v3.0.5

Author: SalvadorBrandolin

README.md

@@ -44,6 +44,7 @@ libraries:
 
 - [Clapeyron.jl](https://github.com/ClapeyronThermo/Clapeyron.jl)
 - [Thermo](https://github.com/CalebBell/thermo)
+- [yaeos (Fortran)](https://github.com/ipqa-research/yaeos)
 
 
 # Example of use
@@ -62,10 +63,12 @@ hexane = Groups("hexane")
 
 print(hexane.unifac.subgroups)
 print(hexane.psrk.subgroups)
+print(hexane.dortmund.subgroups)
 print(hexane.joback.subgroups)
 print(hexane.agani.primary.subgroups)
 ```
 
+    {'CH3': 2, 'CH2': 4}
     {'CH3': 2, 'CH2': 4}
     {'CH3': 2, 'CH2': 4}
     {'-CH3': 2, '-CH2-': 4}
@@ -78,12 +81,14 @@ propanol = Groups("CCCO", "smiles")
 
 print(propanol.unifac.subgroups)
 print(propanol.psrk.subgroups)
+print(propanol.dortmund.subgroups)
 print(propanol.joback.subgroups)
 print(propanol.agani.primary.subgroups)
 ```
 
     {'CH3': 1, 'CH2': 2, 'OH': 1}
     {'CH3': 1, 'CH2': 2, 'OH': 1}
+    {'CH3': 1, 'CH2': 2, 'OH (P)': 1}
     {'-CH3': 1, '-CH2-': 2, '-OH (alcohol)': 1}
     {'CH3': 1, 'CH2': 2, 'OH': 1}
 

docs/source/tutorial/writers.ipynb

@@ -160,6 +160,54 @@
     "\n",
     "GE.gammas()"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### yaeos (https://github.com/ipqa-research/yaeos)\n",
+    "\n",
+    "`ugropy` also provides a translator of its subgroups dictionaries to the\n",
+    "`yaeos` Fortran source code."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "use yaeos__models_ge_group_contribution_unifac, only: Groups\n",
+      "\n",
+      "type(Groups) :: molecules(3)\n",
+      "\n",
+      "molecules(1)%groups_ids = [1, 2]\n",
+      "molecules(1)%number_of_groups = [2, 4]\n",
+      "\n",
+      "molecules(2)%groups_ids = [1, 2, 14]\n",
+      "molecules(2)%number_of_groups = [1, 1, 1]\n",
+      "\n",
+      "molecules(3)%groups_ids = [1, 2, 3, 7, 8]\n",
+      "molecules(3)%number_of_groups = [2, 3, 1, 1, 1]\n",
+      "\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "from ugropy import Groups, unifac, writers\n",
+    "\n",
+    "names = [\"hexane\", \"ethanol\", \"limonene\"]\n",
+    "\n",
+    "grps = [Groups(n).unifac.subgroups for n in names]\n",
+    "\n",
+    "fortran_code = writers.to_yaeos(grps, unifac)\n",
+    "\n",
+    "print(fortran_code)"
+   ]
   }
  ],
  "metadata": {

pyproject.toml

@@ -35,7 +35,7 @@ markers = [
 
 [project]
 name = "ugropy"
-version = "3.0.0"
+version = "3.0.5"
 authors = [{name = "Brandolín, Salvador Eduardo", email = "[email protected]"}]
 license = {text = "The MIT License"}
 readme = "README.md"

tests/core/ilp_solvers/test_ilp_solver.py

@@ -0,0 +1,13 @@
+import pytest
+
+from ugropy import DefaultSolver
+
+
+def test_ilp_solver():
+    problem = DefaultSolver([], {})
+
+    with pytest.raises(NotImplementedError):
+        super(DefaultSolver, problem).solve_one_problem([])
+
+    with pytest.raises(NotImplementedError):
+        super(DefaultSolver, problem).solve()

tests/writers/test_to_clapeyron.py

@@ -243,7 +243,7 @@ def test_making_it_explode():
             molecules_names=["limonene", "ethanol"],
             psrk_groups=[{"CH3": 1, "CH2": 1, "OH": 1}],
         )
-        
+
     with pytest.raises(ValueError):
         to_clapeyron(
             molecules_names=["limonene", "ethanol"],

