def calculate(self, name, atoms): data = DeltaCodesDFTTask.calculate(self, name, atoms) try: steps = atoms.get_calculator().get_number_of_iterations() except (AttributeError, NotImplemented): steps = None data['calculator steps'] = steps return data
'ecut':ecut, 'xc':'PBE', 'pps':'fhi', 'nstep':700, 'diemac': 1000, 'width':w, 'kpts':kd, 'chksymbreak':0, 'ecutsm':0.05, 'nsym':1, } calcfactory = Factory(Abinit, 'Abinit', 'label', **calcopts) taskopts = {} task = Task( calcfactory=calcfactory, tag=tag, fit=fit, use_lock_files=True, **taskopts) if __name__ == '__main__': keys = task.collection.names for m in ['Mn']: keys.remove(m) # EOS fails: reason unknown # run just only system to check if scripts work #task.run(keys) task.run(['Si'])
def __init__(self, **kwargs): DeltaCodesDFTTask.__init__(self, **kwargs)
fit = (5, 0.02) w = 0.06 ecut = 1200 kd = 8.0 tag = 'dcdft_%s_gpaw_pw' % xc.lower() task = Task( calcfactory=Factory(xc=xc, mode=PW(ecut), occupations=FermiDirac(w), maxiter=250, kptdensity=kd, ), tag=tag, fit=fit, use_lock_files=True, ) if __name__ == '__main__': if element is None: keys = set(parameters.keys()).intersection(set(task.collection.names)) for s in elements_slow: keys.remove(s) # those are slow, run separately else: keys = [element] task.run(keys)
return calculator calcopts = { "toldfe": 1.0e-7, "ecut": ecut, "xc": "PBE", "pps": "fhi", "nstep": 700, "diemac": 1000, "width": w, "kpts": kd, "chksymbreak": 0, "ecutsm": 0.05, "nsym": 1, } calcfactory = Factory(Abinit, "Abinit", "label", **calcopts) taskopts = {} task = Task(calcfactory=calcfactory, tag=tag, fit=fit, use_lock_files=True, **taskopts) if __name__ == "__main__": keys = task.collection.names for m in ["Mn"]: keys.remove(m) # EOS fails: reason unknown # run just only system to check if scripts work # task.run(keys) task.run(["Si"])
z = zipfile.ZipFile(name) try: # new in 2.6 z.extractall() except AttributeError: # http://stackoverflow.com/questions/7806563/how-to-unzip-a-zip-file-with-python-2-4 for f in z.namelist(): fd = open(f, "w") fd.write(z.read(f)) fd.close() # AttributeError if unzip not found except (urllib2.HTTPError, AttributeError): raise NotAvailable('Retrieval of zip failed') os.chdir('..') task = Task( tag=tag, use_lock_files=True, ) # header h = ['#element', 'V0', 'B0', 'B1'] if not os.path.exists('%s_raw.csv' % tag): # read calculated results from json file and write into csv task.read() task.analyse() f1 = open('%s_raw.csv' % tag, 'wb') csvwriter1 = csv.writer(f1) csvwriter1.writerow(h) for n in task.collection.names:
#'occupation':0.001, # 0.001 #'maxsteps':None, #'maxtime':None #}, ft=w, symmetry=True, spinpol=True, # must set explicitly calculate_stress=False, deletenc=True, # start fresh every time kptdensity=kd, ) taskopts = {} task = Task( calcfactory=calcfactory, tag=tag, fit=fit, use_lock_files=True, **taskopts) if __name__ == '__main__': keys = set(psp.keys()).intersection(set(task.collection.names)) for m in ['Be', 'Cr', 'Kr', 'Xe']: keys.remove(m) # EOS fails: maybe need higher ecut? for m in ['Zn', 'Zr']: keys.remove(m) # do not converge # run just only system to check if scripts work keys = ['Si'] task.run(keys)
z = zipfile.ZipFile(name) try: # new in 2.6 z.extractall() except AttributeError: # http://stackoverflow.com/questions/7806563/how-to-unzip-a-zip-file-with-python-2-4 for f in z.namelist(): fd = open(f, "w") fd.write(z.read(f)) fd.close() # AttributeError if unzip not found except (urllib.error.HTTPError, AttributeError): raise NotAvailable('Retrieval of zip failed') os.chdir('..') task = Task( tag=tag, use_lock_files=True, ) # header h = ['#element', 'V0', 'B0', 'B1'] if not os.path.exists('%s_raw.csv' % tag): # read calculated results from json file and write into csv task.read() task.analyse() f1 = open('%s_raw.csv' % tag, 'wb') csvwriter1 = csv.writer(f1) csvwriter1.writerow(h) for n in task.collection.names:
def __init__(self, inititer=0, **kwargs): DeltaCodesDFTTask.__init__(self, **kwargs) self.inititer = inititer