diff --git a/phasecalculator/io/phasetransferxmlcreator.py b/phasecalculator/io/phasetransferxmlcreator.py
new file mode 100755
index 0000000000000000000000000000000000000000..dce1d740356b26ed458523196c904e02427f6b29
--- /dev/null
+++ b/phasecalculator/io/phasetransferxmlcreator.py
@@ -0,0 +1,192 @@
+# -*- coding: utf-8 -*-
+# phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+# Copyright (C) 2019 Mark D. Driver
+#
+# phasecalculator is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+"""
+Module for creating Solvent and Phase XML for phase transfer calculations.
+
+@author: Mark
+"""
+
+import logging
+import phasexmlcreator.multicomponentassembler as multiassem
+import phasexmlcreator.phasexmlmaker as phasemake
+import phasexmlcreator.solventxmlmaker as solvmake
+import puresolventinformation.information as pureinfo
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+def create_phase_and_solvent_files(mole_fraction_dict_list, temperature_info, solvent_filename, phase_filename, **kwargs):
+ """Create phase XML and solvent XML files for given composiiton and
+ temperature information.
+
+ Parameters
+ ----------
+ mole_fraction_dict_list : list of dicts
+ List of dictionaries of name: mole fraction pairs per phase/solvent to
+ create.
+ temperature_info : list of dicts
+ Temperature information with dictionaries containing value and unit.
+ solvent_filename : str
+ Solvent XML output filename.
+ phase_filename : str
+ Phase XML output filename.
+ solvent_filename : str, optional
+ Filename for file containing solvent information. Defaults to file in
+ phasexmlcreator module.
+ ssip_filename_list : list of str, optional
+ Filenames for SSIP XML files. Defaults to SSIP files in pureinformation
+ module.
+ name_inchikey_map : dict, optional
+ inchikey: name pairs. Defaults to names of solvents in pureinformation
+ module.
+
+ Returns
+ -------
+ None.
+
+ """
+ solvent_info_list = generate_solv_info_list(mole_fraction_dict_list, **kwargs)
+ write_solvent_file(solvent_info_list, solvent_filename)
+ write_phase_file(solvent_info_list, temperature_info, phase_filename)
+
+def create_solvent_file(mole_fraction_dict_list, solvent_filename, **kwargs):
+ """Create solvent XML file for given compositions.
+
+ Parameters
+ ----------
+ mole_fraction_dict_list : list of dicts
+ List of dictionaries of name: mole fraction pairs per solvent to
+ create.
+ solvent_filename : str
+ Solvent XML output filename.
+ solvent_filename : str, optional
+ Filename for file containing solvent information. Defaults to file in
+ phasexmlcreator module.
+ ssip_filename_list : list of str, optional
+ Filenames for SSIP XML files. Defaults to SSIP files in pureinformation
+ module.
+ name_inchikey_map : dict, optional
+ inchikey: name pairs. Defaults to names of solvents in pureinformation
+ module.
+
+ Returns
+ -------
+ None.
+
+ """
+ solvent_info_list = generate_solv_info_list(mole_fraction_dict_list, **kwargs)
+ write_solvent_file(solvent_info_list, solvent_filename)
+
+def create_phase_file(mole_fraction_dict_list, temperature_info, phase_filename, **kwargs):
+ """Create phase XML file for given compositions and temperatures.
+
+ Parameters
+ ----------
+ mole_fraction_dict_list : list of dicts
+ List of dictionaries of name: mole fraction pairs per phase to
+ create.
+ temperature_info : list of dicts
+ Temperature information with dictionaries containing value and unit.
+ phase_filename : str
+ Phase XML output filename.
+ solvent_filename : str, optional
+ Filename for file containing solvent information. Defaults to file in
+ phasexmlcreator module.
+ ssip_filename_list : list of str, optional
+ Filenames for SSIP XML files. Defaults to SSIP files in pureinformation
+ module.
+ name_inchikey_map : dict, optional
+ inchikey: name pairs. Defaults to names of solvents in pureinformation
+ module.
+
+ Returns
+ -------
+ None.
+
+ """
+ phase_info_list = generate_solv_info_list(mole_fraction_dict_list, **kwargs)
+ write_phase_file(phase_info_list, temperature_info, phase_filename)
+
+def write_solvent_file(solvent_info_list, solvent_filename):
+ """Write solvent XML file for given compositions.
+
+ Parameters
+ ----------
+ solvent_info_list : list of dicts
+ List of dictionaries of information to create XML for given solvent
+ compositions.
+ solvent_filename : str
+ Output filename.
+
+ Returns
+ -------
+ None.
+
+ """
+ solvmake.write_solvent_information_to_file(solvent_info_list, solvent_filename)
+
+
+def write_phase_file(phase_info_list, temperature_info, phase_filename):
+ """Write phase XML file for given compositions and temperatures.
+
+ Parameters
+ ----------
+ phase_info_list : list of dicts
+ List of dictionaries of information to create XML for given phase
+ compositions.
+ temperature_info : list of dicts
+ Temperature information with dictionaries containing value and unit.
+ phase_filename : str
+ Output filename.
+
+ Returns
+ -------
+ None.
+
+ """
+ phasemake.write_phase_information_to_file(phase_info_list, temperature_info, phase_filename)
+
+def generate_solv_info_list(mole_fraction_dict_list, **kwargs):
+ """Generate solvent info from read in SSIP files and solvent information.