tests/writers/test_to_yaeos.py

@@ -0,0 +1,88 @@
+from ugropy import dortmund, psrk, unifac, writers
+
+
+def test_to_yaeos_dortmund():
+    names = ["ethane", "ethanol", "cyclohexane", "water"]
+
+    groups = [dortmund.get_groups(name).subgroups for name in names]
+
+    fortran_code = writers.to_yaeos(groups, dortmund)
+
+    expected = (
+        "use yaeos__models_ge_group_contribution_unifac, only: Groups\n"
+        "\n"
+        "type(Groups) :: molecules(4)\n"
+        "\n"
+        "molecules(1)%groups_ids = [1]\n"
+        "molecules(1)%number_of_groups = [2]\n"
+        "\n"
+        "molecules(2)%groups_ids = [1, 2, 14]\n"
+        "molecules(2)%number_of_groups = [1, 1, 1]\n"
+        "\n"
+        "molecules(3)%groups_ids = [78]\n"
+        "molecules(3)%number_of_groups = [6]\n"
+        "\n"
+        "molecules(4)%groups_ids = [16]\n"
+        "molecules(4)%number_of_groups = [1]\n"
+        "\n"
+    )
+
+    assert fortran_code == expected
+
+
+def test_to_yaeos_psrk():
+    names = ["ethane", "ethanol", "cyclohexane", "oxygen"]
+
+    groups = [psrk.get_groups(name).subgroups for name in names]
+
+    fortran_code = writers.to_yaeos(groups, psrk)
+
+    expected = (
+        "use yaeos__models_ge_group_contribution_unifac, only: Groups\n"
+        "\n"
+        "type(Groups) :: molecules(4)\n"
+        "\n"
+        "molecules(1)%groups_ids = [1]\n"
+        "molecules(1)%number_of_groups = [2]\n"
+        "\n"
+        "molecules(2)%groups_ids = [1, 2, 14]\n"
+        "molecules(2)%number_of_groups = [1, 1, 1]\n"
+        "\n"
+        "molecules(3)%groups_ids = [2]\n"
+        "molecules(3)%number_of_groups = [6]\n"
+        "\n"
+        "molecules(4)%groups_ids = [119]\n"
+        "molecules(4)%number_of_groups = [1]\n"
+        "\n"
+    )
+
+    assert fortran_code == expected
+
+
+def test_to_yaeos_unifac():
+    names = ["ethane", "ethanol", "toluene", "water"]
+
+    groups = [unifac.get_groups(name).subgroups for name in names]
+
+    fortran_code = writers.to_yaeos(groups, unifac)
+
+    expected = (
+        "use yaeos__models_ge_group_contribution_unifac, only: Groups\n"
+        "\n"
+        "type(Groups) :: molecules(4)\n"
+        "\n"
+        "molecules(1)%groups_ids = [1]\n"
+        "molecules(1)%number_of_groups = [2]\n"
+        "\n"
+        "molecules(2)%groups_ids = [1, 2, 14]\n"
+        "molecules(2)%number_of_groups = [1, 1, 1]\n"
+        "\n"
+        "molecules(3)%groups_ids = [9, 11]\n"
+        "molecules(3)%number_of_groups = [5, 1]\n"
+        "\n"
+        "molecules(4)%groups_ids = [16]\n"
+        "molecules(4)%number_of_groups = [1]\n"
+        "\n"
+    )
+
+    assert fortran_code == expected

ugropy/writers/clapeyron.py

@@ -63,7 +63,7 @@ def to_clapeyron(
             "PSRK groups list must have the same amount of elements than"
             "the molecules name list."
         )
-        
+
     if dortmund_groups and len(dortmund_groups) != len(molecules_names):
         raise ValueError(
             "Dortmund groups list must have the same amount of elements than"

ugropy/writers/yaeosf.py

@@ -23,7 +23,6 @@ def to_yaeos(mol_subgroups_list: List[dict], model: GibbsModel) -> str:
     str
         Yaeos Fortran source code.
     """
-
     n_mol = len(mol_subgroups_list)
 
     code = (