#!/usr/bin/env python #### this script modifies the default FATES parameter file to generate # a file used in testing E3SM # Parser code was based off of modify_fates_paramfile.py import os import argparse import code # For development: code.interact(local=dict(globals(), **locals())) from scipy.io import netcdf import xml.etree.ElementTree as et debug = True # --------------------------------------------------------------------------------------- class param_type: def __init__(self,name,values_text): self.name = name self.values = values_text.replace(" ","") #[float(x) for x in values_text.split(',')] # --------------------------------------------------------------------------------------- def load_xml(xmlfile): xmlroot = et.parse(xmlfile).getroot() print("\nOpenend: "+xmlfile) base_cdl = xmlroot.find('base_file').text new_cdl = xmlroot.find('new_file').text pftparams = xmlroot.find('pft_trim_list').text.replace(" ","") paramroot = xmlroot.find('parameters') grouplist = [] for group in paramroot: if(not('ids' in group.attrib.keys())): print("pft_mod_group must have an ids attribute with comma delimited pft indices") print("exiting") exit(2) pft_str = group.attrib['ids'].strip() pft_strvec = pft_str.split(',') pft_ids = [int(s) for s in pft_strvec] print("Processing PFT group: "+group.tag+" ids: "+pft_str) #paramlist = [] #for param in paramroot: # print("parsing "+param.tag) # paramlist.append(param_type(param.tag,param.text)) code.interact(local=dict(globals(), **locals())) return(base_cdl,new_cdl,pftparams,paramlist) # Little function for assembling the call to the system to make the modification # ---------------------------------------------------------------------------------------- def parse_syscall_str(fnamein,fnameout,pft_index,param_name,param_val): if(pft_index==0): sys_call_str = "../tools/modify_fates_paramfile.py"+" --fin " + fnamein + \ " --fout " + fnameout + " --var " + param_name + " --silent " +\ " --val " + "\" "+param_val+"\"" + " --nohist --overwrite --all" else: pft_str_index="{}".format(pft_index) sys_call_str = "../tools/modify_fates_paramfile.py"+" --fin " + fnamein + \ " --fout " + fnameout + " --var " + param_name + " --silent " +\ " --val " + "\" "+param_val+"\"" + " --nohist --overwrite --pft "+pft_str_index if(debug): print(sys_call_str) return(sys_call_str) def main(): # Parse arguments parser = argparse.ArgumentParser(description='Parse command line arguments to this script.') parser.add_argument('--f', dest='xmlfile', type=str, help="XML control file Required.", required=True) args = parser.parse_args() # Load the xml file, which contains the base cdl, the output cdl, # and the parameters to be modified #[base_cdl,new_cdl,pftlist,paramlist] = load_xml(args.xmlfile) xmlroot = et.parse(args.xmlfile).getroot() print("\nOpened: "+args.xmlfile) base_cdl = xmlroot.find('base_file').text new_cdl = xmlroot.find('new_file').text # Convert the base cdl file into a temp nc binary base_nc = os.popen('mktemp').read().rstrip('\n') gencmd = "ncgen -o "+base_nc+" "+base_cdl os.system(gencmd) # Generate a temp output file name new_nc = os.popen('mktemp').read().rstrip('\n') # Use FatesPFTIndexSwapper.py to prune out unwanted PFTs pft_trim_list = xmlroot.find('pft_trim_list').text.replace(" ","") swapcmd="../tools/FatesPFTIndexSwapper.py --pft-indices="+pft_trim_list+" --fin="+base_nc+" --fout="+new_nc+" --nohist" #+" 1>/dev/null" os.system(swapcmd) # On subsequent parameters, overwrite the file paramroot = xmlroot.find('parameters') grouplist = [] for group in paramroot: if(group.tag.strip() == 'non_pft_group'): print("Processing non_pft_group") for param in group: print("parsing "+param.tag) change_str = parse_syscall_str(new_nc,new_nc,0,param.tag,param.text.replace(" ","")) os.system(change_str) elif(group.tag.strip() == 'pft_group'): if(not('ids' in group.attrib.keys())): print("pft_mod_group must have an ids attribute with comma delimited pft indices") print("exiting") exit(2) pft_str = group.attrib['ids'].strip() pft_strvec = pft_str.split(',') pft_ids = [int(s) for s in pft_strvec] print("Processing PFT group: "+group.tag+" ids: "+pft_str) for param in group: print("parsing "+param.tag) param_vec = [str_val for str_val in param.text.replace(" ", "").split(',')] # The number of parameters does not need to equal to the number of PFTs # but it does need to be equally divisible by it v_per_p = float(len(param_vec))/float(len(pft_ids)) if( int(100.0*v_per_p) != 100*int(v_per_p) ): print("inconsistent number of parameter values and number of pfts specified") print("exiting") exit(2) for j,pft_id in enumerate(pft_ids): j0 = j*int(v_per_p) j1 = (j+1)*int(v_per_p) #code.interact(local=dict(globals(), **locals())) param_str = ",".join(param_vec[j0:j1]) change_str = parse_syscall_str(new_nc,new_nc,pft_id,param.tag,param_str) os.system(change_str) else: print("Unidentified group, should be: non_pft_group or pft_group") print("exiting") exit(2) # Append history fp_nc = netcdf.netcdf_file(new_nc, 'a') fp_nc.history = "This file was generated by BatchPatchParams.py:\n"\ "CDL Base File = {}\n"\ "XML patch file = {}"\ .format(base_cdl,args.xmlfile) fp_nc.close() # Sort the new file newer_nc = os.popen('mktemp').read().rstrip('\n') os.system("../tools/ncvarsort.py --fin "+new_nc+" --fout "+newer_nc+" --overwrite") # Dump the new file to the cdl os.system("ncdump "+newer_nc+" > "+new_cdl) print("\nBatch parameter transfer complete\n") print("\nGenerated: {}\n".format(new_cdl)) # This is the actual call to main if __name__ == "__main__": main()