+
+ Parameters
+ ----------
+ mole_fraction_dict_list : list of dicts
+ List of dictionaries of name: mole fraction pairs per phase/solvent to
+ create.
+ solvent_filename : str, optional
+ Filename for file containing solvent information. Defaults to file in
+ phasexmlcreator module.
+ ssip_filename_list : list of str, optional
+ Filenames for SSIP XML files. Defaults to SSIP files in pureinformation
+ module.
+ name_inchikey_map : dict, optional
+ inchikey: name pairs. Defaults to names of solvents in pureinformation
+ module.
+
+ Returns
+ -------
+ solv_info_list : list of dicts
+ List of dictionaries of information to create XML for given solvent
+ compositions.
+
+ """
+ solvent_filename = kwargs.get("solvent_filename", multiassem.solvconcreader.DEFAULT_SOLVENT_INFORMATION_FILE)
+ ssip_filename_list = kwargs.get("ssip_filename_list",pureinfo.get_ssip_file_dict().values())
+ name_inchikey_map = kwargs.get("name_inchikey_map", pureinfo.get_name_inchikey_mapping())
+ return multiassem.generate_solv_info_from_files(mole_fraction_dict_list, solvent_filename, ssip_filename_list, name_inchikey_map)
diff --git a/phasecalculator/test/iotest/phasetransferxmlcreatortest.py b/phasecalculator/test/iotest/phasetransferxmlcreatortest.py
new file mode 100755
index 0000000000000000000000000000000000000000..23660ad4e62e589e1a59cd7673dcdd8c155dc4f1
--- /dev/null
+++ b/phasecalculator/test/iotest/phasetransferxmlcreatortest.py
@@ -0,0 +1,282 @@
+# -*- coding: utf-8 -*-
+# phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+# Copyright (C) 2019 Mark D. Driver
+#
+# phasecalculator is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+"""
+Test case for phasetransferxmlcreator module.
+
+@author: mark
+"""
+
+import logging
+import unittest
+import pathlib
+import os
+from lxml import etree
+import phasecalculator.io.phasetransferxmlcreator as phasexmlmaker
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+class PhasetransferXMLCreatorTestCase(unittest.TestCase):
+
+ def setUp(self):
+ """Set up for tests.
+
+ Returns
+ -------
+ None.
+
+ """
+ self.maxDiff = None
+ parent_directory = pathlib.Path(__file__).parents[1]
+ self.expected_water_xml = """<ssip:SSIPMolecule xmlns:cml="http://www.xml-cml.org/schema" xmlns:ssip="http://www-hunter.ch.cam.ac.uk/SSIP" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ssip:ssipSoftwareVersion="6.0.0" ssip:parameterVersion="1.0.0" xsi:schemaLocation="http://www.xml-cml.org/schema http://www-hunter.ch.cam.ac.uk/schema/cmlschema.xsd http://www-hunter.ch.cam.ac.uk/SSIP http://www-hunter.ch.cam.ac.uk/schema/SSIP.xsd">
+ <cml:molecule ssip:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" cml:id="XLYOFNOQVPJJNP-UHFFFAOYSA-N">
+ <cml:atomArray>
+ <cml:atom cml:elementType="O" cml:id="a1" cml:formalCharge="0" cml:x3="-0.197781963496" cml:y3="-7.5088692891E-35" cml:z3="0.34665983175"/>
+ <cml:atom cml:elementType="H" cml:id="a2" cml:formalCharge="0" cml:x3="0.760536914227" cml:y3="-9.28739754019E-37" cml:z3="0.204548524786"/>
+ <cml:atom cml:elementType="H" cml:id="a3" cml:formalCharge="0" cml:x3="-0.56175495073" cml:y3="5.1742035555E-35" cml:z3="-0.551208356536"/>
+ </cml:atomArray>
+ <cml:bondArray>
+ <cml:bond cml:atomRefs2="a1 a2" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a1 a3" cml:order="1"/>
+ </cml:bondArray>
+ </cml:molecule>
+ <ssip:SurfaceInformation>
+ <ssip:Surfaces>
+ <ssip:Surface>
+ <ssip:TotalSurfaceArea ssip:unit="Ã…^2">37.46449353147367</ssip:TotalSurfaceArea>
+ <ssip:NegativeSurfaceArea ssip:unit="Ã…^2">18.417074471275452</ssip:NegativeSurfaceArea>
+ <ssip:PositiveSurfaceArea ssip:unit="Ã…^2">19.047419060197754</ssip:PositiveSurfaceArea>
+ <ssip:ElectronDensityIsosurface ssip:unit="e bohr^-3">0.002</ssip:ElectronDensityIsosurface>
+ <ssip:NumberOFMEPSPoints>2267</ssip:NumberOFMEPSPoints>
+ <ssip:VdWVolume ssip:unit="Ã…^3">21.118225673870302</ssip:VdWVolume>
+ <ssip:ElectrostaticPotentialMax ssip:unit="kJ mol^-1">222.31155482388002</ssip:ElectrostaticPotentialMax>
+ <ssip:ElectrostaticPotentialMin ssip:unit="kJ mol^-1">-185.78297861082</ssip:ElectrostaticPotentialMin>
