Modified build script to fix problems introduced in Juan's new CFML_F…

…lipR_Mod

bin/Linux/pycrysfml.py

@@ -421,6 +421,7 @@ def __init__(self):
         except: self.this = this
     __swig_destroy__ = _pycrysfml.delete_atom_list_type
     __del__ = lambda self : None;
+    def set_form_factors(self, *args): return _pycrysfml.atom_list_type_set_form_factors(self, *args)
     def get_atom_list_element(self, *args): return _pycrysfml.atom_list_type_get_atom_list_element(self, *args)
     def set_atom_list_element(self, *args): return _pycrysfml.atom_list_type_set_atom_list_element(self, *args)
     def get_atom_list_natoms(self): return _pycrysfml.atom_list_type_get_atom_list_natoms(self)
@@ -1426,8 +1427,8 @@ class FortFuncs(_object):
     if _newclass:write_restraints_obscalc = staticmethod(_pycrysfml.FortFuncs_write_restraints_obscalc)
     __swig_getmethods__["get_maxnumref"] = lambda x: _pycrysfml.FortFuncs_get_maxnumref
     if _newclass:get_maxnumref = staticmethod(_pycrysfml.FortFuncs_get_maxnumref)
-    __swig_getmethods__["hkl_lat_absent"] = lambda x: _pycrysfml.FortFuncs_hkl_lat_absent
-    if _newclass:hkl_lat_absent = staticmethod(_pycrysfml.FortFuncs_hkl_lat_absent)
+    __swig_getmethods__["mhkl_absent"] = lambda x: _pycrysfml.FortFuncs_mhkl_absent
+    if _newclass:mhkl_absent = staticmethod(_pycrysfml.FortFuncs_mhkl_absent)
     __swig_getmethods__["init_err_refl"] = lambda x: _pycrysfml.FortFuncs_init_err_refl
     if _newclass:init_err_refl = staticmethod(_pycrysfml.FortFuncs_init_err_refl)
     __swig_getmethods__["init_reflist"] = lambda x: _pycrysfml.FortFuncs_init_reflist
@@ -1518,6 +1519,10 @@ class FortFuncs(_object):
     if _newclass:z4frgn = staticmethod(_pycrysfml.FortFuncs_z4frgn)
     __swig_getmethods__["z4frz1"] = lambda x: _pycrysfml.FortFuncs_z4frz1
     if _newclass:z4frz1 = staticmethod(_pycrysfml.FortFuncs_z4frz1)
+    __swig_getmethods__["additional_scattering_factors"] = lambda x: _pycrysfml.FortFuncs_additional_scattering_factors
+    if _newclass:additional_scattering_factors = staticmethod(_pycrysfml.FortFuncs_additional_scattering_factors)
+    __swig_getmethods__["allocate_scattering_species"] = lambda x: _pycrysfml.FortFuncs_allocate_scattering_species
+    if _newclass:allocate_scattering_species = staticmethod(_pycrysfml.FortFuncs_allocate_scattering_species)
     __swig_getmethods__["calc_strfactor"] = lambda x: _pycrysfml.FortFuncs_calc_strfactor
     if _newclass:calc_strfactor = staticmethod(_pycrysfml.FortFuncs_calc_strfactor)
     __swig_getmethods__["calc_hkl_strfactor"] = lambda x: _pycrysfml.FortFuncs_calc_hkl_strfactor
@@ -1656,6 +1661,8 @@ class FortFuncs(_object):
     if _newclass:sym_prod_st = staticmethod(_pycrysfml.FortFuncs_sym_prod_st)
     __swig_getmethods__["write_bin_spacegroup"] = lambda x: _pycrysfml.FortFuncs_write_bin_spacegroup
     if _newclass:write_bin_spacegroup = staticmethod(_pycrysfml.FortFuncs_write_bin_spacegroup)
+    __swig_getmethods__["write_magnetic_space_group"] = lambda x: _pycrysfml.FortFuncs_write_magnetic_space_group
+    if _newclass:write_magnetic_space_group = staticmethod(_pycrysfml.FortFuncs_write_magnetic_space_group)
     __swig_getmethods__["write_spacegroup"] = lambda x: _pycrysfml.FortFuncs_write_spacegroup
     if _newclass:write_spacegroup = staticmethod(_pycrysfml.FortFuncs_write_spacegroup)
     __swig_getmethods__["write_sym"] = lambda x: _pycrysfml.FortFuncs_write_sym
@@ -2747,9 +2754,9 @@ def FortFuncs_get_maxnumref(*args):
   return _pycrysfml.FortFuncs_get_maxnumref(*args)
 FortFuncs_get_maxnumref = _pycrysfml.FortFuncs_get_maxnumref
 
