some bug fixed

jackey-qiu · May 11, 2021 · f013e3d · f013e3d
1 parent 26e8f44
commit f013e3d
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Showing 2 changed files with 51 additions and 3 deletions.
diff --git a/EnginePool/models/structure_tools/sxrd_dafy.py b/EnginePool/models/structure_tools/sxrd_dafy.py
@@ -618,12 +618,43 @@ def calc_f_all(self, h, k, l):
         return abs(ftot)*self.inst.inten
 
     def calc_f_all_RAXS(self, h, k, l, a,b,c,A_list,P_list, E, E0, f1f2, res_el, mode = 'MD'):
-        f_ctr = self.calc_f_all(h, k, l)
+        '''
+        Calculate the structure factors for the sample
+        Here the surface structure is diveded into the subtrate itself and the sorbate atoms
+        The format of domain has a structure like: domain = {'domain1':{'slab':slab,'wt':weight,'sorbate':sorbate}}
+        '''
+        #here the chemically equivalent domains will be added up in-coherently always
+        ftot=0
+        # key = (h[0],k[0],l[0],l[-1])
+        # if key in self.fb:
+            # fb = self.fb[key]
+        # else:
+            # fb = self.calc_fb(h, k, l)
+            # self.fb[key] = fb
+        fb = self.calc_fb(h, k, l)
+
         if mode == 'MD':
             f_raxs, scale = self.calc_fs_sorbate_RAXS_MD(h, k, l,self.domain[key]['sorbate'],self.domain[key]['sorbate_sym'],a,b,c,E,E0,f1f2,res_el)
         elif mode == 'MI':
             f_raxs, scale = self.calc_fs_sorbate_RAXS_MI(f1f2,E, E0, a, b, c, A_list,P_list)
-        return scale*(f_ctr + f_raxs)
+
+        if self.coherence==True:
+            for key in self.domain.keys():
+                f_water = self.calc_f_layered_water_copper(h, k, l, rgh = self.domain[key])
+                if self.domain[key]['wt']!=0:
+                    if type(self.domain[key]['sorbate'])==type([]):
+                        ftot = ftot+(fb+self.calc_fs(h, k, l,[self.domain[key]['slab']])+self.calc_fs_sorbate(h, k, l,self.domain[key]['sorbate'],self.domain[key]['sorbate_sym'])+f_raxs+f_water)*self.domain[key]['wt']
+                    else:
+                        ftot = ftot+(fb+self.calc_fs(h, k, l,[self.domain[key]['slab']])+self.calc_fs_sorbate(h, k, l,[self.domain[key]['sorbate']],self.domain[key]['sorbate_sym'])+f_raxs+f_water)*self.domain[key]['wt']
+        else:
+            for key in self.domain.keys():
+                f_water = self.calc_f_layered_water_copper(h, k, l, rgh = self.domain[key])
+                if self.domain[key]['wt']!=0:
+                    if type(self.domain[key]['sorbate'])==type([]):
+                        ftot = ftot+abs(fb+self.calc_fs(h, k, l,[self.domain[key]['slab']])+self.calc_fs_sorbate(h, k, l,self.domain[key]['sorbate'],self.domain[key]['sorbate_sym'])+f_raxs+f_water)*self.domain[key]['wt']
+                    else:
+                        ftot = ftot+abs(fb+self.calc_fs(h, k, l,[self.domain[key]['slab']])+self.calc_fs_sorbate(h, k, l,[self.domain[key]['sorbate']],self.domain[key]['sorbate_sym'])+f_raxs+f_water)*self.domain[key]['wt']
+        return abs(ftot)*self.inst.inten*scale
 
     def calc_f_ideal(self, h, k, l):
         '''
@@ -2658,7 +2689,7 @@ def _extract_f1f2(f1f2,E):
         if len(f1f2)!=len(E):
             f1f2=_extract_f1f2(f1f2,E)
         scaling_factor = np.exp(-a*(E-E0)**2/E0**2+b*(E-E0)/E0)*c
-        return (f1f2[:,0]+1.0J*f1f2[:,1])*A_list*np.exp(1.0J*np.pi*2*P_list)),scaling_factor
+        return (f1f2[:,0]+1.0J*f1f2[:,1])*A_list*np.exp(1.0J*np.pi*2*P_list),scaling_factor
 
     def calc_fs_sorbate_RAXS_MD(self, h, k, l,slabs, sorbate_sym,a,b,c,E,E0,f1f2,res_el='Pb'):
         '''Calculate the structure factors from the surface

diff --git a/FilterPool/data_superrod.py b/FilterPool/data_superrod.py
@@ -562,6 +562,7 @@ def concatenate_all_ctr_datasets(self):
         all_ctr_data = []
         self.ctr_data_info = {}
         self.scaling_tag = []
+        self.data_type = []
         for i,each in enumerate(self.items):
             if hasattr(each,'mask'):
                 h,k,x,y,LB,dL = each.extra_data['h'][each.mask][:,np.newaxis],each.extra_data['k'][each.mask][:,np.newaxis],each.x[each.mask][:,np.newaxis],each.extra_data['Y'][each.mask][:,np.newaxis],each.extra_data['LB'][each.mask][:,np.newaxis],each.extra_data['dL'][each.mask][:,np.newaxis]
@@ -572,6 +573,10 @@ def concatenate_all_ctr_datasets(self):
                 self.scaling_tag.append('specular_rod')
             else:
                 self.scaling_tag.append('nonspecular_rod')
+            if x[0]>100:#x column is energy for raxs (in ev); but x column is L for CTR (smaller than 10 usually)
+                self.data_type.append('RAXS')
+            else:
+                self.data_type.append('CTR')
             #mask = np.ones(len(h))[:,np.newaxis]
             fbulk = np.zeros(len(h))[:,np.newaxis]
             temp_data = np.hstack((h,k,x,y,LB,dL,fbulk))
@@ -590,6 +595,18 @@ def split_fullset(self,full_set,scale_factors):
             sub_sets.append(full_set[cum_sum[i]:cum_sum[i+1]]*scale_factors[i])
         return sub_sets
 
+    def get_ctr_raxs_data(self, full_set, scale_factors):
+        sub_sets = self.split_fullset(full_set, scale_factors)
+        sub_sets_ctr = []
+        sub_sets_raxs = []
+        for i in range(len(self.data_type)):
+            each = self.data_type[i]
+            if each == 'CTR':
+                sub_sets_ctr.append(sub_sets[i])
+            elif each == 'RAXS':
+                sub_sets_raxs.append(sub_sets[i])
+        return sub_sets_ctr,sub_sets_raxs
+
     def __getitem__(self,key):
         '''__getitem__(self,key) --> DataSet