+ </ssip:Surface>
+ </ssip:Surfaces>
+ </ssip:SurfaceInformation>
+ <ssip:SSIPs>
+ <ssip:SSIP ssip:value="2.8" ssip:nearestAtomID="a2" cml:x3="1.7703677783019898" cml:y3="-0.037716579245226" cml:z3="-0.12404973071057998"/>
+ <ssip:SSIP ssip:value="2.8" ssip:nearestAtomID="a3" cml:x3="-0.78007076629588" cml:y3="-0.131868324564555" cml:z3="-1.585252051411308"/>
+ <ssip:SSIP ssip:value="-4.5" ssip:nearestAtomID="a1" cml:x3="-0.78007076629588" cml:y3="-1.185660785500926" cml:z3="1.34163366293468"/>
+ <ssip:SSIP ssip:value="-4.5" ssip:nearestAtomID="a1" cml:x3="-0.9035034763341259" cml:y3="0.8351649972210169" cml:z3="1.5735514132586688"/>
+ </ssip:SSIPs>
+</ssip:SSIPMolecule>"""
+ self.expected_butanol_xml = """<ssip:SSIPMolecule xmlns:cml="http://www.xml-cml.org/schema" xmlns:ssip="http://www-hunter.ch.cam.ac.uk/SSIP" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ssip:ssipSoftwareVersion="6.0.0" ssip:parameterVersion="1.0.0" xsi:schemaLocation="http://www.xml-cml.org/schema http://www-hunter.ch.cam.ac.uk/schema/cmlschema.xsd http://www-hunter.ch.cam.ac.uk/SSIP http://www-hunter.ch.cam.ac.uk/schema/SSIP.xsd">
+ <cml:molecule ssip:stdInChIKey="LRHPLDYGYMQRHN-UHFFFAOYSA-N" cml:id="LRHPLDYGYMQRHN-UHFFFAOYSA-N">
+ <cml:atomArray>
+ <cml:atom cml:elementType="C" cml:id="a1" cml:formalCharge="0" cml:x3="0.453161473082" cml:y3="-1.03446801266" cml:z3="-0.0905306598548"/>
+ <cml:atom cml:elementType="H" cml:id="a10" cml:formalCharge="0" cml:x3="-0.711314642651" cml:y3="-1.77936986861" cml:z3="1.57182493824"/>
+ <cml:atom cml:elementType="H" cml:id="a11" cml:formalCharge="0" cml:x3="-2.35918900768" cml:y3="-0.976902587046" cml:z3="-0.14772459368"/>
+ <cml:atom cml:elementType="H" cml:id="a12" cml:formalCharge="0" cml:x3="-1.77474726333" cml:y3="-2.19616982792" cml:z3="-1.27745306344"/>
+ <cml:atom cml:elementType="H" cml:id="a13" cml:formalCharge="0" cml:x3="-2.519145554" cml:y3="-4.00559237167" cml:z3="0.302707946329"/>
+ <cml:atom cml:elementType="H" cml:id="a14" cml:formalCharge="0" cml:x3="-3.10209800172" cml:y3="-2.77368664521" cml:z3="1.42866821719"/>
+ <cml:atom cml:elementType="H" cml:id="a15" cml:formalCharge="0" cml:x3="-4.0901443513" cml:y3="-3.10664597908" cml:z3="-1.18904146578"/>
+ <cml:atom cml:elementType="C" cml:id="a2" cml:formalCharge="0" cml:x3="-0.564202390594" cml:y3="-2.0116665412" cml:z3="0.507612692817"/>
+ <cml:atom cml:elementType="C" cml:id="a3" cml:formalCharge="0" cml:x3="-1.92163762747" cml:y3="-1.98241261328" cml:z3="-0.206572876019"/>
+ <cml:atom cml:elementType="C" cml:id="a4" cml:formalCharge="0" cml:x3="-2.92693672032" cml:y3="-2.98225012861" cml:z3="0.367318952425"/>
+ <cml:atom cml:elementType="O" cml:id="a5" cml:formalCharge="0" cml:x3="-4.208010389" cml:y3="-2.9017666367" cml:z3="-0.248445606999"/>
+ <cml:atom cml:elementType="H" cml:id="a6" cml:formalCharge="0" cml:x3="0.655827908609" cml:y3="-1.26752859656" cml:z3="-1.14312376632"/>
+ <cml:atom cml:elementType="H" cml:id="a7" cml:formalCharge="0" cml:x3="0.0848553777946" cml:y3="-0.00239243828223" cml:z3="-0.0456709489122"/>
+ <cml:atom cml:elementType="H" cml:id="a8" cml:formalCharge="0" cml:x3="1.40666917559" cml:y3="-1.07214682201" cml:z3="0.448356319391"/>
+ <cml:atom cml:elementType="H" cml:id="a9" cml:formalCharge="0" cml:x3="-0.154987987004" cml:y3="-3.03150093117" cml:z3="0.472873914607"/>
+ </cml:atomArray>
+ <cml:bondArray>
+ <cml:bond cml:atomRefs2="a1 a2" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a1 a6" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a1 a7" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a1 a8" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a2 a10" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a2 a3" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a2 a9" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a3 a11" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a3 a12" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a3 a4" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a4 a13" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a4 a14" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a4 a5" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a5 a15" cml:order="1"/>