-def FortFuncs_hkl_lat_absent(*args):
-  return _pycrysfml.FortFuncs_hkl_lat_absent(*args)
-FortFuncs_hkl_lat_absent = _pycrysfml.FortFuncs_hkl_lat_absent
+def FortFuncs_mhkl_absent(*args):
+  return _pycrysfml.FortFuncs_mhkl_absent(*args)
+FortFuncs_mhkl_absent = _pycrysfml.FortFuncs_mhkl_absent
 
 def FortFuncs_init_err_refl():
   return _pycrysfml.FortFuncs_init_err_refl()
@@ -2931,6 +2938,14 @@ def FortFuncs_z4frz1(*args):
   return _pycrysfml.FortFuncs_z4frz1(*args)
 FortFuncs_z4frz1 = _pycrysfml.FortFuncs_z4frz1
 
+def FortFuncs_additional_scattering_factors(*args):
+  return _pycrysfml.FortFuncs_additional_scattering_factors(*args)
+FortFuncs_additional_scattering_factors = _pycrysfml.FortFuncs_additional_scattering_factors
+
+def FortFuncs_allocate_scattering_species(*args):
+  return _pycrysfml.FortFuncs_allocate_scattering_species(*args)
+FortFuncs_allocate_scattering_species = _pycrysfml.FortFuncs_allocate_scattering_species
+
 def FortFuncs_calc_strfactor(*args):
   return _pycrysfml.FortFuncs_calc_strfactor(*args)
 FortFuncs_calc_strfactor = _pycrysfml.FortFuncs_calc_strfactor
@@ -3207,6 +3222,10 @@ def FortFuncs_write_bin_spacegroup(*args):
   return _pycrysfml.FortFuncs_write_bin_spacegroup(*args)
 FortFuncs_write_bin_spacegroup = _pycrysfml.FortFuncs_write_bin_spacegroup
 
+def FortFuncs_write_magnetic_space_group(*args):
+  return _pycrysfml.FortFuncs_write_magnetic_space_group(*args)
+FortFuncs_write_magnetic_space_group = _pycrysfml.FortFuncs_write_magnetic_space_group
+
 def FortFuncs_write_spacegroup(*args):
   return _pycrysfml.FortFuncs_write_spacegroup(*args)
 FortFuncs_write_spacegroup = _pycrysfml.FortFuncs_write_spacegroup
@@ -4663,6 +4682,24 @@ def __init__(self):
 sbvs_par_type_swigregister = _pycrysfml.sbvs_par_type_swigregister
 sbvs_par_type_swigregister(sbvs_par_type)
 
+class scattering_species_type(_object):
+    __swig_setmethods__ = {}
+    __setattr__ = lambda self, name, value: _swig_setattr(self, scattering_species_type, name, value)
+    __swig_getmethods__ = {}
+    __getattr__ = lambda self, name: _swig_getattr(self, scattering_species_type, name)
+    __repr__ = _swig_repr
+    def __init__(self): 
+        this = _pycrysfml.new_scattering_species_type()
+        try: self.this.append(this)
+        except: self.this = this
+    __swig_destroy__ = _pycrysfml.delete_scattering_species_type
+    __del__ = lambda self : None;
+    __swig_setmethods__["data_ptr"] = _pycrysfml.scattering_species_type_data_ptr_set
+    __swig_getmethods__["data_ptr"] = _pycrysfml.scattering_species_type_data_ptr_get
+    if _newclass:data_ptr = _swig_property(_pycrysfml.scattering_species_type_data_ptr_get, _pycrysfml.scattering_species_type_data_ptr_set)
+scattering_species_type_swigregister = _pycrysfml.scattering_species_type_swigregister
+scattering_species_type_swigregister(scattering_species_type)
+
 class space_group_type(_object):
     __swig_setmethods__ = {}
     __setattr__ = lambda self, name, value: _swig_setattr(self, space_group_type, name, value)

