updated a bit

turbogenius/pyturbo/basis_set.py

@@ -117,6 +117,17 @@ def __init__(
         )
 
         if not all(check_flags):
+            logger.error(f'-------------they should be equal-------------')
+            logger.error(f'len(self.exponent) = {len(self.exponent)}')
+            logger.error(f'len(self.coefficient) = {len(self.coefficient)}')
+            logger.error(f'len(self.prim_factor) = {len(self.prim_factor)}')
+            logger.error(f'len(self.shell_index) = {len(self.shell_index)}')
+            logger.error(f'-------------they should be equal-------------')
+            logger.error(f'len(self.nucleus_index) = {len(self.nucleus_index)}')
+            logger.error(f'len(self.shell_ang_mom) = {len(self.shell_ang_mom)}')
+            logger.error(f'len(self.shell_ang_mom_turbo_notation) = {len(self.shell_ang_mom_turbo_notation)}')
+            logger.error(f'self.shell_ang_mom={self.shell_ang_mom}')
+            logger.error(f'self.shell_ang_mom_turbo_notation={self.shell_ang_mom_turbo_notation}')
             raise ValueError
 
     def __str__(self) -> str:

turbogenius/pyturbo/io_fort10.py

@@ -1637,6 +1637,8 @@ def mo_coefficient(self, new_mo_coefficient):
         # logger.debug(len(new_mo_coefficient))
         # logger.debug(len(self.__mo_coefficient))
         # logger.debug(new_mo_coefficient[0][-1])
+        logger.info(f'Replacing MO coeffs (real). num = {len(new_mo_coefficient)}')
+        logger.info(f'num total = {np.sum([len(mos) for mos in new_mo_coefficient])}')
         assert len(new_mo_coefficient) == len(self.__mo_coefficient)
         total_num_sed = len(new_mo_coefficient) * len(new_mo_coefficient[0])
         logger.debug(f"Total num sed = {total_num_sed}")
@@ -1657,6 +1659,8 @@ def mo_coefficient(self, new_mo_coefficient):
     @mo_coefficient_imag.setter
     def mo_coefficient_imag(self, new_mo_coefficient_imag):
         self.read()
+        logger.info(f'Replacing MO coeffs (imag). num = {len(new_mo_coefficient_imag)}')
+        logger.info(f'num total = {np.sum([len(mos) for mos in new_mo_coefficient_imag])}')
         # logger.debug(len(new_mo_coefficient))
         # logger.debug(len(self.__mo_coefficient_imag))
         # logger.debug(new_mo_coefficient[0][-1])
@@ -2002,7 +2006,7 @@ def read(self):
 
                 orb_type_chr = str(return_orb_type_chr(shell_ang_mom_turbo_notation.v))
 
-                if orb_type_chr in {"s", "p", "d", "f", "g", "h", "i"}:
+                if orb_type_chr in {"s", "s100", "s131", "p", "p103", "p150", "d", "f", "g", "h", "i"}:
                     contraction_flag = return_contraction_flag(
                         shell_ang_mom_turbo_notation.v
                     )
@@ -2027,6 +2031,10 @@ def read(self):
                     self.__shell_index.append(shell_index)
                     self.__exponent.append(Value())
                     self.__coefficient.append(Value())
+
+                else:
+                    raise NotImplementedError
+
 
                 p = p[4 + param_num.v :]
 

turbogenius/pyturbo/makefort10.py

@@ -101,10 +101,10 @@ def generate_input(self, input_name: str, basis_sets_unique_element: bool = True
             atomic_number = self.structure.atomic_numbers[num]
 
             if self.structure.has_celldm:
-                logger.warning("Cartesian coord.")
+                #logger.warning("Cartesian coord.")
                 x, y, z = self.structure.positions[num]
             else:
-                logger.warning("Fractional coord.")
+                #logger.warning("Fractional coord.")
                 x, y, z = self.structure.positions_frac[num]
 
             # we need this operation even if basis_sets_unique_element is True
@@ -543,7 +543,12 @@ def read_default_namelist(
 
         # twobody part
         for i in range(num_twobody):
-            namelist.set_parameter(f"twobodypar({i+1})", 0.5, "&electrons")
+            if jastrow_type == -15:
+                namelist.set_parameter(f"twobodypar({i+1})", 0.5, "&electrons")
+            elif jastrow_type == -6:
+                namelist.set_parameter(f"twobodypar({i+1})", 1.0, "&electrons")
+            else:
+                namelist.set_parameter(f"twobodypar({i+1})", 0.5, "&electrons")
         namelist.comment_out("twobodypar")
 
         # spin (i.e., neldiff)

turbogenius/pyturbo/pseudopotentials.py

@@ -91,7 +91,12 @@ def __init__(
         logger.debug(f"power={self.power}")
 
         # assertion!!
-        assert len(set(self.nucleus_index)) == len(self.max_ang_mom_plus_1)
+        if len(set(self.nucleus_index)) != len(self.max_ang_mom_plus_1):
+            logger.error(f"set(self.nucleus_index) = {set(self.nucleus_index)}")
+            logger.error(f"len(self.max_ang_mom_plus_1) = {len(self.max_ang_mom_plus_1)}")
+            logger.error(f"self.nucleus_index = {self.nucleus_index}")
+            logger.error(f"self.max_ang_mom_plus_1 = {self.max_ang_mom_plus_1}")
+            raise ValueError
         assert len(set(self.nucleus_index)) == len(self.z_core)
         assert len(set(self.nucleus_index)) == len(self.cutoff)
         assert len(self.ang_mom) == len(self.exponent)

turbogenius/pyturbo/utils/utility.py

@@ -54,7 +54,12 @@ def return_element_symbol(atomic_number):
 
 def return_atomic_number(element):
     element = str(element)
-    return Element(element).number
+    try:
+        E = Element(element)
+        number = E.number
+    except ValueError:
+        number = 0.0
+    return number
 
 
 def remove_file(file):

turbogenius/trexio_to_turborvb.py

@@ -311,6 +311,7 @@ def trexio_to_turborvb_wf(
 
     # Pseudopotentials
     if has_ecp:
+        logger.info(f"ecp_z_core={ecp_z_core}")
         cutoff = [0.0] * len(ecp_z_core)
         pseudopotentials = Pseudopotentials(
             max_ang_mom_plus_1=ecp_max_ang_mom_plus_1,