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CoolProp/Web/scripts/CPWeb/SphinxTools.py
Ian Bell 6f8b4c95e2 Use requests with retry adapter for PubChem SDF downloads (#2730) 
Replaces urllib with requests + HTTPAdapter/Retry to get automatic
retries (up to 3) with exponential backoff on 429/5xx and network
errors; 404 is treated as a definitive miss and skips to 2D without
retrying.

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
2026-04-16 20:08:58 -04:00

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import CoolProp
CP = CoolProp.CoolProp
import os
import codecs
import re
import requests
from requests.adapters import HTTPAdapter
from urllib3.util.retry import Retry
web_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..'))
root_dir = os.path.abspath(os.path.join(web_dir, '..'))
fluid_template = u""".. _fluid_{fluid:s}:
{fluid_stars:s}
{fluid:s}
{fluid_stars:s}
{references:s}
{aliases:s}
{molecule_viewer_rst:s}Fluid Information
=================
.. csv-table::
:header-rows: 1
:escape: @
:widths: 40, 60
:delim: ;
:file: {fluid:s}-info.csv
REFPROP Validation Data
=======================
.. note::
This figure compares the results generated from CoolProp and those generated from REFPROP. They are all results obtained in the form :math:`Y(T,\\rho)`, where :math:`Y` is the parameter of interest and which for all EOS is a direct evaluation of the EOS
You can download the script that generated the following figure here: :download:`(link to script)<REFPROPplots/{fluid:s}.py>`, right-click the link and then save as... or the equivalent in your browser. You can also download this figure :download:`as a PDF<REFPROPplots/{fluid:s}.pdf>`.
.. image:: REFPROPplots/{fluid:s}.png
Consistency Plots
=================
The following figure shows all the flash routines that are available for this fluid. A red + is a failure of the flash routine, a black dot is a success. Hopefully you will only see black dots. The red curve is the maximum temperature curve, and the blue curve is the melting line if one is available for the fluid.
In this figure, we start off with a state point given by T,P and then we calculate each of the other possible output pairs in turn, and then try to re-calculate T,P from the new input pair. If we don't arrive back at the original T,P values, there is a problem in the flash routine in CoolProp. For more information on how these figures were generated, see :py:mod:`CoolProp.Plots.ConsistencyPlots`
.. note::
You can download the script that generated the following figure here: :download:`(link to script)<Consistencyplots/{fluid:s}.py>`, right-click the link and then save as... or the equivalent in your browser. You can also download this figure :download:`as a PDF<Consistencyplots/{fluid:s}.pdf>`.
.. image:: Consistencyplots/{fluid:s}.png
Superancillary Plots
====================
The following figure shows the accuracy of the superancillary functions relative to extended precision calculations carried out in C++ with the teqp library. The results of the iterative calculations with REFPROP and CoolProp are also shown.
.. note::
You can download the script that generated the following figure here: :download:`(link to script)<Superancillaryplots/{fluid:s}.py>`, right-click the link and then save as... or the equivalent in your browser. You can also download this figure :download:`as a PDF<Superancillaryplots/{fluid:s}.pdf>`.