bin/help.txt

@@ -92,6 +92,7 @@ CLASSES
         reflection_list_type
         reflection_type
         sbvs_par_type
+        scattering_species_type
         space_group_type
         spgr_info_type
         sxd_val_type
@@ -316,6 +317,8 @@ CLASSES
      |  ----------------------------------------------------------------------
      |  Static methods defined here:
      |  
+     |  additional_scattering_factors = FortFuncs_additional_scattering_factors(...)
+     |  
      |  ag_theta = FortFuncs_ag_theta(...)
      |  
      |  al_theta = FortFuncs_al_theta(...)
@@ -340,6 +343,8 @@ CLASSES
      |  
      |  allocate_point_list = FortFuncs_allocate_point_list(...)
      |  
+     |  allocate_scattering_species = FortFuncs_allocate_scattering_species(...)
+     |  
      |  allocate_vparam = FortFuncs_allocate_vparam(...)
      |  
      |  angs_4c_bisecting = FortFuncs_angs_4c_bisecting(...)
@@ -642,8 +647,6 @@ CLASSES
      |  
      |  hk_equiv = FortFuncs_hk_equiv(...)
      |  
-     |  hkl_lat_absent = FortFuncs_hkl_lat_absent(...)
-     |  
      |  hklgen_sxtal_list = FortFuncs_hklgen_sxtal_list(...)
      |  
      |  hklgen_sxtal_reflection = FortFuncs_hklgen_sxtal_reflection(...)
@@ -756,6 +759,8 @@ CLASSES
      |  
      |  matrix_inverse = FortFuncs_matrix_inverse(...)
      |  
+     |  mhkl_absent = FortFuncs_mhkl_absent(...)
+     |  
      |  molcrys_to_atomlist = FortFuncs_molcrys_to_atomlist(...)
      |  
      |  molec_to_atomlist = FortFuncs_molec_to_atomlist(...)
@@ -1080,6 +1085,8 @@ CLASSES
      |  
      |  write_mag_structure_factors = FortFuncs_write_mag_structure_factors(...)
      |  
+     |  write_magnetic_space_group = FortFuncs_write_magnetic_space_group(...)
+     |  
      |  write_magnetic_structure = FortFuncs_write_magnetic_structure(...)
      |  
      |  write_mcif = FortFuncs_write_mcif(...)
@@ -1163,7 +1170,7 @@ CLASSES
      |  __swig_destroy__ = <built-in function delete_FortFuncs>
      |  
      |  
-     |  __swig_getmethods__ = {'ag_theta': <function <lambda>>, 'al_theta': <f...
+     |  __swig_getmethods__ = {'additional_scattering_factors': <function <lam...
      |  
      |  __swig_setmethods__ = {}
 
@@ -1502,6 +1509,8 @@ CLASSES
      |  
      |  set_atom_list_natoms(self, *args)
      |  
+     |  set_form_factors(self, *args)
+     |  
      |  ----------------------------------------------------------------------
      |  Data descriptors defined here:
      |  
@@ -5002,6 +5011,40 @@ CLASSES
      |  
      |  __swig_setmethods__ = {'data_ptr': <built-in function sbvs_par_type_da...
 
