Add ShengBTE IO Functions #1518
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| # coding: utf-8 | ||
| # Copyright (c) Pymatgen Development Team. | ||
| # Distributed under the terms of the MIT License | ||
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| import f90nml | ||
| import numpy as np | ||
| import re | ||
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| """ | ||
| This module defines IO ShengBTE for reading, updating, and writing the | ||
| CONTROL input file | ||
| """ | ||
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| __author__ = "Rees Chang" | ||
| __copyright__ = "Copyright 2019, The Materials Project" | ||
| __version__ = "0.1" | ||
| __email__ = "rc564@cornell.edu" | ||
| __date__ = "June 27, 2019" | ||
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| class Control: | ||
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| """ | ||
| Class for reading, updating, and writing ShengBTE CONTROL files. | ||
| Currently only supports ShengBTE options relevant to CSLD. | ||
| """ | ||
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| def __init__(self, | ||
| alloc_dict=None, | ||
| crystal_dict=None, | ||
| params_dict=None, | ||
| flags_dict=None): | ||
| """ | ||
| Args: | ||
| alloc_dict (dict): ShengBTE 'allocations' parameters | ||
| crystal_dict (dict): ShengBTE 'crystal' parameters | ||
| params_dict (dict): ShengBTE 'parameters' parameters | ||
| flags_dict (dict): ShengBTE 'flags' parameters | ||
| """ | ||
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| self.alloc_dict = { | ||
| 'nelements': None, | ||
| 'natoms': None, | ||
| 'ngrid': None, | ||
| 'norientations': 0, | ||
| } | ||
| if alloc_dict: | ||
| self.alloc_dict.update(alloc_dict) | ||
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| self.crystal_dict = { | ||
| 'lfactor': 0.1, | ||
| 'lattvec': None, #required | ||
| 'types': None, #required | ||
| 'elements': None, #required | ||
| 'positions': None, #required | ||
| 'masses': None, | ||
| 'gfactors': None, | ||
| 'epsilon': None, | ||
| 'born': None, | ||
| 'scell': None, #required | ||
| 'orientations': None | ||
| } | ||
| if crystal_dict: | ||
| self.crystal_dict.update(crystal_dict) | ||
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| self.params_dict = { | ||
| 'T': 300, #required | ||
| 'T_min': None, | ||
| 'T_max': None, | ||
| 'T_step': None, | ||
| 'omega_max': None, | ||
| 'scalebroad': 0.5, #required | ||
| 'rmin': None, | ||
| 'rmax': None, | ||
| 'dr': None, | ||
| 'maxiter': None, | ||
| 'nticks': None, | ||
| 'eps': None | ||
| } | ||
| if params_dict: | ||
| self.params_dict.update(params_dict) | ||
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| self.flags_dict = { | ||
| 'nonanalytic': None, | ||
| 'convergence': None, | ||
| 'isotopes': None, | ||
| 'autoisotopes': None, | ||
| 'nanowires': None, | ||
| 'onlyharmonic': None, | ||
| 'espresso': None | ||
| } | ||
| if flags_dict: | ||
| self.flags_dict.update(flags_dict) | ||
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| def check_required_params(): | ||
| """ | ||
| Raise error if any required parameters are missing | ||
| """ | ||
| required_params = {'crystal': | ||
| ['lattvec', | ||
| 'types', | ||
| 'elements', | ||
| 'positions', | ||
| 'scell'], | ||
| 'parameters': | ||
| ['T', | ||
| 'scalebroad'], | ||
| } | ||
| required_namelists = list(required_params.keys()) | ||
| for required_namelist in required_namelists: | ||
| required_namelist_params = required_params[required_namelist] | ||
| for required_namelist_param in required_namelist_params: | ||
| if required_namelist == 'allocations' and \ | ||
| self.alloc_dict[required_namelist_param] is None: | ||