.. image:: Superancillaryplots/{fluid:s}.png
"""
table_template = """ Parameter, Value
**General**;
Molar mass [kg/mol];{mm:s}
CAS number; {CAS:s}
ASHRAE class; {ASHRAE:s}
Formula; {formula:s}
Acentric factor; {acentric:s}
InChI; {inchi:s}
InChIKey; {inchikey:s}
SMILES; {smiles:s}
ChemSpider ID; {ChemSpider_id:s}
**Limits**;
Maximum temperature [K];{Tmax:s}
Maximum pressure [Pa];{pmax:s}
**Triple point**;
Triple point temperature [K];{Tt:s}
Triple point pressure [Pa]; {pt:s}
**Critical point**;
Critical point temperature [K]; {Tc:s}
Critical point density [kg/m3]; {rhoc_mass:s}
Critical point density [mol/m3]; {rhoc_molar:s}
Critical point pressure [Pa]; {pc:s}
{reducing_string:s}
"""
reducing_template = """**Reducing point**;
Reducing point temperature [K]; {Tr:s}
Reducing point density [mol/m3]; {rhor_molar:s}
"""
bibtex_keys = ['EOS', 'CP0', 'CONDUCTIVITY', 'VISCOSITY', 'MELTING_LINE', 'SURFACE_TENSION']
bibtex_map = {'EOS': 'Equation of State',
'CP0': 'Ideal gas specific heat',
'CONDUCTIVITY': 'Thermal Conductivity',
'VISCOSITY': 'Viscosity',
'MELTING_LINE': 'Melting Line',
'SURFACE_TENSION': 'Surface Tension'}
from pybtex.database.input import bibtex
parser = bibtex.Parser()
bibdata = parser.parse_file(os.path.join(root_dir, "CoolPropBibTeXLibrary.bib"))
from CoolProp.BibtexParser import BibTeXerClass
BTC = BibTeXerClass(os.path.join(root_dir, "CoolPropBibTeXLibrary.bib"))
# See http://stackoverflow.com/questions/19751402/does-pybtex-support-accent-special-characters-in-bib-file/19754245#19754245
import pybtex
style = pybtex.plugin.find_plugin('pybtex.style.formatting', 'plain')()
backend = pybtex.plugin.find_plugin('pybtex.backends', 'html')()
parser = pybtex.database.input.bibtex.Parser()
_INCHIKEY_RE = re.compile(r'^[A-Z]{14}-[A-Z]{10}-[A-Z]$')
def fetch_pubchem_sdf(inchikey, cache_dir):
"""
Fetch SDF from PubChem for *inchikey*, trying 3-D conformer first then 2-D.
Results are cached in *cache_dir* so subsequent runs never hit the network.
Returns (sdf_string, is_3d) or (None, None) when unavailable.
"""
os.makedirs(cache_dir, exist_ok=True)
for record_type, is_3d in (('3d', True), ('2d', False)):
cache_path = os.path.join(cache_dir, f'{inchikey}_{record_type}.sdf')
fail_flag = cache_path + '.failed'
if os.path.exists(cache_path):
with open(cache_path, 'r', encoding='utf-8') as fh:
return fh.read(), is_3d
if os.path.exists(fail_flag):
continue
url = (f'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/'
f'{inchikey}/SDF?record_type={record_type}')
session = requests.Session()
retry = Retry(total=3, backoff_factor=1,
status_forcelist=[429, 500, 502, 503, 504],
allowed_methods=['GET'])
session.mount('https://', HTTPAdapter(max_retries=retry))
try:
resp = session.get(url, timeout=15)
if resp.status_code == 404:
open(fail_flag, 'w').close()
continue
resp.raise_for_status()
content = resp.text
with open(cache_path, 'w', encoding='utf-8') as fh:
fh.write(content)
print(f' fetched {record_type.upper()} SDF for {inchikey}')
return content, is_3d
except Exception as exc:
print(f' PubChem {record_type.upper()} SDF unavailable for {inchikey}: {exc}')
open(fail_flag, 'w').close()
return None, None
def generate_3dmol_rst(fluid, sdf_data, is_3d):
"""
Return an RST string containing a ``.. raw:: html`` block with an embedded
interactive py3Dmol viewer. The SDF data is inlined as a JS template
literal so no external file serving is required.