+    class scattering_species_type(__builtin__.object)
+     |  Methods defined here:
+     |  
+     |  __del__ lambda self
+     |  
+     |  __getattr__ lambda self, name
+     |  
+     |  __init__(self)
+     |  
+     |  __repr__ = _swig_repr(self)
+     |  
+     |  __setattr__ lambda self, name, value
+     |  
+     |  ----------------------------------------------------------------------
+     |  Data descriptors defined here:
+     |  
+     |  __dict__
+     |      dictionary for instance variables (if defined)
+     |  
+     |  __weakref__
+     |      list of weak references to the object (if defined)
+     |  
+     |  data_ptr
+     |  
+     |  ----------------------------------------------------------------------
+     |  Data and other attributes defined here:
+     |  
+     |  __swig_destroy__ = <built-in function delete_scattering_species_type>
+     |  
+     |  
+     |  __swig_getmethods__ = {'data_ptr': <built-in function scattering_speci...
+     |  
+     |  __swig_setmethods__ = {'data_ptr': <built-in function scattering_speci...
+
     class space_group_type(__builtin__.object)
      |  Methods defined here:
      |  
@@ -5659,6 +5702,8 @@ FUNCTIONS
 
     FloatVector_swigregister(...)
 
+    FortFuncs_additional_scattering_factors(...)
+
     FortFuncs_ag_theta(...)
 
     FortFuncs_al_theta(...)
@@ -5683,6 +5728,8 @@ FUNCTIONS
 
     FortFuncs_allocate_point_list(...)
 
+    FortFuncs_allocate_scattering_species(...)
+
     FortFuncs_allocate_vparam(...)
 
     FortFuncs_angs_4c_bisecting(...)
@@ -5985,8 +6032,6 @@ FUNCTIONS
 
     FortFuncs_hk_equiv(...)
 
-    FortFuncs_hkl_lat_absent(...)
-
     FortFuncs_hklgen_sxtal_list(...)
 
     FortFuncs_hklgen_sxtal_reflection(...)
@@ -6099,6 +6144,8 @@ FUNCTIONS
 
     FortFuncs_matrix_inverse(...)
 
+    FortFuncs_mhkl_absent(...)
+
     FortFuncs_molcrys_to_atomlist(...)
 
     FortFuncs_molec_to_atomlist(...)
@@ -6425,6 +6472,8 @@ FUNCTIONS
 
     FortFuncs_write_mag_structure_factors(...)
 
+    FortFuncs_write_magnetic_space_group(...)
+
     FortFuncs_write_magnetic_structure(...)
 
     FortFuncs_write_mcif(...)
@@ -6797,6 +6846,8 @@ FUNCTIONS
 
     sbvs_par_type_swigregister(...)
 
+    scattering_species_type_swigregister(...)
+
     space_group_type_swigregister(...)
 
     spgr_info_type_swigregister(...)

fix_makefile_deps.py

@@ -2,6 +2,7 @@
 # Joseph Lesniewski - NIST Center for Neutron Research
 # Summer 2014
 # hack out EoS and SAn modules from Makefile
+# May 2016 Edit hack out new CFML_FlipR_Mod
 lines = [line.strip() for line in open("./Makefile.deps")]
 out = open("./Makefile.deps", "w")
 for line in lines:
@@ -12,6 +13,8 @@
 				pass
 			elif 'CFML_EoS_Mod' in item:
 				pass
+			elif 'CFML_FlipR_Mod' in item:
+				pass
 			else:
 				out.write(item + " ")
 		out.write("\n")
@@ -20,6 +23,8 @@
 			pass
 		elif 'CFML_EoS_Mod' in line:
 			pass
+		elif 'CFML_FlipR_Mod' in line:
+			pass
 		else:
 			out.write(line+"\n")
 out.close()

