Add Pseudo Unit Test for SO2

src/FCIdump/README.rst

@@ -10,6 +10,9 @@ Documentation
 .. Do not edit this section. It was auto-generated from the
 .. NEEDED_MODULES file.
 
+`fcidump <http://github.com/LCPQ/quantum_package/tree/master/src/FCIdump/fcidump.irp.f#L1>`_
+  Undocumented
+
 
 
 Needed Modules

tests/SO2.xyz

@@ -0,0 +1,5 @@
+3
+SO2 Geo: Experiment Mult: 1 symmetry: 32
+O    0.0    1.2371    0.7215
+O    0.0   -1.2371    0.7215
+S    0.0    0.0       0.0

tests/unit_test/unit_test.py

@@ -12,6 +12,9 @@ sys.path = [EZFIO + "/Python"] + sys.path
 
 from ezfio import ezfio
 from collections import defaultdict
+from collections import namedtuple
+
+Energy = namedtuple('Energy', ['without_pseudo', 'with_pseudo'])
 
 # ~#~#~ #
 # O p t #
@@ -34,7 +37,7 @@ has_hf_alredy = False
 global filename_check
 
 
-def init_folder(geo, basis, mult=1, ezfio_name=None):
+def init_folder(geo, basis, mult=1, pseudo=False, ezfio_name=None):
     '''
     Take a geo in arg (aka a existing geo.xyz in test/)
     And create the geo.ezfio with the adeguate basis and multipliciti
@@ -47,15 +50,21 @@ def init_folder(geo, basis, mult=1, ezfio_name=None):
     if not ezfio_name:
         ezfio_name = geo
 
-    cmd = "qp_create_ezfio_from_xyz -b {0} -m {1} {2}.xyz -o {3}.ezfio"
+    if pseudo:
+        cmd = "qp_create_ezfio_from_xyz -b {0} -m {1} {2}.xyz -p -o {3}.ezfio"
+    else:
+        cmd = "qp_create_ezfio_from_xyz -b {0} -m {1} {2}.xyz -o {3}.ezfio"
+
     subprocess.check_call([cmd.format(basis, mult, geo, ezfio_name)],
                           shell=True)
 
+    subprocess.call(["rm {0}.xyz".format(geo)], shell=True)
+
 
 def get_error_message(l_exepected, l_cur):
     l_msg = ["Need {0} get {1} error is {2}".format(i, j, abs(i - j))
              for i, j in zip(l_exepected, l_cur)]
-    return "\n".join(l_msg)
+    return "\n" + "\n".join(l_msg)
 
 
 #  _
@@ -146,18 +155,20 @@ def check_mo_guess(geo, basis, mult=1):
 # /  |_   _   _ |        _. |      _   _
 # \_ | | (/_ (_ |<   \/ (_| | |_| (/_ _>
 #
-def run_hf(geo, basis, mult=1):
+def run_hf(geo, basis, mult=1, pseudo=False, remove_after_sucess=True):
     """
     Run a simle by default hf
     EZFIO path = geo.ezfio
     """
+
     # ~#~#~#~#~#~#~#~#~#~ #
     # R e f _ e n e r g y #
     # ~#~#~#~#~#~#~#~#~#~ #
 
-    ref_energy = defaultdict(dict)
+    ref_energy = defaultdict(defaultdict)
 
-    ref_energy["sto-3g"]["methane"] = -39.7267433402
+    ref_energy["sto-3g"]["methane"] = Energy(-39.7267433402, None)
+    ref_energy["vdz"]["SO2"] = Energy(None, -41.48912297776174)
 
     # ~#~#~#~#~#~#~#~#~#~#~#~#~#~#~ #
     # G l o b a l _ v a r i a b l e #
@@ -170,7 +181,7 @@ def run_hf(geo, basis, mult=1):
     # I n i t #
     # ~#~#~#~ #
 
-    init_folder(geo, basis, mult)
+    init_folder(geo, basis, mult, pseudo)
     ezfio.set_file("{0}.ezfio".format(geo))
 
     # ~#~#~#~#~#~#~#~#~#~#~#~#~ #
@@ -187,7 +198,7 @@ def run_hf(geo, basis, mult=1):
     ezfio.hartree_fock_thresh_scf = 1.e-10
     ezfio.hartree_fock_n_it_scf_max = 100
 
-    ezfio.pseudo_integrals_do_pseudo = False
+    ezfio.pseudo_integrals_do_pseudo = pseudo
 