"""
# Escape SDF content for safe embedding inside a JS template literal
sdf_js = sdf_data.replace('\\', '\\\\').replace('`', '\\`').replace('${', '\\${')
dim_label = '3D conformer' if is_3d else '2D structure'
html = (
f'<div class="molecule-viewer" style="text-align:center;margin:1em 0;">\n'
f' <div id="mol3d_{fluid}" style="width:400px;height:320px;'
f'position:relative;display:inline-block;border:1px solid #ccc;border-radius:6px;"></div>\n'
f' <p style="margin-top:0.4em;color:#666;font-size:0.85em;">\n'
f' {fluid} \u2014 {dim_label} (interactive: click and drag to rotate)\n'
f' </p>\n'
f'</div>\n'
f'<script>\n'
f'(function() {{\n'
f' var sdf = `{sdf_js}`;\n'
f' function init() {{\n'
f' if (typeof $3Dmol === "undefined") {{ setTimeout(init, 150); return; }}\n'
f' var v = $3Dmol.createViewer(\n'
f' document.getElementById("mol3d_{fluid}"),\n'
f' {{backgroundColor: "white"}});\n'
f' v.addModel(sdf, "sdf");\n'
f' v.setStyle({{}}, {{stick: {{radius: 0.15}}, sphere: {{scale: 0.3}}}});\n'
f' v.zoomTo();\n'
f' v.resize();\n'
f' v.render();\n'
f' }}\n'
f' if (document.readyState === "loading") {{\n'
f' document.addEventListener("DOMContentLoaded", init);\n'
f' }} else {{\n'
f' init();\n'
f' }}\n'
f'}})();\n'
f'</script>'
)
indented = '\n'.join(' ' + line for line in html.split('\n'))
return (
'Molecular Structure\n'
'===================\n'
'\n'
'.. raw:: html\n'
'\n'
f'{indented}\n'
'\n'
)
def formula2RST(formula):
"""
See: https://docutils.sourceforge.io/docs/ref/rst/roles.html#subscript
"""
return formula.replace('_{', r'\ :sub:`').replace('}',r'`\ ').replace(r'\ :sub:`1`\ ', '')
def entry2html(entry):
for e in entry:
return e.text.render(backend).replace('{', '').replace('}', '').replace('\n', ' ')
def generate_bibtex_string(fluid):
string = ''
for key in bibtex_keys:
header_string = ''
sect_strings = []
try:
# get the item
bibtex_key = CoolProp.CoolProp.get_BibTeXKey(fluid, key).strip()
for thekey in bibtex_key.split(','):
if thekey.strip() in bibdata.entries.keys():
html = BTC.getEntry(key=thekey.strip(), fmt='html')
if len(sect_strings) == 0:
sect = bibtex_map[key]
header_string = sect + '\n' + '-' * len(sect) + '\n\n'
sect_strings.append('.. raw:: html\n\n ' + html + '\n\n')
except ValueError as E:
print("error: %s" % E)
string += header_string + '\n\n.. raw:: html\n\n <br><br> \n\n'.join(sect_strings)
return string
class FluidInfoTableGenerator(object):
def __init__(self, name):
self.name = name
def write(self, path):
def tos(n):
''' convert number to nicely formatted string '''
n = str(n)
if 'e' in n:
l, r = n.split('e')
n = rf' :math:`{l}@\times 10^{{{r}}}`'
else:
return n
return n
molar_mass = CoolProp.CoolProp.PropsSI(self.name, 'molemass')
Tt = CoolProp.CoolProp.PropsSI(self.name, 'Ttriple')
Tc = CoolProp.CoolProp.PropsSI(self.name, 'Tcrit')
Tr = CoolProp.CoolProp.PropsSI(self.name, 'T_reducing')
pc = CoolProp.CoolProp.PropsSI(self.name, 'pcrit')
pt = CoolProp.CoolProp.PropsSI(self.name, 'ptriple')
if pt is None:
pt = "Unknown"
Tmax = CoolProp.CoolProp.PropsSI(self.name, 'Tmax')
pmax = CoolProp.CoolProp.PropsSI(self.name, 'pmax')
acentric = CoolProp.CoolProp.PropsSI(self.name, 'acentric')