| raise AttributeError('Missing argument: {}>{}'.format(required_namelist, | ||
| required_namelist_param)) | ||
| elif required_namelist == 'crystal' and \ | ||
| self.crystal_dict[required_namelist_param] is None: | ||
| raise AttributeError('Missing argument: {}>{}'.format(required_namelist, | ||
| required_namelist_param)) | ||
| elif required_namelist == 'parameters' and \ | ||
| self.params_dict[required_namelist_param] is None: | ||
| raise AttributeError('Missing argument: {}>{}'.format(required_namelist, | ||
| required_namelist_param)) | ||
| elif required_namelist == 'flags' and \ | ||
| self.flags_dict[required_namelist_param] is None: | ||
| raise AttributeError('Missing argument: {}>{}'.format(required_namelist, | ||
| required_namelist_param)) | ||
| check_required_params() | ||
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| @classmethod | ||
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| def from_file(cls, filepath): | ||
| """ | ||
| Read a CONTROL namelist file and output a 'Control' object | ||
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| Args: | ||
| filepath (String): Path of the CONTROL file. | ||
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| Returns: | ||
| 'Control' object with parameters instantiated. | ||
| """ | ||
| nml = f90nml.read(filepath) | ||
| sdict = nml.todict() | ||
| if 't' in sdict['parameters']: | ||
| sdict['parameters']['T'] = sdict['parameters']['t'] | ||
| del sdict['parameters']['t'] | ||
| if 't_min' in sdict['parameters']: | ||
| sdict['parameters']['T_min'] = sdict['parameters']['t_min'] | ||
| del sdict['parameters']['t_min'] | ||
| if 't_max' in sdict['parameters']: | ||
| sdict['parameters']['T_max'] = sdict['parameters']['t_max'] | ||
| del sdict['parameters']['t_max'] | ||
| if 't_step' in sdict['parameters']: | ||
| sdict['parameters']['T_step'] = sdict['parameters']['t_step'] | ||
| del sdict['parameters']['t_step'] | ||
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| alloc_dict = sdict['allocations'] | ||
| crystal_dict = sdict['crystal'] | ||
| params_dict = sdict['parameters'] | ||
| flags_dict = sdict['flags'] | ||
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| return cls(alloc_dict, crystal_dict, params_dict, flags_dict) | ||
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| @classmethod | ||
| def from_dict(cls, sdict): | ||
| """ | ||
| Write a CONTROL file from a Python dictionary. | ||
| Description and default parameters can be found at | ||
| https://bitbucket.org/sousaw/shengbte/src/master/. | ||
| Note some parameters are mandatory. Optional parameters | ||
| default here to None and will not be written to file. | ||
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| Args: | ||
| dict: A Python dictionary of ShengBTE input parameters. | ||
| filename: Filename to save the CONTROL file | ||
| """ | ||
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| try: | ||
| alloc_dict = sdict['allocations'] | ||
| except: | ||
| alloc_dict = {} | ||
| try: | ||
| crystal_dict = sdict['crystal'] | ||
| except: | ||
| crystal_dict = {} | ||
| try: | ||
| params_dict = sdict['parameters'] | ||
| except: | ||
| params_dict = {} | ||
| try: | ||
| flags_dict = sdict['flags'] | ||
| except: | ||
| flags_dict = {} | ||
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| return cls(alloc_dict, crystal_dict, params_dict, flags_dict) | ||
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| def to_file(self, filename): | ||
|
There was a problem hiding this comment. Can you set the filename default to "CONTROL" |
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| """ | ||
| Writes ShengBTE CONTROL file from 'Control' object | ||