hklgen/pycrysfml.py

@@ -421,6 +421,7 @@ def __init__(self):
         except: self.this = this
     __swig_destroy__ = _pycrysfml.delete_atom_list_type
     __del__ = lambda self : None;
+    def set_form_factors(self, *args): return _pycrysfml.atom_list_type_set_form_factors(self, *args)
     def get_atom_list_element(self, *args): return _pycrysfml.atom_list_type_get_atom_list_element(self, *args)
     def set_atom_list_element(self, *args): return _pycrysfml.atom_list_type_set_atom_list_element(self, *args)
     def get_atom_list_natoms(self): return _pycrysfml.atom_list_type_get_atom_list_natoms(self)
@@ -1426,8 +1427,8 @@ class FortFuncs(_object):
     if _newclass:write_restraints_obscalc = staticmethod(_pycrysfml.FortFuncs_write_restraints_obscalc)
     __swig_getmethods__["get_maxnumref"] = lambda x: _pycrysfml.FortFuncs_get_maxnumref
     if _newclass:get_maxnumref = staticmethod(_pycrysfml.FortFuncs_get_maxnumref)
-    __swig_getmethods__["hkl_lat_absent"] = lambda x: _pycrysfml.FortFuncs_hkl_lat_absent
-    if _newclass:hkl_lat_absent = staticmethod(_pycrysfml.FortFuncs_hkl_lat_absent)
+    __swig_getmethods__["mhkl_absent"] = lambda x: _pycrysfml.FortFuncs_mhkl_absent
+    if _newclass:mhkl_absent = staticmethod(_pycrysfml.FortFuncs_mhkl_absent)
     __swig_getmethods__["init_err_refl"] = lambda x: _pycrysfml.FortFuncs_init_err_refl
     if _newclass:init_err_refl = staticmethod(_pycrysfml.FortFuncs_init_err_refl)
     __swig_getmethods__["init_reflist"] = lambda x: _pycrysfml.FortFuncs_init_reflist
@@ -1518,6 +1519,10 @@ class FortFuncs(_object):
     if _newclass:z4frgn = staticmethod(_pycrysfml.FortFuncs_z4frgn)
     __swig_getmethods__["z4frz1"] = lambda x: _pycrysfml.FortFuncs_z4frz1
     if _newclass:z4frz1 = staticmethod(_pycrysfml.FortFuncs_z4frz1)
+    __swig_getmethods__["additional_scattering_factors"] = lambda x: _pycrysfml.FortFuncs_additional_scattering_factors
+    if _newclass:additional_scattering_factors = staticmethod(_pycrysfml.FortFuncs_additional_scattering_factors)
+    __swig_getmethods__["allocate_scattering_species"] = lambda x: _pycrysfml.FortFuncs_allocate_scattering_species
+    if _newclass:allocate_scattering_species = staticmethod(_pycrysfml.FortFuncs_allocate_scattering_species)
     __swig_getmethods__["calc_strfactor"] = lambda x: _pycrysfml.FortFuncs_calc_strfactor
     if _newclass:calc_strfactor = staticmethod(_pycrysfml.FortFuncs_calc_strfactor)
     __swig_getmethods__["calc_hkl_strfactor"] = lambda x: _pycrysfml.FortFuncs_calc_hkl_strfactor
@@ -1656,6 +1661,8 @@ class FortFuncs(_object):
     if _newclass:sym_prod_st = staticmethod(_pycrysfml.FortFuncs_sym_prod_st)
     __swig_getmethods__["write_bin_spacegroup"] = lambda x: _pycrysfml.FortFuncs_write_bin_spacegroup
     if _newclass:write_bin_spacegroup = staticmethod(_pycrysfml.FortFuncs_write_bin_spacegroup)
+    __swig_getmethods__["write_magnetic_space_group"] = lambda x: _pycrysfml.FortFuncs_write_magnetic_space_group
+    if _newclass:write_magnetic_space_group = staticmethod(_pycrysfml.FortFuncs_write_magnetic_space_group)
     __swig_getmethods__["write_spacegroup"] = lambda x: _pycrysfml.FortFuncs_write_spacegroup
     if _newclass:write_spacegroup = staticmethod(_pycrysfml.FortFuncs_write_spacegroup)
     __swig_getmethods__["write_sym"] = lambda x: _pycrysfml.FortFuncs_write_sym
@@ -2747,9 +2754,9 @@ def FortFuncs_get_maxnumref(*args):
   return _pycrysfml.FortFuncs_get_maxnumref(*args)
 FortFuncs_get_maxnumref = _pycrysfml.FortFuncs_get_maxnumref
 