+ </cml:bondArray>
+ </cml:molecule>
+ <ssip:SurfaceInformation>
+ <ssip:Surfaces>
+ <ssip:Surface>
+ <ssip:TotalSurfaceArea ssip:unit="Ã…^2">122.2095781704891</ssip:TotalSurfaceArea>
+ <ssip:NegativeSurfaceArea ssip:unit="Ã…^2">20.900319182402814</ssip:NegativeSurfaceArea>
+ <ssip:PositiveSurfaceArea ssip:unit="Ã…^2">101.30925898808572</ssip:PositiveSurfaceArea>
+ <ssip:ElectronDensityIsosurface ssip:unit="e bohr^-3">0.002</ssip:ElectronDensityIsosurface>
+ <ssip:NumberOFMEPSPoints>9580</ssip:NumberOFMEPSPoints>
+ <ssip:VdWVolume ssip:unit="Ã…^3">99.3920085615431</ssip:VdWVolume>
+ <ssip:ElectrostaticPotentialMax ssip:unit="kJ mol^-1">213.86532254634</ssip:ElectrostaticPotentialMax>
+ <ssip:ElectrostaticPotentialMin ssip:unit="kJ mol^-1">-172.51370353134</ssip:ElectrostaticPotentialMin>
+ </ssip:Surface>
+ </ssip:Surfaces>
+ </ssip:SurfaceInformation>
+ <ssip:SSIPs>
+ <ssip:SSIP ssip:value="2.784040024744081" ssip:nearestAtomID="a15" cml:x3="-3.8161781356582187" cml:y3="-3.342557618498982" cml:z3="-2.192649106294994"/>
+ <ssip:SSIP ssip:value="0.773639545237379" ssip:nearestAtomID="a12" cml:x3="-2.239105576984704" cml:y3="-3.099174713898159" cml:z3="-2.0252301249653697"/>
+ <ssip:SSIP ssip:value="0.5071846345423165" ssip:nearestAtomID="a13" cml:x3="-2.8499750929763277" cml:y3="-4.524230524251444" cml:z3="-0.8462517897648159"/>
+ <ssip:SSIP ssip:value="0.4784372492163057" ssip:nearestAtomID="a6" cml:x3="0.9270005337214728" cml:y3="-1.649107340870889" cml:z3="-2.251805301783455"/>
+ <ssip:SSIP ssip:value="0.46383776537503163" ssip:nearestAtomID="a9" cml:x3="0.136470579099108" cml:y3="-4.205322913496092" cml:z3="0.352187567944962"/>
+ <ssip:SSIP ssip:value="0.4557099985213939" ssip:nearestAtomID="a8" cml:x3="2.420223369759191" cml:y3="-1.188501408973558" cml:z3="1.0796321860050409"/>
+ <ssip:SSIP ssip:value="0.4355872186992693" ssip:nearestAtomID="a7" cml:x3="-0.30271267022695597" cml:y3="1.1313523827905538" cml:z3="0.031343697635518995"/>
+ <ssip:SSIP ssip:value="0.43429343831228867" ssip:nearestAtomID="a14" cml:x3="-2.937811637006091" cml:y3="-2.45801773806002" cml:z3="2.5781764284587028"/>
+ <ssip:SSIP ssip:value="0.33435822085360595" ssip:nearestAtomID="a11" cml:x3="-2.5158938537831497" cml:y3="0.207568717565752" cml:z3="0.059691722864448994"/>
+ <ssip:SSIP ssip:value="0.0" ssip:nearestAtomID="a3" cml:x3="-1.4487933333328935" cml:y3="-2.074966666667215" cml:z3="0.05005333333293337"/>
+ <ssip:SSIP ssip:value="0.0" ssip:nearestAtomID="a3" cml:x3="-1.4487933333328935" cml:y3="-2.074966666667215" cml:z3="0.05005333333293337"/>
+ <ssip:SSIP ssip:value="-5.3386085001748205" ssip:nearestAtomID="a5" cml:x3="-5.4850745889327115" cml:y3="-3.640825199834338" cml:z3="0.48092898414517593"/>
+ <ssip:SSIP ssip:value="-5.365217010700665" ssip:nearestAtomID="a5" cml:x3="-5.353424285394745" cml:y3="-1.7849561367024218" cml:z3="0.11271581239149799"/>
+ </ssip:SSIPs>
+</ssip:SSIPMolecule>"""
+ self.mol_info_list = [{"concentration_value":10.8702104695089,
+ "inchikey":"LRHPLDYGYMQRHN-UHFFFAOYSA-N",
+ "mole_fraction":0.16452830188679246,
+ "ssip_molecule":self.expected_butanol_xml},
+ {"concentration_value":55.3496115427303,
+ "inchikey":"XLYOFNOQVPJJNP-UHFFFAOYSA-N",
+ "mole_fraction":0.8354716981132075,
+ "ssip_molecule":self.expected_water_xml,},
+ ]
+ self.mole_fraction_dict_list = [{"water":0.8354716981132075,
+ "1-butanol":0.16452830188679246}]
+ self.solvent_info_list = phasexmlmaker.generate_solv_info_list(self.mole_fraction_dict_list)
+ self.expected_phase_file = (parent_directory /"resources" / "expected_phase.xml").absolute().as_posix()
+ self.expected_solvent_file = (parent_directory /"resources" / "expected_solvent.xml").absolute().as_posix()
+ self.temperature_info = [{"temperature_value": 298.0, "temperature_units": "KELVIN"}]
+ self.phase_filename = "actual_phase.xml"
+ self.solvent_filename = "actual_solvent.xml"
+ def tearDown(self):
+ """Clean up after tests.