| """ | ||
| positions = np.asarray(self.crystal_dict['positions']) | ||
| num_sites, _ = positions.shape | ||
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| nelements = str(self.alloc_dict['nelements']) | ||
| natoms = str(self.alloc_dict['natoms']) | ||
| ngrid = self.alloc_dict['ngrid'] | ||
| norientations = str(self.alloc_dict['norientations']) | ||
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| lfactor = str(self.crystal_dict['lfactor']) | ||
| lattvec1 = self.crystal_dict['lattvec'][0] | ||
| lattvec2 = self.crystal_dict['lattvec'][1] | ||
| lattvec3 = self.crystal_dict['lattvec'][2] | ||
| elements = self.crystal_dict['elements'] | ||
| types = self.crystal_dict['types'] | ||
| scell = self.crystal_dict['scell'] | ||
| # new from here | ||
| if self.crystal_dict['epsilon'] is not None: | ||
| epsilon1 = self.crystal_dict['epsilon'][0] | ||
| epsilon2 = self.crystal_dict['epsilon'][1] | ||
| epsilon3 = self.crystal_dict['epsilon'][2] | ||
| else: | ||
| epsilon1 = np.full(3, None) | ||
| epsilon2 = np.full(3, None) | ||
| epsilon3 = np.full(3, None) | ||
| if self.crystal_dict['born'] is not None: | ||
| born = np.asarray(self.crystal_dict['born']) | ||
| else: | ||
| born = np.full((num_sites, 3, 3), None) | ||
| orientations = np.asarray(self.crystal_dict['orientations']) | ||
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| temperature = str(int(self.params_dict['T'])) | ||
| scalebroad = str(self.params_dict['scalebroad']) | ||
| t_min = str(self.params_dict['T_min']) | ||
| t_max = str(self.params_dict['T_max']) | ||
| t_step = str(self.params_dict['T_step']) | ||
| omega_max = str(self.params_dict['omega_max']) | ||
| rmin = str(self.params_dict['rmin']) | ||
| rmax = str(self.params_dict['rmax']) | ||
| dr = str(self.params_dict['dr']) | ||
| maxiter = str(self.params_dict['maxiter']) | ||
| nticks = str(self.params_dict['nticks']) | ||
| eps = str(self.params_dict['eps']) | ||
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| onlyharmonic = self.flags_dict['onlyharmonic'] | ||
| isotopes = self.flags_dict['isotopes'] | ||
| nonanalytic = self.flags_dict['nonanalytic'] | ||
| nanowires = self.flags_dict['nanowires'] | ||
| convergence = self.flags_dict['convergence'] | ||
| autoisotopes = self.flags_dict['autoisotopes'] | ||
| espresso = self.flags_dict['espresso'] | ||
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| def boolean_to_string(boolean): | ||
| if boolean is not None: | ||
| if boolean is True: | ||
| return '.TRUE.' | ||
| else: | ||
| return '.FALSE.' | ||
| else: | ||
| return 'None' | ||
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| #Write strings for types, positions, and born | ||
| indent = ' ' | ||
| types_string = 'types=' | ||
| positions_string = '' | ||
| born_string = '' | ||
| for line in range(num_sites): | ||
| if line != num_sites-1: | ||
| types_string += str(types[line])+' ' | ||
| else: | ||
| types_string += str(types[line])+',\n' | ||
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| positions_string += indent+'positions(:,' + str(line+1) + ')=' + str(positions[line,0]) + ' ' \ | ||
| + str(positions[line,1]) + ' ' + str(positions[line,2]) + ',\n' | ||
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| for i in range(3): | ||
| born_string += indent+'born(:,'+str(i+1)+','+str(line+1)+')='+str(born[line][i][0])+' '\ | ||
| +str(born[line][i][1])+' '+str(born[line][i][2])+',\n' | ||
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| #Write string for orientations | ||
| num_orientations = self.alloc_dict['norientations'] | ||
| orientations_string = '' | ||
| for o in range(num_orientations): | ||
| if o != num_orientations-1: | ||