-def FortFuncs_hkl_lat_absent(*args):
-  return _pycrysfml.FortFuncs_hkl_lat_absent(*args)
-FortFuncs_hkl_lat_absent = _pycrysfml.FortFuncs_hkl_lat_absent
+def FortFuncs_mhkl_absent(*args):
+  return _pycrysfml.FortFuncs_mhkl_absent(*args)
+FortFuncs_mhkl_absent = _pycrysfml.FortFuncs_mhkl_absent
 
 def FortFuncs_init_err_refl():
   return _pycrysfml.FortFuncs_init_err_refl()
@@ -2931,6 +2938,14 @@ def FortFuncs_z4frz1(*args):
   return _pycrysfml.FortFuncs_z4frz1(*args)
 FortFuncs_z4frz1 = _pycrysfml.FortFuncs_z4frz1
 
+def FortFuncs_additional_scattering_factors(*args):
+  return _pycrysfml.FortFuncs_additional_scattering_factors(*args)
+FortFuncs_additional_scattering_factors = _pycrysfml.FortFuncs_additional_scattering_factors
+
+def FortFuncs_allocate_scattering_species(*args):
+  return _pycrysfml.FortFuncs_allocate_scattering_species(*args)
+FortFuncs_allocate_scattering_species = _pycrysfml.FortFuncs_allocate_scattering_species
+
 def FortFuncs_calc_strfactor(*args):
   return _pycrysfml.FortFuncs_calc_strfactor(*args)
 FortFuncs_calc_strfactor = _pycrysfml.FortFuncs_calc_strfactor
@@ -3207,6 +3222,10 @@ def FortFuncs_write_bin_spacegroup(*args):
   return _pycrysfml.FortFuncs_write_bin_spacegroup(*args)
 FortFuncs_write_bin_spacegroup = _pycrysfml.FortFuncs_write_bin_spacegroup
 
+def FortFuncs_write_magnetic_space_group(*args):
+  return _pycrysfml.FortFuncs_write_magnetic_space_group(*args)
+FortFuncs_write_magnetic_space_group = _pycrysfml.FortFuncs_write_magnetic_space_group
+
 def FortFuncs_write_spacegroup(*args):
   return _pycrysfml.FortFuncs_write_spacegroup(*args)
 FortFuncs_write_spacegroup = _pycrysfml.FortFuncs_write_spacegroup
@@ -4663,6 +4682,24 @@ def __init__(self):
 sbvs_par_type_swigregister = _pycrysfml.sbvs_par_type_swigregister
 sbvs_par_type_swigregister(sbvs_par_type)
 
+class scattering_species_type(_object):
+    __swig_setmethods__ = {}
+    __setattr__ = lambda self, name, value: _swig_setattr(self, scattering_species_type, name, value)
+    __swig_getmethods__ = {}
+    __getattr__ = lambda self, name: _swig_getattr(self, scattering_species_type, name)
+    __repr__ = _swig_repr
+    def __init__(self): 
+        this = _pycrysfml.new_scattering_species_type()
+        try: self.this.append(this)
+        except: self.this = this
+    __swig_destroy__ = _pycrysfml.delete_scattering_species_type
+    __del__ = lambda self : None;
+    __swig_setmethods__["data_ptr"] = _pycrysfml.scattering_species_type_data_ptr_set
+    __swig_getmethods__["data_ptr"] = _pycrysfml.scattering_species_type_data_ptr_get
+    if _newclass:data_ptr = _swig_property(_pycrysfml.scattering_species_type_data_ptr_get, _pycrysfml.scattering_species_type_data_ptr_set)
+scattering_species_type_swigregister = _pycrysfml.scattering_species_type_swigregister
+scattering_species_type_swigregister(scattering_species_type)
+
 class space_group_type(_object):
     __swig_setmethods__ = {}
     __setattr__ = lambda self, name, value: _swig_setattr(self, space_group_type, name, value)