+
+ Returns
+ -------
+ None.
+
+ """
+ if os.path.isfile(self.phase_filename):
+ os.remove(self.phase_filename)
+ if os.path.isfile(self.solvent_filename):
+ os.remove(self.solvent_filename)
+ def test_create_phase_and_solvent_files(self):
+ """Test
+
+ Returns
+ -------
+ None.
+
+ """
+ phasexmlmaker.create_phase_and_solvent_files(self.mole_fraction_dict_list, self.temperature_info, self.solvent_filename, self.phase_filename)
+ with open(self.phase_filename, "r") as act_file:
+ actual_contents = act_file.read()
+ with open(self.expected_phase_file, "r") as exp_file:
+ expected_contents = exp_file.read()
+ self.assertMultiLineEqual(expected_contents, actual_contents)
+ with open(self.solvent_filename, "r") as act_file:
+ actual_contents = act_file.read()
+ with open(self.expected_solvent_file, "r") as exp_file:
+ expected_contents = exp_file.read()
+ self.assertMultiLineEqual(expected_contents, actual_contents)
+ def test_create_solvent_file(self):
+ """Test
+
+ Returns
+ -------
+ None.
+
+ """
+ phasexmlmaker.create_solvent_file(self.mole_fraction_dict_list, self.solvent_filename)
+ with open(self.solvent_filename, "r") as act_file:
+ actual_contents = act_file.read()
+ with open(self.expected_solvent_file, "r") as exp_file:
+ expected_contents = exp_file.read()
+ self.assertMultiLineEqual(expected_contents, actual_contents)
+ def test_create_phase_file(self):
+ """Test
+
+ Returns
+ -------
+ None.
+
+ """
+ phasexmlmaker.create_phase_file(self.mole_fraction_dict_list, self.temperature_info, self.phase_filename)
+ with open(self.phase_filename, "r") as act_file:
+ actual_contents = act_file.read()
+ with open(self.expected_phase_file, "r") as exp_file:
+ expected_contents = exp_file.read()
+ self.assertMultiLineEqual(expected_contents, actual_contents)
+ def test_write_solvent_file(self):
+ """Test
+
+ Returns
+ -------
+ None.
+
+ """
+ phasexmlmaker.write_solvent_file(self.solvent_info_list, self.solvent_filename)
+ with open(self.solvent_filename, "r") as act_file:
+ actual_contents = act_file.read()
+ with open(self.expected_solvent_file, "r") as exp_file:
+ expected_contents = exp_file.read()
+ self.assertMultiLineEqual(expected_contents, actual_contents)
+ def test_write_phase_file(self):
+ """Test
+
+ Returns
+ -------
+ None.
+
+ """
+ phasexmlmaker.write_phase_file(self.solvent_info_list, self.temperature_info, self.phase_filename)
+ with open(self.phase_filename, "r") as act_file:
+ actual_contents = act_file.read()
+ with open(self.expected_phase_file, "r") as exp_file:
+ expected_contents = exp_file.read()
+ self.assertMultiLineEqual(expected_contents, actual_contents)
+ def test_generate_solv_info_list(self):
+ """Test
+
+ Returns
+ -------
+ None.
+
+ """
+ expected_list = self.mol_info_list
+ expected_keys = [
+ "concentration_value",
+ "inchikey",
+ "mole_fraction",
+ "ssip_molecule",
+ ]
+ actual_info_list = self.solvent_info_list
+ self.assertEqual(1, len(actual_info_list))
+ actual_information = actual_info_list[0]
+ self.assertEqual("1-butanol0.165water0.835", actual_information["solvent_name"])
+ self.assertEqual("1-butanol0.165water0.835", actual_information["solvent_id"])
+ actual_list = actual_information["ssip_info_list"]
+ for entry, information_dict in enumerate(actual_list):
+ with self.subTest(entry=entry):
+ expected_dict = expected_list[entry]
+ self.assertListEqual(expected_keys, sorted(information_dict.keys()))
+ self.assertEqual(
+ expected_dict["inchikey"], information_dict["inchikey"]
+ )
+ self.assertAlmostEqual(expected_dict["concentration_value"], information_dict["concentration_value"])
+ self.assertAlmostEqual(expected_dict["mole_fraction"], information_dict["mole_fraction"])
+ self.assertMultiLineEqual(
+ expected_dict["ssip_molecule"],
+ etree.tounicode(information_dict["ssip_molecule"]),
+ )
\ No newline at end of file
diff --git a/phasecalculator/test/phasecalculatortests.py b/phasecalculator/test/phasecalculatortests.py
index 587a90606c990efa96b74377549fbf9c70afab9b..da7899498f9810343064b177d6d89fae1bfe226d 100755
--- a/phasecalculator/test/phasecalculatortests.py
+++ b/phasecalculator/test/phasecalculatortests.py
@@ -23,12 +23,13 @@ Created on Tue Jan 7 16:34:17 2020
import logging
import unittest
import sys
+from phasecalculator.test.iotest.phasetransferxmlcreatortest import PhasetransferXMLCreatorTestCase