     # ~#~#~ #
     # R u n #
@@ -201,15 +212,25 @@ def run_hf(geo, basis, mult=1):
     # ~#~#~#~#~ #
 
     cur_e = ezfio.get_hartree_fock_energy()
+
     ref_e = ref_energy[basis][geo]
+    if pseudo:
+        ref_e = ref_e.with_pseudo
+    else:
+        ref_e = ref_e.without_pseudo
 
     if abs(cur_e - ref_e) <= precision:
+
+        if remove_after_sucess:
+            subprocess.call(["rm -R {0}.ezfio".format(geo)], shell=True)
+
         return True
+
     else:
         raise ValueError(get_error_message([ref_e], [cur_e]))
 
 
-def run_full_ci_10k_pt2_end(geo, basis):
+def run_full_ci_10k_pt2_end(geo, basis, pseudo):
     """
     Run a Full_ci with 10k with the TruePT2
     EZFIO path = geo.ezfio
@@ -222,8 +243,8 @@ def run_full_ci_10k_pt2_end(geo, basis):
     ref_energy_var = defaultdict(dict)
     ref_energy_pt2 = defaultdict(dict)
 
-    ref_energy_var["sto-3g"]["methane"] = -0.398058753535695E+02
+    ref_energy_var["sto-3g"]["methane"] = Energy(-0.398058753535695E+02, None)
-    ref_energy_pt2["sto-3g"]["methane"] = -0.398059182483741E+02
+    ref_energy_pt2["sto-3g"]["methane"] = Energy(-0.398059182483741E+02, None)
 
     # ~#~#~#~ #
     # I n i t #
@@ -256,6 +277,13 @@ def run_full_ci_10k_pt2_end(geo, basis):
     ref_var = ref_energy_var[basis][geo]
     ref_pt2 = ref_energy_pt2[basis][geo]
 
+    if pseudo:
+        ref_var = ref_var.with_pseudo
+        ref_pt2 = ref_pt2.with_pseudo
+    else:
+        ref_var = ref_var.without_pseudo
+        ref_pt2 = ref_pt2.without_pseudo
+
     t = [abs(cur_var - ref_var) <= precision,
          abs(cur_pt2 - ref_pt2) <= precision]
 
@@ -266,15 +294,16 @@ def run_full_ci_10k_pt2_end(geo, basis):
                                            [cur_var, cur_pt2]))
 
 
-def hf_then_10k_test(geo, basis):
+def hf_then_10k_test(geo, basis, mult=1, pseudo=False):
-    if not has_hf_alredy:
+
-        run_hf(geo, basis)
+    run_hf(geo, basis, mult, pseudo, remove_after_sucess=False)
 
     try:
-        run_full_ci_10k_pt2_end(geo, basis)
+        run_full_ci_10k_pt2_end(geo, basis, pseudo)
-        return_code = True
     except:
-        return_code = False
+        raise
+    else:
+        return_code = True
 
     # ~#~#~#~#~#~#~#~ #
     # F i n a l i z e #
@@ -335,15 +364,27 @@ def check_convert(path_out):
     else:
         raise ValueError(get_error_message([ref_e], [cur_e]))
 
+
 # ___
 #  |  _   _ _|_
 #  | (/_ _>  |_
 #
 class ValueTest(unittest.TestCase):
 
-    def test_full_ci_10k_pt2_end(self):
+    def test_hf_then_full_ci_10k_pt2_end(self):
-        self.assertTrue(hf_then_10k_test("methane", "sto-3g"))
+        self.assertTrue(hf_then_10k_test(geo="methane",
+                                         basis="sto-3g",
+                                         mult=1,
+                                         pseudo=False))
 
+    def test_hf(self):
+        self.assertTrue(run_hf(geo="SO2",
+                               basis="vdz",
+                               mult=1,
+                               pseudo=True))
+
+
+class ConvertTest(unittest.TestCase):
     def test_check_convert_hf_energy(self):
         self.assertTrue(check_convert("HBO.out"))
 
@@ -351,11 +392,12 @@ class ValueTest(unittest.TestCase):
 class InputTest(unittest.TestCase):
 
     def test_check_disk_acess(self):
-        self.assertTrue(check_disk_acess("methane", "un-ccemd-ref"))
+        self.assertTrue(check_disk_acess(geo="methane",
+                                         basis="un-ccemd-ref"))
 
     def test_check_mo_guess(self):
-        self.assertTrue(check_mo_guess("methane", "maug-cc-pVDZ"))
+        self.assertTrue(check_mo_guess(geo="methane",
-
+                                       basis="maug-cc-pVDZ"))
 
 if __name__ == '__main__':
     unittest.main()