Fixes Tests Implementations

.gitignore

@@ -1,3 +1,5 @@
 *.pyc
 
 .idea/
+
+simfiles

config.example.yml

@@ -1,8 +1,8 @@
 crystal_pol:
-    mem: 42
+    mem: 28
     n_procs: 20
     level: "b3lyp/aug-cc-pVDZ"
     pop: "chelpg"
     mult: [0, 1]
     n_atoms: 18
-    comment: "DC-MBI UAEnvolvida"
+    comment: "Crystal"

crystal.example.gjf

@@ -1,5 +1,5 @@
-%mem=42GB
+%mem=30GB
-%Nprocs=20
+%Nprocs=24
 #p ${LEVEL} POP=${POP} density=current NoSymm (CHARGE - A partir do segundo)
 
 ${COMMENTARY} passo 1

crystalpol/gaussian.py

@@ -3,7 +3,7 @@ from crystalpol.shared.system.crystal import Crystal
 from crystalpol.shared.config import Config
 
 from pathlib import Path, PosixPath
-from typing import TextIO
+from typing import TextIO, Union
 import subprocess
 import textwrap
 import shutil
@@ -25,8 +25,14 @@ class Gaussian:
 
     def run(self, cycle: int, crystal: Crystal) -> None:
 
-        file = Path("simfiles", f"crystal-{str(cycle).zfill(2)}.gjf")
+        self.create_simulation_dir()
 
+        file = Path(
+            "simfiles",
+            f"crystal-{str(cycle).zfill(2)}",
+            f"crystal-{str(cycle).zfill(2)}.gjf"
+        )
+        self.create_step_dir(cycle)
         self.make_gaussian_input(cycle, file, crystal)
 
         if shutil.which("bash") is not None:
@@ -35,7 +41,7 @@ class Gaussian:
                     "bash",
                     "-c",
                     "exec -a {}-step{} {} {}".format(
-                        self.qmprog, cycle, self.qmprog, file.name
+                        self.qmprog, cycle, self.qmprog, str(file)
                     ),
                 ]
             )
@@ -47,6 +53,19 @@ class Gaussian:
 
         return self.read_charges_from_gaussian_output()
 
+    def create_step_dir(self, cycle):
+        step_dir = Path(
+            "simfiles",
+            f"crystal-{str(cycle).zfill(2)}"
+        )
+        if not os.path.exists(step_dir):
+            os.makedirs(step_dir)
+        else:
+            raise RuntimeError(
+                f"Step directory '{str(step_dir)}' already exists. "
+                f"Please remove it before proceeding."
+            )
+
     def create_simulation_dir(self):
         if not os.path.exists(self.config.simulation_dir):
             os.makedirs(self.config.simulation_dir)
@@ -56,17 +75,17 @@ class Gaussian:
                 f"Please remove it before proceeding."
             )
 
-    def make_gaussian_input(self, cycle: int, file: PosixPath, crystal: Crystal) -> str:
+    def make_gaussian_input(self, cycle: int, file: Union[PosixPath, Path], crystal: Crystal) -> str:
 
         with open(file, 'w+') as fh:
 
-            fh.write(f"%Mem={self.config.mem}MB\n")
+            fh.write(f"%Mem={self.config.mem}Gb\n")
 
             fh.write(f"%Nprocs={self.config.n_procs}\n")
 
             kwords_line = f"#P {self.config.level} " \
-                          f"Pop = {self.config.pop} " \
+                          f"Pop={self.config.pop} " \
-                          f"Density = Current " \
+                          f"Density=Current " \
                           f"NoSymm "
 
             if cycle > 1:
@@ -77,17 +96,19 @@ class Gaussian:
 
             fh.write(f"\n{self.config.comment} - Cycle number {cycle}\n")
             fh.write("\n")
-            fh.write(f"{self.config.mult[0]}, {self.config.mult[1]}\n")
+            fh.write(f"{self.config.mult[0]} {self.config.mult[1]}\n")
 
             for atom in crystal[0][0]:
                 symbol = atom_symbol[atom.na]
                 fh.write(
                     f"{symbol:<2s}    "
-                    f"{atom.rx:>10.5f}   "
+                    f"{float(atom.rx):>10.5f}    "
-                    f"{atom.ry:>10.5f}   "
+                    f"{float(atom.ry):>10.5f}    "
-                    f"{atom.rz:>10.5f}\n"
+                    f"{float(atom.rz):>10.5f}\n"
                 )
 
+            fh.write("\n")
+
             if cycle > 1:
                 self.make_gaussian_charges(fh, crystal)
 
@@ -96,8 +117,6 @@ class Gaussian:
 
     def make_gaussian_charges(self, fh: TextIO, crystal: Crystal) -> None:
 
-        fh.write("\n")
-
         for index_cell, cell in enumerate(crystal):
             for index_mol, molecule in enumerate(cell):
                 if (index_cell == 0 and index_mol != 0) or (index_cell != 0):
@@ -105,10 +124,12 @@ class Gaussian:
                         symbol = atom_symbol[atom.na]
                         fh.write(
                             f"{symbol:<2s}    "
-                            f"{atom.rx:>10.5f}   "
+                            f"{float(atom.rx):>10.5f}    "
-                            f"{atom.ry:>10.5f}   "
+                            f"{float(atom.ry):>10.5f}    "
-                            f"{atom.rz:>10.5f}\n"
+                            f"{float(atom.rz):>10.5f}\n"
                         )
 