logging.basicConfig()
LOGGER = logging.getLogger(__name__)
LOGGER.setLevel(logging.WARN)
-IO_TEST_CASES = []
+IO_TEST_CASES = [PhasetransferXMLCreatorTestCase,]
RUNNERS_TEST_CASES = []
diff --git a/phasecalculator/test/resources/expected_phase.xml b/phasecalculator/test/resources/expected_phase.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f28ca30b17d6533e4b85bf094331db9eb5ddaf25
--- /dev/null
+++ b/phasecalculator/test/resources/expected_phase.xml
@@ -0,0 +1,90 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<phase:MixtureCollection xmlns:phase="http://www-hunter.ch.cam.ac.uk/PhaseSchema" xmlns:ssip="http://www-hunter.ch.cam.ac.uk/SSIP" xmlns:cml="http://www.xml-cml.org/schema">
+ <phase:Mixtures>
+ <phase:Mixture phase:soluteID="298.000KELVIN">
+ <phase:Phases>
+ <phase:Phase phase:solventID="1-butanol0.165water0.835298.000KELVIN" phase:units="MOLAR">
+ <phase:Molecules>
+ <phase:Molecule phase:stdInChIKey="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:moleFraction="0.1645"><cml:molecule ssip:stdInChIKey="LRHPLDYGYMQRHN-UHFFFAOYSA-N" cml:id="LRHPLDYGYMQRHN-UHFFFAOYSA-N">
+ <cml:atomArray>
+ <cml:atom cml:elementType="C" cml:id="a1" cml:formalCharge="0" cml:x3="0.453161473082" cml:y3="-1.03446801266" cml:z3="-0.0905306598548"/>
+ <cml:atom cml:elementType="H" cml:id="a10" cml:formalCharge="0" cml:x3="-0.711314642651" cml:y3="-1.77936986861" cml:z3="1.57182493824"/>
+ <cml:atom cml:elementType="H" cml:id="a11" cml:formalCharge="0" cml:x3="-2.35918900768" cml:y3="-0.976902587046" cml:z3="-0.14772459368"/>
+ <cml:atom cml:elementType="H" cml:id="a12" cml:formalCharge="0" cml:x3="-1.77474726333" cml:y3="-2.19616982792" cml:z3="-1.27745306344"/>
+ <cml:atom cml:elementType="H" cml:id="a13" cml:formalCharge="0" cml:x3="-2.519145554" cml:y3="-4.00559237167" cml:z3="0.302707946329"/>
+ <cml:atom cml:elementType="H" cml:id="a14" cml:formalCharge="0" cml:x3="-3.10209800172" cml:y3="-2.77368664521" cml:z3="1.42866821719"/>
+ <cml:atom cml:elementType="H" cml:id="a15" cml:formalCharge="0" cml:x3="-4.0901443513" cml:y3="-3.10664597908" cml:z3="-1.18904146578"/>
+ <cml:atom cml:elementType="C" cml:id="a2" cml:formalCharge="0" cml:x3="-0.564202390594" cml:y3="-2.0116665412" cml:z3="0.507612692817"/>
+ <cml:atom cml:elementType="C" cml:id="a3" cml:formalCharge="0" cml:x3="-1.92163762747" cml:y3="-1.98241261328" cml:z3="-0.206572876019"/>
+ <cml:atom cml:elementType="C" cml:id="a4" cml:formalCharge="0" cml:x3="-2.92693672032" cml:y3="-2.98225012861" cml:z3="0.367318952425"/>
+ <cml:atom cml:elementType="O" cml:id="a5" cml:formalCharge="0" cml:x3="-4.208010389" cml:y3="-2.9017666367" cml:z3="-0.248445606999"/>
+ <cml:atom cml:elementType="H" cml:id="a6" cml:formalCharge="0" cml:x3="0.655827908609" cml:y3="-1.26752859656" cml:z3="-1.14312376632"/>
+ <cml:atom cml:elementType="H" cml:id="a7" cml:formalCharge="0" cml:x3="0.0848553777946" cml:y3="-0.00239243828223" cml:z3="-0.0456709489122"/>
+ <cml:atom cml:elementType="H" cml:id="a8" cml:formalCharge="0" cml:x3="1.40666917559" cml:y3="-1.07214682201" cml:z3="0.448356319391"/>
+ <cml:atom cml:elementType="H" cml:id="a9" cml:formalCharge="0" cml:x3="-0.154987987004" cml:y3="-3.03150093117" cml:z3="0.472873914607"/>
+ </cml:atomArray>
+ <cml:bondArray>
+ <cml:bond cml:atomRefs2="a1 a2" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a1 a6" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a1 a7" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a1 a8" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a2 a10" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a2 a3" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a2 a9" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a3 a11" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a3 a12" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a3 a4" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a4 a13" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a4 a14" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a4 a5" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a5 a15" cml:order="1"/>
+ </cml:bondArray>
+ </cml:molecule>
+ <ssip:SurfaceInformation>
+ <ssip:Surfaces>
+ <ssip:Surface>
+ <ssip:TotalSurfaceArea ssip:unit="Ã…^2">122.2095781704891</ssip:TotalSurfaceArea>
+ <ssip:NegativeSurfaceArea ssip:unit="Ã…^2">20.900319182402814</ssip:NegativeSurfaceArea>
