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run.py
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run.py
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import sys
import os
import shutil
from pcrfilehelper import pcrFileHelper
from diffpy.pyfullprof.fpoutputfileparsers import FPOutFileParser
from diffpy.pyfullprof.fit import Fit
from paramlist import ParamList
from outfilecheckerror import check
from subrun import SubRun
import setting
error_info={
0:"no error",
-1: "no out file",
1: "out file error",
-30: "error in run and break",
-31: "asym error",
-32: "no rwp in out file",
-33: "Singular matrix",
-10: "no rwp task"
}
class Run:
def __init__(self):
return
#reset Run
def reset(self,pcrfilename,tmp_dir_path="tmp"):
self.tmp_path="/"+tmp_dir_path+"/"
self.pcrRW=None
self.outR=None
self.fit=None
self.params=None
self.err = 0
self.step_index=-1
self.errmsg=""
self.job_name=pcrfilename
self.Rwp=10000
self.R={"Rp":0,"Rwp":0,"Re":0,"Chi2":0}
#file pcr and out
self.pcrfilename=os.path.realpath(pcrfilename)
self.outfilename=os.path.splitext(self.pcrfilename)[0]+".out"
self.codefile=os.path.splitext(self.pcrfilename)[0]
self.dirname=os.path.dirname(self.pcrfilename)
self.base_pcrfilename=os.path.basename(self.pcrfilename)
self.base_outfilename=os.path.basename(self.outfilename)
self.tmpdir=os.path.dirname(self.pcrfilename)+self.tmp_path
shutil.copyfile(self.pcrfilename,self.pcrfilename+"_back")
if os.path.exists(self.tmpdir)==False:
os.mkdir(self.tmpdir)
os.chdir(self.dirname) # change the dir to the pcr dir
self.resetLoad()
if self.err !=0:
print(error_info[self.err])
self.runfp()
self.push() # the number 0 version
shutil.copy(self.pcrfilename,self.pcrfilename+"_back") #backup the pcrfile
return
def resetLoad(self):
self.pcrRW=pcrFileHelper()
try:
self.pcrRW.readFromPcrFile(self.pcrfilename)
except Exception,e:
print Exception,":",e
return -0x80
self.fit=self.pcrRW.fit
self.job=self.fit.get("Pattern")[0].get("Job") # get the type of job
self.datafile=self.fit.get("Pattern")[0].get("Datafile") # the name of data file
self.phase_num=len(self.fit.get("Phase"))
if self.job==0:
asylim=self.fit.get("Pattern")[0].get("AsymLim")
if asylim < 5: asylim=setting.run_set.AsymLim
self.fit.get("Pattern")[0].set("AsymLim",asylim)
if self.job == 2:
self.err = -10 # no Rwp task
if setting.run_set.Atom_Aniso_Temp_Enable==True:
for atom_i in self.fit.get("Phase")[0].get("Atom"):
atom_i.set("N_t",2)
self.real_datafile=os.path.splitext(self.pcrfilename)[0]+".dat" # the absolute path of the data file
#read outfile and get rwp
if os.path.exists(self.outfilename) == False:
self.throwerr(-1, "no out file ")
elif self.err>=0:
self.outR=FPOutFileParser(self.pcrRW.fit,self.outfilename)
if self.outR.getStatus()== False:
self.throwerr(1, "out file error")
elif self.err == 0:
self.Rwp=self.getRwp()
#end read outfile
self.params=ParamList(self.fit.getParamList(),self.job,self.fit)
return self.err
def runfp(self):
self.err=0
subrun=SubRun()
subrun.reset("fp2k",self.base_pcrfilename,"not saved to the current PCR file:")
self.err=subrun.run()
self.err=check(self.outfilename)
self.err=self.resetLoad()
#only save the right result
if(self.err==0):
self.push()
#get the Rwp
def getRwp(self,num=-1):
if num<0:
num=self.getCycleNum()+num+1
if self.err==0:
Rwp=self.outR.getResidues(num)[0][1]
r_factor=self.outR.getResidues(num)[0]
self.R={"Rp":r_factor[0],"Rwp":r_factor[1],"Re":r_factor[2],"Chi2":r_factor[3]}
return Rwp
def getCycleNum(self):
if self.err == 0:
Num=self.outR.getNumCycles()
return Num
#----------------------------------------------------------------------
def back_no_step(self):
self.back(0)
# step=0 represent only pop but step_index don't change
def back(self,step=1):
self.err=0
if self.step_index<0:
return
if self.step_index-step < 0:
step=self.step_index
print "back",self.step_index,step
self.pop(step)
self.resetLoad()
return
def push(self):
self.step_index+=1
tmp=self.tmpdir+"step="+str(self.step_index)
copyfile(self.pcrfilename,tmp+".pcr")
copyfile(self.outfilename,tmp+".out")
return
def pop(self , step = 1):
n=step
if self.step_index == 0: n = 0
tmp=self.tmpdir+"step="+str(self.step_index-n)
print "$$pop",tmp
if(os.path.exists(tmp+".pcr")):
copyfile(tmp+".pcr", self.pcrfilename)
if(os.path.exists(tmp+".out")):
copyfile(tmp+".out",self.outfilename)
else:
self.throwerr(-1,"no out file")
self.step_index -= step
if self.step_index < 0:
self.step_index = 0
return 1
# write to pcr
def writepcr(self):
self.pcrRW.writeToPcrFile(self.pcrfilename)
return
def setParam(self,index,code=False):
if code ==False:
self.params.turnoff_param(index)
else:
self.params.turnon_param(index)
return
def throwerr(self, errcode, str):
self.err = errcode
self.errmsg = str
print(self.errmsg)
def copyfile(source,destin):
shutil.copyfile(source,destin)
'''
step_index=open(source,"r")
context=step_index.read()
step_index.close()
step_index=open(destin,"w")
step_index.write(context)
step_index.close()
'''