def test_read_extra_abivars(self): vars_out = {'ecut': 40} f = open('extra_abivars', 'w') f.write(str(vars_out)) f.close() vars_in = read_extra_abivars() self.assertEqual(vars_out, vars_in) os.remove('extra_abivars')
def create(self): """ create single abinit G0W0 flow """ manager = 'slurm' if 'ceci' in self.spec['mode'] else 'shell' # an AbiStructure object has an overwritten version of get_sorted_structure that sorts according to Z # this could also be pulled into the constructor of Abistructure #abi_structure = self.structure.get_sorted_structure() from abipy import abilab item = copy.copy(self.structure.item) self.structure.__class__ = abilab.Structure self.structure = self.structure.get_sorted_structure_z() self.structure.item = item abi_structure = self.structure manager = TaskManager.from_user_config() # Initialize the flow. flow = Flow(self.work_dir, manager, pickle_protocol=0) # flow = Flow(self.work_dir, manager) # kpoint grid defined over density 40 > ~ 3 3 3 if self.spec['converge'] and not self.all_converged: # (2x2x2) gamma centered mesh for the convergence test on nbands and ecuteps # if kp_in is present in the specs a kp_in X kp_in x kp_in mesh is used for the convergence studie if 'kp_in' in self.spec.keys(): if self.spec['kp_in'] > 9: print( 'WARNING:\nkp_in should be < 10 to generate an n x n x n mesh\nfor larger values a grid with ' 'density kp_in will be generated') scf_kppa = self.spec['kp_in'] else: scf_kppa = 2 else: # use the specified density for the final calculation with the converged nbands and ecuteps of other # stand alone calculations scf_kppa = self.spec['kp_grid_dens'] gamma = True # 'standard' parameters for stand alone calculation scf_nband = self.get_bands(self.structure) nscf_nband = [10 * scf_nband] nksmall = None ecuteps = [8] ecutsigx = 44 extra_abivars = dict(paral_kgb=1, inclvkb=2, ecut=44, pawecutdg=88, gwmem='10', getden=-1, istwfk="*1", timopt=-1, nbdbuf=8, prtsuscep=0) # read user defined extra abivars from file 'extra_abivars' should be dictionary extra_abivars.update(read_extra_abivars()) #self.bands_fac = 0.5 if 'gwcomp' in extra_abivars.keys() else 1 #self.convs['nscf_nbands']['test_range'] = tuple([self.bands_fac*x for x in self.convs['nscf_nbands']['test_range']]) response_models = ['godby'] if 'ppmodel' in extra_abivars.keys(): response_models = [extra_abivars.pop('ppmodel')] if self.option is not None: for k in self.option.keys(): if k in ['ecuteps', 'nscf_nbands']: pass else: extra_abivars.update({k: self.option[k]}) if k == 'ecut': extra_abivars.update({'pawecutdg': self.option[k] * 2}) try: grid = read_grid_from_file(s_name(self.structure) + ".full_res")['grid'] all_done = read_grid_from_file( s_name(self.structure) + ".full_res")['all_done'] workdir = os.path.join(s_name(self.structure), 'w' + str(grid)) except (IOError, OSError): grid = 0 all_done = False workdir = None if not all_done: if (self.spec['test'] or self.spec['converge']) and not self.all_converged: if self.spec['test']: print('| setting test calculation') tests = SingleAbinitGWWork(self.structure, self.spec).tests response_models = [] else: if grid == 0: print('| setting convergence calculations for grid 0') #tests = SingleAbinitGWWorkFlow(self.structure, self.spec).convs tests = self.convs else: print('| extending grid') #tests = expand(SingleAbinitGWWorkFlow(self.structure, self.spec).convs, grid) tests = expand(self.convs, grid) ecuteps = [] nscf_nband = [] for test in tests: if tests[test]['level'] == 'scf': if self.option is None: extra_abivars.update( {test + '_s': tests[test]['test_range']}) elif test in self.option: extra_abivars.update({test: self.option[test]}) else: extra_abivars.update( {test + '_s': tests[test]['test_range']}) else: for value in tests[test]['test_range']: if test == 'nscf_nbands': nscf_nband.append( value * self.get_bands(self.structure)) #scr_nband takes nscf_nbands if not specified #sigma_nband takes scr_nbands if not specified if test == 'ecuteps': ecuteps.append(value) if test == 'response_model': response_models.append(value) elif self.all_converged: print( '| setting up for testing the converged values at the high kp grid ' ) # add a bandstructure and dos calculation if os.path.isfile('bands'): nksmall = -30 #negative value > only bandstructure else: nksmall = 30 # in this case a convergence study has already been performed. # The resulting parameters are passed as option ecuteps = [ self.option['ecuteps'], self.option['ecuteps'] + self.convs['ecuteps']['test_range'][1] - self.convs['ecuteps']['test_range'][0] ] nscf_nband = [ self.option['nscf_nbands'], self.option['nscf_nbands'] + self.convs['nscf_nbands']['test_range'][1] - self.convs['nscf_nbands']['test_range'][0] ] # for