+        fh.write("\n")
+
     def read_charges_from_gaussian_output(self) -> None:
-        pass
+        pass

tests/shared/test_gaussian.py

@@ -4,6 +4,7 @@ from crystalpol.shared.system.atom import Atom
 from crystalpol.shared.config import Config
 from crystalpol.gaussian import Gaussian
 
+from pathlib import Path
 from io import StringIO
 
 from unittest import mock, TestCase
@@ -38,6 +39,7 @@ class TestGaussian(TestCase):
     @mock.patch('crystalpol.gaussian.os')
     def test_create_simulation_dir(self, os_mock):
         os_mock.path.exists.return_value = False
+        os_mock.makedirs = mock.MagicMock()
 
         gaussian = Gaussian(
             Config(
@@ -53,6 +55,7 @@ class TestGaussian(TestCase):
     @mock.patch('crystalpol.gaussian.os')
     def test_create_simulation_dir_raises_exception(self, os_mock):
         os_mock.path.exists.return_value = True
+        os_mock.makedirs = mock.MagicMock()
         gaussian = Gaussian(
             Config(
                 mem=1,
@@ -64,6 +67,7 @@ class TestGaussian(TestCase):
         with self.assertRaises(RuntimeError):
             gaussian.create_simulation_dir()
 
+    # @mock.patch('crystalpol.gaussian.os')
     @mock.patch('crystalpol.gaussian.open')
     def test_make_gaussian_input_cycle_1(self, open_mock):
 
@@ -78,16 +82,17 @@ class TestGaussian(TestCase):
                 n_atoms=10
             )
         )
-        gaussian_input = gaussian.make_gaussian_input(1, crystal)
+        gaussian_input = gaussian.make_gaussian_input(1, Path(), crystal)
         expected_output = """\
-%Mem=1MB
+%Mem=1Gb
 %Nprocs=1
-#P b3lyp/aug-cc-pVDZ Pop = chelpg Density = Current NoSymm
+#P b3lyp/aug-cc-pVDZ Pop=chelpg Density=Current NoSymm
 
 crystalpol - Cycle number 1
 
-0, 1
+0 1
-H        0.00000      0.00000      0.00000
+H        0.00000       0.00000       0.00000
+
 """
         self.assertEqual(gaussian_input, expected_output)
 
@@ -107,16 +112,17 @@ H        0.00000      0.00000      0.00000
         )
         gaussian_input = gaussian.make_gaussian_input(2, "test", crystal)
         expected_output = """\
-%Mem=1MB
+%Mem=1Gb
 %Nprocs=1
-#P b3lyp/aug-cc-pVDZ Pop = chelpg Density = Current NoSymm charge
+#P b3lyp/aug-cc-pVDZ Pop=chelpg Density=Current NoSymm charge
 
 crystalpol - Cycle number 2
 
-0, 1
+0 1
-H        0.00000      0.00000      0.00000
+H        0.00000       0.00000       0.00000
+
+H        0.00000       0.00000       0.00000
 
-H        0.00000      0.00000      0.00000
 """
         self.assertEqual(gaussian_input, expected_output)
 
@@ -136,13 +142,15 @@ H        0.00000      0.00000      0.00000
         file.seek(0)
 
         charges_string = file.read()
-        expected_charges = '\nH        0.00000      0.00000      0.00000\n'
+        expected_charges = 'H        0.00000       0.00000       0.00000\n\n'
 
         self.assertEqual(charges_string, expected_charges)
 
+    @mock.patch('crystalpol.gaussian.os')
     @mock.patch('crystalpol.gaussian.subprocess.call', autospec=True, return_value=0)
     @mock.patch('crystalpol.gaussian.Gaussian.make_gaussian_input')
-    def test_run(self, subprocess_call_mock, make_gaussian_input_mock):
+    def test_run(self, make_gaussian_input_mock, subprocess_call_mock, os_mock):
+        os_mock.path.exists.return_value = False
 
         gaussian = Gaussian(
             Config(
@@ -155,9 +163,11 @@ H        0.00000      0.00000      0.00000
 
         self.assertTrue(subprocess_call_mock.called)
 
+    @mock.patch('crystalpol.gaussian.os')
     @mock.patch('crystalpol.gaussian.subprocess.call', autospec=True, return_value=1)
     @mock.patch('crystalpol.gaussian.Gaussian.make_gaussian_input')
-    def test_run_raises_exception(self, subprocess_call_mock, make_gaussian_input_mock):
+    def test_run_raises_exception(self, subprocess_call_mock, make_gaussian_input_mock, os_mock):
+        os_mock.path.exists.return_value = False
 
         gaussian = Gaussian(
             Config(

tests/test_polarization.py

@@ -6,7 +6,6 @@ from crystalpol.shared.system.molecule import Molecule
 from unittest import TestCase, mock
 import unittest
 
-
 GEOM_DATA = """\
     Cl      0.529511   -1.626652    1.247344
     N       3.703161    2.470259    1.679277
@@ -85,9 +84,12 @@ class TestPolarization(TestCase):
         self.assertEqual(len(pol.crystal), 2)
         self.assertEqual(len(pol.crystal[0]), 1)
 
-
     @mock.patch('builtins.open', mock.mock_open(read_data=GEOM_DATA))
-    def test_run(self):
+    @mock.patch('crystalpol.gaussian.subprocess.call', autospec=True, return_value=0)
+    @mock.patch('crystalpol.gaussian.os')
+    def test_run(self, os_mock, subprocess_call_mock):
+        os_mock.path.exists.return_value = False
+
         pol = Polarization("geom_file", "outfile", self.config)
 
         pol.run()