rhoc_mass = CoolProp.CoolProp.PropsSI(self.name, 'rhomass_critical')
rhoc_molar = CoolProp.CoolProp.PropsSI(self.name, 'rhomolar_critical')
rhor_molar = CoolProp.CoolProp.PropsSI(self.name, 'rhomolar_reducing')
CAS = CoolProp.CoolProp.get_fluid_param_string(self.name, "CAS")
ASHRAE = CoolProp.CoolProp.get_fluid_param_string(self.name, "ASHRAE34")
formula = CoolProp.CoolProp.get_fluid_param_string(self.name, "formula")
if formula:
formula = formula2RST(formula)
else:
formula = 'Not applicable'
formula = formula.replace('_{1}', '')
InChI = CoolProp.CoolProp.get_fluid_param_string(self.name, "INCHI")
InChiKey = CoolProp.CoolProp.get_fluid_param_string(self.name, "INCHIKEY")
smiles = CoolProp.CoolProp.get_fluid_param_string(self.name, "SMILES")
ChemSpider_id = CoolProp.CoolProp.get_fluid_param_string(self.name, "CHEMSPIDER_ID")
twoDurl = CoolProp.CoolProp.get_fluid_param_string(self.name, "2DPNG_URL")
# Generate (or not) the reducing data
reducing_data = ''
if abs(Tr - Tc) > 1e-3:
reducing_data = reducing_template.format(Tr=tos(Tr),
rhor_molar=tos(rhor_molar))
args = dict(mm=tos(molar_mass),
Tt=tos(Tt),
pt=tos(pt),
Tc=tos(Tc),
rhoc_mass=tos(rhoc_mass),
rhoc_molar=tos(rhoc_molar),
pc=tos(pc),
acentric=tos(acentric),
CAS=tos(CAS),
ASHRAE=tos(ASHRAE),
Tmax=tos(Tmax),
pmax=tos(pmax),
reducing_string=reducing_data,
formula=formula,
inchi=InChI,
inchikey=InChiKey,
smiles=smiles,
ChemSpider_id=ChemSpider_id,
twoDurl=twoDurl
)
out = table_template.format(**args)
with open(os.path.join(path, self.name + '-info.csv'), 'w') as fp:
print("writing %s" % os.path.join(path, self.name + '-info.csv'))
fp.write(out)
class FluidGenerator(object):
def __init__(self, fluid):
self.fluid = fluid
def write(self, path):
# Write CSV table data for fluid information
ITG = FluidInfoTableGenerator(self.fluid)
ITG.write(path)
del_old = CP.get_config_string(CP.LIST_STRING_DELIMITER)
CP.set_config_string(CP.LIST_STRING_DELIMITER, '|')
try:
aliases = ', '.join(['``' + a.strip() + '``' for a in CoolProp.CoolProp.get_fluid_param_string(self.fluid, 'aliases').strip().split('|') if a])
finally:
CP.set_config_string(CP.LIST_STRING_DELIMITER, del_old)
if aliases:
aliases = 'Aliases\n=======\n\n' + aliases + '\n'
references = generate_bibtex_string(self.fluid)
if references:
references = 'References\n==========\n' + references + '\n'
# Generate interactive 3-D molecule viewer (py3Dmol via PubChem SDF)
molecule_viewer_rst = ''
inchikey = CoolProp.CoolProp.get_fluid_param_string(self.fluid, "INCHIKEY")
if inchikey and _INCHIKEY_RE.match(inchikey):
sdf_cache = os.path.join(path, 'molecule_sdf')
sdf_data, is_3d = fetch_pubchem_sdf(inchikey, sdf_cache)
if sdf_data:
molecule_viewer_rst = generate_3dmol_rst(self.fluid, sdf_data, is_3d)
# Write RST file for fluid
out = fluid_template.format(aliases=aliases,
fluid=self.fluid,
fluid_stars='*' * len(self.fluid),
references=references,
molecule_viewer_rst=molecule_viewer_rst
)
with codecs.open(os.path.join(path, self.fluid + '.rst'), 'w', encoding='utf-8') as fp:
print("writing %s" % os.path.join(path, self.fluid + '.rst'))
fp.write(out)
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