option in self.option: # if option not in ['ecuteps', 'nscf_nband']: # extra_abivars.update({option + '_s': self.option[option]}) else: print('| all is done for this material') return logger.info('ecuteps : ', ecuteps) logger.info('extra : ', extra_abivars) logger.info('nscf_nb : ', nscf_nband) work = g0w0_extended_work(abi_structure, self.pseudo_table, scf_kppa, nscf_nband, ecuteps, ecutsigx, scf_nband, accuracy="normal", spin_mode="unpolarized", smearing=None, response_models=response_models, charge=0.0, sigma_nband=None, scr_nband=None, gamma=gamma, nksmall=nksmall, **extra_abivars) flow.register_work(work, workdir=workdir) return flow.allocate()
def create(self): """ create single abinit G0W0 flow """ manager = 'slurm' if 'ceci' in self.spec['mode'] else 'shell' # an AbiStructure object has an overwritten version of get_sorted_structure that sorts according to Z # this could also be pulled into the constructor of Abistructure #abi_structure = self.structure.get_sorted_structure() from abipy import abilab item = copy.copy(self.structure.item) self.structure.__class__ = abilab.Structure self.structure = self.structure.get_sorted_structure_z() self.structure.item = item abi_structure = self.structure manager = TaskManager.from_user_config() # Initialize the flow. flow = Flow(self.work_dir, manager, pickle_protocol=0) # flow = Flow(self.work_dir, manager) # kpoint grid defined over density 40 > ~ 3 3 3 if self.spec['converge'] and not self.all_converged: # (2x2x2) gamma centered mesh for the convergence test on nbands and ecuteps # if kp_in is present in the specs a kp_in X kp_in x kp_in mesh is used for the convergence studie if 'kp_in' in self.spec.keys(): if self.spec['kp_in'] > 9: print('WARNING:\nkp_in should be < 10 to generate an n x n x n mesh\nfor larger values a grid with ' 'density kp_in will be generated') scf_kppa = self.spec['kp_in'] else: scf_kppa = 2 else: # use the specified density for the final calculation with the converged nbands and ecuteps of other # stand alone calculations scf_kppa = self.spec['kp_grid_dens'] gamma = True # 'standard' parameters for stand alone calculation nb = self.get_bands(self.structure) nscf_nband = [10 * nb] nksmall = None ecuteps = [8] ecutsigx = 44 extra_abivars = dict( paral_kgb=1, inclvkb=2, ecut=44, pawecutdg=88, gwmem='10', getden=-1, istwfk="*1", timopt=-1, nbdbuf=8 ) # read user defined extra abivars from file 'extra_abivars' should be dictionary extra_abivars.update(read_extra_abivars()) #self.bands_fac = 0.5 if 'gwcomp' in extra_abivars.keys() else 1 #self.convs['nscf_nbands']['test_range'] = tuple([self.bands_fac*x for x in self.convs['nscf_nbands']['test_range']]) response_models = ['godby'] if 'ppmodel' in extra_abivars.keys(): response_models = [extra_abivars.pop('ppmodel')] if self.option is not None: for k in self.option.keys(): if k in ['ecuteps', 'nscf_nbands']: pass else: extra_abivars.update({k: self.option[k]}) if k == 'ecut': extra_abivars.update({'pawecutdg': self.option[k]*2}) try: grid = read_grid_from_file(s_name(self.structure)+".full_res")['grid'] all_done = read_grid_from_file(s_name(self.structure)+".full_res")['all_done'] workdir = os.path.join(s_name(self.structure), 'w'+str(grid)) except (IOError, OSError): grid = 0 all_done = False workdir = None if not all_done: if (self.spec['test'] or self.spec['converge']) and not self.all_converged: if self.spec['test']: print('| setting test calculation') tests = SingleAbinitGWWork(self.structure, self.spec).tests response_models = [] else: if grid == 0: print('| setting convergence calculations for grid 0') #tests = SingleAbinitGWWorkFlow(self.structure, self.spec).convs tests = self.convs else: print('| extending grid') #tests = expand(SingleAbinitGWWorkFlow(self.structure, self.spec).convs, grid) tests = expand(self.convs, grid) ecuteps = [] nscf_nband = [] for test in tests: if tests[test]['level'] == 'scf': if self.option is None: extra_abivars.update({test + '_s': tests[test]['test_range']}) elif test in self.option: extra_abivars.update({test: self.option[test]}) else: extra_abivars.update({test + '_s': tests[test]['test_range']}) else: for value in tests[test]['test_range']: if test == 'nscf_nbands': nscf_nband.append(value * self.get_bands(self.structure)) #scr_nband takes nscf_nbands if not specified #sigma_nband takes scr_nbands if not specified if test == 'ecuteps': ecuteps.append(value) if test == 'response_model': response_models.append(value) elif self.all_converged: print('| setting up for testing the converged values at the high kp grid ') # add a bandstructure and dos calculation nksmall = 30 # in this case a convergence study has already been performed. # The resulting parameters are passed as option ecuteps = [self.option['ecuteps'], self.option['ecuteps'] + self.convs['ecuteps']['test_range'][1] - self.convs['ecuteps']['test_range'][0]] nscf_nband = [self.option['nscf_nbands'], self.option['nscf_nbands'] + self.convs['nscf_nbands'][ 'test_range'][1] - self.convs['nscf_nbands']['test_range'][0]] # for option in self.option: # if option not in ['ecuteps', 'nscf_nband']: # extra_abivars.update({option + '_s': self.option[option]}) else: print('| all is done for this material') return logger.info('ecuteps : ', ecuteps) logger.info('extra : ', extra_abivars) logger.info('nscf_nb : ', nscf_nband) work = g0w0_extended_work(abi_structure, self.pseudo_table, scf_kppa, nscf_nband, ecuteps, ecutsigx, accuracy="normal", spin_mode="unpolarized", smearing=None, response_models=response_models, charge=0.0, sigma_nband=None, scr_nband=None, gamma=gamma, nksmall=nksmall, **extra_abivars) flow.register_work(work, workdir=workdir) return flow.allocate()
def process_data(self, structure): """ Process the data of a set of GW calculations: for 'single' and 'test' calculations the data is read and outputted for the parameter scanning part of a convergence calculation the data is read and parameters that provide converged results are determined for the 'full' part of a convergence calculation the data is read and it is tested if the slopes are in agreement with the scanning part """ data = GWConvergenceData(spec=self, structure=structure) if self.data['converge']: done = False try: data.read_full_res_from_file() if data.full_res['all_done']: done = True print('| no action needed al is done already') except (IOError, OSError, SyntaxError): pass data.set_type() while not done: if data.type['parm_scr']: data.read() if len(data.data) == 0: print('| parm_scr type calculation but no data found.') break if len(data.data) < 9: # todo this should be calculated print('| parm_scr type calculation but no complete data found,' ' check if all calculations are done.') break if data.find_conv_pars_scf('ecut', 'full_width', self['tol'])[0]: print('| parm_scr type calculation, converged scf values found') else: print('| parm_scr type calculation, no converged scf values found') data.full_res.update({'remark': 'No converged SCf parameter found. Continue anyway.'}) data.conv_res['values'].update({'ecut': 40*eV_to_Ha}) data.conv_res['control'].update({'ecut': True}) #if ecut is provided in extra_abivars overwrite in any case .. if 'ecut' in read_extra_abivars().keys(): data.conv_res['values'].update({'ecut': read_extra_abivars()['ecut']*eV_to_Ha}) # if converged ok, if not increase the grid parameter of the next set of calculations extrapolated = data.find_conv_pars(self['tol']) if data.conv_res['control']['nbands']: print('| parm_scr type calculation, converged values found, extrapolated value: %s' % extrapolated[4]) else: print('| parm_scr type calculation, no converged values found, increasing grid') data.full_res['grid'] += 1 data.print_full_res() data.print_conv_res() # plot data: print_gnuplot_header('plots', s_name(structure)+' tol = '+str(self['tol']), filetype=None) data.print_gnuplot_line('plots') data.print_plot_data() done = True elif data.type['full']: if not data.read_conv_res_from_file(s_name(structure)+'.conv_res'): print('| Full type calculation but the conv_res file is not available, trying to reconstruct') data.read() data.find_conv_pars(self['tol']) data.print_conv_res() data.read(subset='.conv') if len(data.data) == 0: print('| Full type calculation but no data found.') break if len(data.data) < 4: print('| Full type calculation but no complete data found.') for item in data.data: print(item) break if data.test_full_kp_results(tol_rel=1, tol_abs=0.0015): print('| Full type calculation and the full results agree with the parm_scr.' ' All_done for this compound.') data.full_res.update({'all_done': True}) data.print_full_res() done = True #data.print_plot_data() self.code_interface.store_results(name=s_name(structure)) else: print('| Full type calculation but the full results do not agree with the parm_scr.') print('| Increase the tol to find better converged parameters and test the full grid again.') print('| TODO') data.full_res.update({'remark': 'no agreement at high dens kp mesh,', 'all_done': True}) # read the system specific tol for System.conv_res # if it's not there create it from the global tol # reduce tol # set data.type to convergence # loop done = True elif self.data['test']: data.read() data.set_type() data.print_plot_data() else: data.read() data.set_type() data.print_plot_data()