def sweep(runspath,resultspath,inputtemplatepath,sweepdicarr):
sweeplog = open(resultspath+"/sweep.log","w+")
sweeplog.write("runspath "+runspath+"\n")
sweeplog.write("resultspath "+resultspath+"\n")
sweeplog.write("inputtemplatepath "+inputtemplatepath+"\n")
rundirlog = open(resultspath+"/rundir.log","w+")
inputtree = etree.parse(inputtemplatepath)
for irun, sweepdic in enumerate(sweepdicarr):
time.sleep(0.1)
runpath, rundir = tstamp_folder.tstamp_folder(runspath)
os.chdir(runpath)
sweeplog.write("\n"+"runpath "+runpath+"\n")
rundirlog.write(runpath+"\n")
inputdscr="Input file generated by sweep.py script\n"
inputdscr=inputdscr+"input.xml template in: %s\n"%(inputtemplatepath)
inputdscr=inputdscr+"results path is: %s\n"%(resultspath)
for xpath,value in sweepdic.items():
sweeplog.write("\t"+"sweepvar "+xpath+"\n")
sweeplog.write("\t"+"value "+str(value)+"\n")
inputdscr=inputdscr+"sweeping variable: "+xpath+"\n"
inputdscr=inputdscr+"value: "+str(value)+"\n"
setinputxml.setByXpath(inputtree,xpath,str(value))
setinputxml.setByXpath(inputtree,"/input/keywords",inputdscr)
inputtree.write(runpath+"/input.xml",pretty_print="true")
sweeplog.close()
rundirlog.close()
def energy(var, data):
runpath = data[0]
runcommand = data[1]
xpath = data[2]
os.chdir(runpath)
os.system("rm -f info.xml")
inputtree = etree.parse("input.xml")
nvar = len(var)
for i in range(nvar):
setinputxml.setByXpath(inputtree, xpath[i], str(var[i]))
inputtree.write("input.xml", pretty_print="true")
os.system(runcommand)
while not os.path.exists("info.xml"):
time.sleep(1)
time.sleep(5)
return -queryinfoxml.getLastTotalEnergy()
def optimize(
runpath, resultspath, inputtemplatepath, vararr, runcommand, ftolerance=1.0e-4, xtolerance=1.0e-4, itmax=500
):
amoebalog = open(resultspath + "/amoeba.log", "w+")
optimizelog = open(resultspath + "/optimize.log", "w+")
optimizelog.write("runpath " + runpath + "\n")
optimizelog.write("resultspath " + resultspath + "\n")
optimizelog.write("inputtemplatepath " + inputtemplatepath + "\n")
optimizelog.write("Variables:\n")
inputtree = etree.parse(inputtemplatepath)
inputdscr = "Input file generated by script optimize.py \n"
inputdscr = inputdscr + "runpath: %s\n" % (runpath)
inputdscr = inputdscr + "resultspath: %s\n" % (resultspath)
inputdscr = inputdscr + "input template from path: %s\n" % (inputtemplatepath)
inputdscr = inputdscr + "optimization varibales:\n"
for var in vararr:
optimizelog.write("xpath: " + var[0] + "\n")
optimizelog.write("guess: " + str(var[1]) + "\n")
optimizelog.write("scale: " + str(var[2]) + "\n")
inputdscr = inputdscr + "xpath: " + str(var[0]) + "\n"
inputdscr = inputdscr + "guess: " + str(var[1]) + "\n"
inputdscr = inputdscr + "scale: " + str(var[2]) + "\n"
optimizelog.flush()
setinputxml.setByXpath(inputtree, "/input/keywords", inputdscr)
inputtree.write(runpath + "/input.xml", pretty_print="true")
guess = []
scale = []
data = []
data.append(runpath)
data.append(runcommand)
data.append([])
for var in vararr:
data[-1].append(var[0]) # build xpath array
guess.append(var[1]) # build array of initial guess values for the variables
scale.append(var[2])
simplex, fvalue, iteration = amoeba.amoeba(guess, scale, energy, ftolerance, xtolerance, itmax, data, amoebalog)
amoebalog.write("%d\t" % (iteration))
amoebalog.write("%1.10f\t" % (fvalue))
for value in simplex:
amoebalog.write("%1.10f\t" % (value))
amoebalog.write("\n")
amoebalog.flush()
optimizelog.write("\nOptimization converged after %d iterations of amoeba.py\n" % (iteration))
optimizelog.write("\nOptimized variables found:\n")
for i, var in enumerate(vararr):
optimizelog.write("xpath: " + var[0] + "\n")
optimizelog.write("optimized value: %1.0f\n\n" % (simplex[i]))
optimizelog.flush()
optimizelog.close()
amoebalog.close()
