing units
d = {}
metadata = self.metadata["results"]
for key, value in tmp.items():
if key in metadata:
from_units = value["units"].replace("Eh", "E_h")
to_units = metadata[key]["units"]
if from_units == to_units:
d[key] = value["data"]
else:
d[key] = Q_(value["data"], from_units).m_as(to_units)
# Put any requested results into variables or tables
self.store_results(data=d, create_tables=True)
# And the output
table = {
"": [
"Units",
"Electronic",
"Translational",
"Rotational",
"Vibrational",
"Total Correction",
"Total (E_h)",
],
"S": [
"J/mol/K",
round(d["S_elec"], 2),
round(d["S_trans"], 2),
round(d["S_rot"], 2),
round(d["S_vib"], 2),
round(d["S_tot"], 2),
],
"Cv": [
"J/mol/K",
round(d["Cv_elec"], 2),
round(d["Cv_trans"], 2),
round(d["Cv_rot"], 2),
round(d["Cv_vib"], 2),
round(d["Cv_tot"], 2),
],
"Cp": [
"J/mol/K",
round(d["Cp_elec"], 2),
round(d["Cp_trans"], 2),
round(d["Cp_rot"], 2),
round(d["Cp_vib"], 2),
round(d["Cp_tot"], 2),
],
"E": [
"kJ/mol",
round(d["E_elec"], 2),
round(d["E_trans"], 2),
round(d["E_rot"], 2),
round(d["E_vib"], 2),
round(d["E_corr"], 2),
round(d["E_tot"], 6),
],
"H": [
"kJ/mol",
round(d["H_elec"], 2),
round(d["H_trans"], 2),
round(d["H_rot"], 2),
round(d["H_vib"], 2),
round(d["H_corr"], 2),
round(d["H_tot"], 6),
],
"G": [
"kJ/mol",
round(d["G_elec"], 2),
round(d["G_trans"], 2),
round(d["G_rot"], 2),
round(d["G_vib"], 2),
round(d["G_corr"], 2),
round(d["G_tot"], 6),
],
}
text = ""
tmp = tabulate(
table,
headers="keys",
tablefmt="simple_outline",
disable_numparse=True,
numalign="decimal",
stralign="center",
colalign=(
"center",
"decimal",
"decimal",
"decimal",
"decimal",
"decimal",
"decimal",
),
)
length = len(tmp.splitlines()[0])
text += "\n"
parameters = self.parameters.current_values_to_dict(
context=seamm.flowchart_variables._data
)
T = parameters["T"]
P = parameters["P"]
text += f"Thermodynamic Functions at {T:.2f~P} and {P:.2f~P}".center(length)
text += "\n"
text += tmp
text += "\n"
printer.normal(__(text, indent=8 * " ", wrap=False, dedent=False))
else:
text = (
"\nThere are no thermochemistry results from Psi4. Perhaps it "
f"failed? Looking for {str(json_file)}."
)
printer.normal(__(text, indent=self.indent + 4 * " "))
raise RuntimeError(text)
