##<Define other pars>##
rgh=domain_creator.define_global_vars(rgh=UserVars(),domain_number=NUMBER_DOMAIN)#global vars
rgh_raxs=domain_creator.define_raxs_vars(rgh=UserVars(),number_spectra=NUMBER_RAXS_SPECTRA,number_domain=1)#RAXR spectra pars
rgh_dlw=domain_creator.define_diffused_layer_water_vars(rgh=UserVars())#Diffused Layered water pars
rgh_dls=domain_creator.define_diffused_layer_sorbate_vars(rgh=UserVars())#Diffused Layered sorbate pars
##<make fit table file>##
if not RUN:
table_container=[]
rgh_instance_list=[rgh]+groups+sorbate_groups+Gaussian_groups+[rgh_gaussian]+[rgh_gaussian_freeze]+[vars()['rgh_domain1_set'+str(i+1)] for i in range(NUMBER_SORBATE_LAYER)]+[rgh_dlw,rgh_dls]
rgh_instance_name_list=['rgh']+group_names+sorbate_group_names+Gaussian_group_names+['rgh_gaussian']+['rgh_gaussian_freeze']+['rgh_domain1_set'+str(i+1) for i in range(NUMBER_SORBATE_LAYER)]+['rgh_dlw','rgh_dls']
table_container=make_grid.set_table_input_all(container=table_container,rgh_instance_list=rgh_instance_list,rgh_instance_name_list=rgh_instance_name_list,par_file=os.path.join(BATCH_PATH_HEAD,'pars_ranges.txt'))
#raxs pars
table_container=make_grid.set_table_input_raxs(container=table_container,rgh_group_instance=rgh_raxs,rgh_group_instance_name='rgh_raxs',par_range={'a':[0,20],'b':[-5,5],'c':[0,10],'A':[0,10],'P':[0,1]},number_spectra=NUMBER_RAXS_SPECTRA,number_domain=1)
#build up the tab file
make_grid.make_table(container=table_container,file_path=os.path.join(OUTPUT_FILE_PATH,'par_table.tab'))
##<fitting function part>##
if COUNT_TIME:t_1=datetime.now()
VARS=vars()
def Sim(data,VARS=VARS):
##<update the basis info>##
INFO_LIB['basis']=np.array([unitcell.a, unitcell.b, unitcell.c])
##<Extract pars>##
layered_water_pars=vars(rgh_dlw)
layered_sorbate_pars=vars(rgh_dls)
raxs_vars=vars(rgh_raxs)
##<update sorbates>##
[domain_creator.update_sorbate_new(domain=Domain1,anchored_atoms=[],func=domain_creator_sorbate.OS_cubic_oligomer,info_lib=INFO_LIB,domain_tag='_D1',rgh=VARS['rgh_domain1_set'+str(i+1)],index_offset=[i*2*NUMBER_EL_MOTIF,NUMBER_EL_MOTIF+i*2*NUMBER_EL_MOTIF],xy_offset=XY_OFFSET,height_offset=HEIGHT_OFFSET,level=LEVEL,symmetry_couple=SYMMETRY,cap=CAP,attach_sorbate_number=EXTRA_SORBATE,first_or_second=SWITCH_EXTRA_SORBATE,mirror=MIRROR_EXTRA_SORBATE,build_grid=BUILD_GRID) for i in range(NUMBER_SORBATE_LAYER)]#domain1
rgh_raxs=domain_creator.define_raxs_vars(rgh=UserVars(),number_spectra=NUMBER_RAXS_SPECTRA,number_domain=NUMBER_DOMAIN)#RAXR spectra pars
rgh_dlw=domain_creator.define_diffused_layer_water_vars(rgh=UserVars())#Diffused Layered water pars
rgh_dls=domain_creator.define_diffused_layer_sorbate_vars(rgh=UserVars())#Diffused Layered sorbate pars
##<make fit table file>##
if not RUN:
table_container=[]
rgh_instance_list=[rgh]+groups+[absorbed_water_pair1_D1,absorbed_water_pair2_D1,absorbed_water_pair1_D2,absorbed_water_pair2_D2]+\
sorbate_groups+[rgh_domain1,rgh_domain2,rgh_dlw,rgh_dls]
rgh_instance_name_list=['rgh']+group_names+['absorbed_water_pair1_D1','absorbed_water_pair2_D1','absorbed_water_pair1_D2','absorbed_water_pair2_D2']+\
sorbate_group_names+['rgh_domain1','rgh_domain2','rgh_dlw','rgh_dls']
table_container=make_grid.set_table_input_all(container=table_container,rgh_instance_list=rgh_instance_list,rgh_instance_name_list=rgh_instance_name_list,par_file=BATCH_PATH_HEAD+'pars_ranges.txt')
#raxs pars
table_container=make_grid.set_table_input_raxs(container=table_container,rgh_group_instance=rgh_raxs,rgh_group_instance_name='rgh_raxs',par_range={'a':[0,1],'b':[0,1],'c':[0,1],'A':[0,1],'P':[0,1]},number_spectra=NUMBER_RAXS_SPECTRA,number_domain=NUMBER_DOMAIN)
#build up the tab file
make_grid.make_table(container=table_container,file_path=OUTPUT_FILE_PATH+'par_table.tab')
##<fitting function part>##
if COUNT_TIME:t_1=datetime.now()
def Sim(data):
##<Extract pars>##
layered_water_pars=vars(rgh_dlw)
layered_sorbate_pars=vars(rgh_dls)
raxs_vars=vars(rgh_raxs)
##<update sorbates>##
domain_creator.update_sorbate(domain=Domain1,anchored_atoms=[],func=domain_creator_sorbate.OS_sqr_antiprism_oligomer,info_lib=INFO_LIB,domain_tag='_D1',rgh=rgh_domain1,index_offset=[0,1],height_offset=HEIGHT_OFFSET)#domain1
domain_creator.update_sorbate(domain=Domain2,anchored_atoms=[],func=domain_creator_sorbate.OS_sqr_antiprism_oligomer,info_lib=INFO_LIB,domain_tag='_D2',rgh=rgh_domain2,index_offset=[0,1],height_offset=HEIGHT_OFFSET)#domain2
#You can add more domains