+ <ssip:PositiveSurfaceArea ssip:unit="Ã…^2">101.30925898808572</ssip:PositiveSurfaceArea>
+ <ssip:ElectronDensityIsosurface ssip:unit="e bohr^-3">0.002</ssip:ElectronDensityIsosurface>
+ <ssip:NumberOFMEPSPoints>9580</ssip:NumberOFMEPSPoints>
+ <ssip:VdWVolume ssip:unit="Ã…^3">99.3920085615431</ssip:VdWVolume>
+ <ssip:ElectrostaticPotentialMax ssip:unit="kJ mol^-1">213.86532254634</ssip:ElectrostaticPotentialMax>
+ <ssip:ElectrostaticPotentialMin ssip:unit="kJ mol^-1">-172.51370353134</ssip:ElectrostaticPotentialMin>
+ </ssip:Surface>
+ </ssip:Surfaces>
+ </ssip:SurfaceInformation>
+ <phase:SSIPs phase:units="MOLAR"><phase:SSIP ssip:value="2.784040024744081" ssip:nearestAtomID="a15" cml:x3="-3.8161781356582187" cml:y3="-3.342557618498982" cml:z3="-2.192649106294994" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.773639545237379" ssip:nearestAtomID="a12" cml:x3="-2.239105576984704" cml:y3="-3.099174713898159" cml:z3="-2.0252301249653697" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.5071846345423165" ssip:nearestAtomID="a13" cml:x3="-2.8499750929763277" cml:y3="-4.524230524251444" cml:z3="-0.8462517897648159" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.4784372492163057" ssip:nearestAtomID="a6" cml:x3="0.9270005337214728" cml:y3="-1.649107340870889" cml:z3="-2.251805301783455" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.46383776537503163" ssip:nearestAtomID="a9" cml:x3="0.136470579099108" cml:y3="-4.205322913496092" cml:z3="0.352187567944962" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.4557099985213939" ssip:nearestAtomID="a8" cml:x3="2.420223369759191" cml:y3="-1.188501408973558" cml:z3="1.0796321860050409" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.4355872186992693" ssip:nearestAtomID="a7" cml:x3="-0.30271267022695597" cml:y3="1.1313523827905538" cml:z3="0.031343697635518995" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.43429343831228867" ssip:nearestAtomID="a14" cml:x3="-2.937811637006091" cml:y3="-2.45801773806002" cml:z3="2.5781764284587028" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.33435822085360595" ssip:nearestAtomID="a11" cml:x3="-2.5158938537831497" cml:y3="0.207568717565752" cml:z3="0.059691722864448994" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.0" ssip:nearestAtomID="a3" cml:x3="-1.4487933333328935" cml:y3="-2.074966666667215" cml:z3="0.05005333333293337" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="0.0" ssip:nearestAtomID="a3" cml:x3="-1.4487933333328935" cml:y3="-2.074966666667215" cml:z3="0.05005333333293337" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="-5.3386085001748205" ssip:nearestAtomID="a5" cml:x3="-5.4850745889327115" cml:y3="-3.640825199834338" cml:z3="0.48092898414517593" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="-5.365217010700665" ssip:nearestAtomID="a5" cml:x3="-5.353424285394745" cml:y3="-1.7849561367024218" cml:z3="0.11271581239149799" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">10.870210</phase:TotalConcentration></phase:SSIP></phase:SSIPs></phase:Molecule>
+ <phase:Molecule phase:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phase:moleculeID="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phase:moleFraction="0.8355"><cml:molecule ssip:stdInChIKey="XLYOFNOQVPJJNP-UHFFFAOYSA-N" cml:id="XLYOFNOQVPJJNP-UHFFFAOYSA-N">
+ <cml:atomArray>
+ <cml:atom cml:elementType="O" cml:id="a1" cml:formalCharge="0" cml:x3="-0.197781963496" cml:y3="-7.5088692891E-35" cml:z3="0.34665983175"/>
+ <cml:atom cml:elementType="H" cml:id="a2" cml:formalCharge="0" cml:x3="0.760536914227" cml:y3="-9.28739754019E-37" cml:z3="0.204548524786"/>
+ <cml:atom cml:elementType="H" cml:id="a3" cml:formalCharge="0" cml:x3="-0.56175495073" cml:y3="5.1742035555E-35" cml:z3="-0.551208356536"/>
+ </cml:atomArray>
+ <cml:bondArray>
+ <cml:bond cml:atomRefs2="a1 a2" cml:order="1"/>
+ <cml:bond cml:atomRefs2="a1 a3" cml:order="1"/>
+ </cml:bondArray>
+ </cml:molecule>
+ <ssip:SurfaceInformation>
+ <ssip:Surfaces>
+ <ssip:Surface>
+ <ssip:TotalSurfaceArea ssip:unit="Ã…^2">37.46449353147367</ssip:TotalSurfaceArea>
+ <ssip:NegativeSurfaceArea ssip:unit="Ã…^2">18.417074471275452</ssip:NegativeSurfaceArea>
+ <ssip:PositiveSurfaceArea ssip:unit="Ã…^2">19.047419060197754</ssip:PositiveSurfaceArea>
+ <ssip:ElectronDensityIsosurface ssip:unit="e bohr^-3">0.002</ssip:ElectronDensityIsosurface>
+ <ssip:NumberOFMEPSPoints>2267</ssip:NumberOFMEPSPoints>
+ <ssip:VdWVolume ssip:unit="Ã…^3">21.118225673870302</ssip:VdWVolume>
+ <ssip:ElectrostaticPotentialMax ssip:unit="kJ mol^-1">222.31155482388002</ssip:ElectrostaticPotentialMax>
+ <ssip:ElectrostaticPotentialMin ssip:unit="kJ mol^-1">-185.78297861082</ssip:ElectrostaticPotentialMin>
+ </ssip:Surface>
+ </ssip:Surfaces>
+ </ssip:SurfaceInformation>
+ <phase:SSIPs phase:units="MOLAR"><phase:SSIP ssip:value="2.8" ssip:nearestAtomID="a2" cml:x3="1.7703677783019898" cml:y3="-0.037716579245226" cml:z3="-0.12404973071057998" phase:moleculeID="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.349612</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="2.8" ssip:nearestAtomID="a3" cml:x3="-0.78007076629588" cml:y3="-0.131868324564555" cml:z3="-1.585252051411308" phase:moleculeID="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.349612</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="-4.5" ssip:nearestAtomID="a1" cml:x3="-0.78007076629588" cml:y3="-1.185660785500926" cml:z3="1.34163366293468" phase:moleculeID="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.349612</phase:TotalConcentration></phase:SSIP><phase:SSIP ssip:value="-4.5" ssip:nearestAtomID="a1" cml:x3="-0.9035034763341259" cml:y3="0.8351649972210169" cml:z3="1.5735514132586688" phase:moleculeID="XLYOFNOQVPJJNP-UHFFFAOYSA-N" phase:units="MOLAR"><phase:TotalConcentration phase:units="MOLAR">55.349612</phase:TotalConcentration></phase:SSIP></phase:SSIPs></phase:Molecule>
+ </phase:Molecules>
+ <phase:Temperature phase:units="KELVIN">298.000</phase:Temperature>
+ </phase:Phase>
+ </phase:Phases>
+ </phase:Mixture>
+ </phase:Mixtures>
+</phase:MixtureCollection>
diff --git a/phasecalculator/test/resources/expected_solvent.xml b/phasecalculator/test/resources/expected_solvent.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3bdad337eb003bd686c5266c9a80c65c10a3376e
--- /dev/null
+++ b/phasecalculator/test/resources/expected_solvent.xml
@@ -0,0 +1,85 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<phase:SolventList xmlns:phase="http://www-hunter.ch.cam.ac.uk/PhaseSchema" xmlns:ssip="http://www-hunter.ch.cam.ac.uk/SSIP" xmlns:cml="http://www.xml-cml.org/schema">
+ <phase:Solvents>
+ <phase:Solvent phase:solventID="1-butanol0.165water0.835" phase:solventName="1-butanol0.165water0.835" phase:units="MOLAR">
+ <phase:Molecules>
+ <phase:Molecule phase:stdInChIKey="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:moleculeID="LRHPLDYGYMQRHN-UHFFFAOYSA-N" phase:moleFraction="0.1645"><cml:molecule ssip:stdInChIKey="LRHPLDYGYMQRHN-UHFFFAOYSA-N" cml:id="LRHPLDYGYMQRHN-UHFFFAOYSA-N">
+ <cml:atomArray>
+ <cml:atom cml:elementType="C" cml:id="a1" cml:formalCharge="0" cml:x3="0.453161473082" cml:y3="-1.03446801266" cml:z3="-0.0905306598548"/>
+ <cml:atom cml:elementType="H" cml:id="a10" cml:formalCharge="0" cml:x3="-0.711314642651" cml:y3="-1.77936986861" cml:z3="1.57182493824"/>
+ <cml:atom cml:elementType="H" cml:id="a11" cml:formalCharge="0" cml:x3="-2.35918900768" cml:y3="-0.976902587046" cml:z3="-0.14772459368"/>
+ <cml:atom cml:elementType="H" cml:id="a12" cml:formalCharge="0" cml:x3="-1.77474726333" cml:y3="-2.19616982792" cml:z3="-1.27745306344"/>
+ <cml:atom cml:elementType="H" cml:id="a13" cml:formalCharge="0" cml:x3="-2.519145554" cml:y3="-4.00559237167" cml:z3="0.302707946329"/>
+ <cml:atom cml:elementType="H" cml:id="a14" cml:formalCharge="0" cml:x3="-3.10209800172" cml:y3="-2.77368664521" cml:z3="1.42866821719"/>
+ <cml:atom cml:elementType="H" cml:id="a15" cml:formalCharge="0" cml:x3="-4.0901443513" cml:y3="-3.10664597908" cml:z3="-1.18904146578"/>
+ <cml:atom cml:elementType="C" cml:id="a2" cml:formalCharge="0" cml:x3="-0.564202390594" cml:y3="-2.0116665412" cml:z3="0.507612692817"/>
+ <cml:atom cml:elementType="C" cml:id="a3" cml:formalCharge="0" cml:x3="-1.92163762747" cml:y3="-1.98241261328" cml:z3="-0.206572876019"/>
+ <cml:atom cml:elementType="C" cml:id="a4" cml:formalCharge="0" cml:x3="-2.92693672032" cml:y3="-2.98225012861" cml:z3="0.367318952425"/>
+ <cml:atom cml:elementType="O" cml:id="a5" cml:formalCharge="0" cml:x3="-4.208010389" cml:y3="-2.9017666367" cml:z3="-0.248445606999"/>
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