| orientations_string += indent+'orientations(:,'+str(o+1)+')='+str(orientations[o][0])+' '+\ | ||
| str(orientations[o][1])+' '+str(orientations[o][2])+',\n' | ||
| else: | ||
| orientations_string += indent + 'orientations(:,' + str(o + 1) + ')=' + str(orientations[o][0]) + ' ' + \ | ||
| str(orientations[o][1]) + ' ' + str(orientations[o][2]) + '\n' | ||
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| #masses, gfactors | ||
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| full_string = '&allocations\n'+indent+'nelements='+nelements+',\n' | ||
| full_string += indent+'natoms='+natoms+',\n' | ||
| full_string += indent+'ngrid(:)='+str(ngrid[0])+' '+str(ngrid[1])+' '+str(ngrid[2])+'\n' | ||
| full_string += indent+'norientations='+norientations+'\n' | ||
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| full_string += '&end\n&crystal\n' | ||
| full_string += indent+'lfactor='+lfactor+',\n' | ||
| full_string += indent+'lattvec(:,1)='+str(lattvec1[0])+' '+str(lattvec1[1])+' '+str(lattvec1[2])+',\n' | ||
| full_string += indent+'lattvec(:,2)='+str(lattvec2[0])+' '+str(lattvec2[1])+' '+str(lattvec2[2])+',\n' | ||
| full_string += indent+'lattvec(:,3)='+str(lattvec3[0])+' '+str(lattvec3[1])+' '+str(lattvec3[2])+',\n' | ||
| full_string += indent+'elements=' | ||
| if isinstance(elements, list): | ||
| for i in range(len(elements)): | ||
| full_string += '\"'+elements[i]+str('\"') | ||
| if i != (len(elements)-1): | ||
| full_string += ' ' | ||
| else: | ||
| full_string += '\n' | ||
| else: | ||
| full_string += '\"'+elements+str('\"\n') | ||
| full_string += indent+types_string | ||
| full_string += positions_string | ||
| full_string += indent+'epsilon(:,1)='+str(epsilon1[0])+' '+str(epsilon1[1])+' '+str(epsilon1[2])+',\n' | ||
| full_string += indent+'epsilon(:,2)='+str(epsilon2[0])+' '+str(epsilon2[1])+' '+str(epsilon2[2])+',\n' | ||
| full_string += indent+'epsilon(:,3)='+str(epsilon3[0])+' '+str(epsilon3[1])+' '+str(epsilon3[2])+',\n' | ||
| full_string += born_string | ||
| full_string += indent+'scell(:)='+str(scell[0])+' '+str(scell[1])+' '+str(scell[2])+'\n' | ||
| full_string += orientations_string | ||
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| full_string += '&end\n¶meters\n' | ||
| full_string += indent+'T='+temperature+'\n' | ||
| full_string += indent+'scalebroad='+scalebroad+'\n' | ||
| full_string += indent+'T_min='+t_min+'\n' | ||
| full_string += indent+'T_max='+t_max+'\n' | ||
| full_string += indent+'T_step='+t_step+'\n' | ||
| full_string += indent+'omega_max='+omega_max+'\n' | ||
| full_string += indent+'rmin='+rmin+'\n' | ||
| full_string += indent+'rmax='+rmax+'\n' | ||
| full_string += indent+'dr='+dr+'\n' | ||
| full_string += indent+'maxiter='+maxiter+'\n' | ||
| full_string += indent+'nticks='+nticks+'\n' | ||
| full_string += indent+'eps='+eps+'\n' | ||
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| full_string += '&end\n&flags\n' | ||
| full_string += indent+'isotopes='+boolean_to_string(isotopes)+'\n' | ||
| full_string += indent+'onlyharmonic='+boolean_to_string(onlyharmonic)+'\n' | ||
| full_string += indent+'nonanalytic='+boolean_to_string(nonanalytic)+'\n' | ||
| full_string += indent+'nanowires='+boolean_to_string(nanowires)+'\n' | ||
| full_string += indent + 'convergence=' + boolean_to_string(convergence) + '\n' | ||
| full_string += indent + 'autoisotopes=' + boolean_to_string(autoisotopes) + '\n' | ||
| full_string += indent + 'espresso=' + boolean_to_string(espresso) + '\n' | ||
| full_string += '&end' | ||
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| def remove_substring(substring, string): | ||
| #Removes lines from 'string' containing 'substring' | ||
| return re.sub('.*'+substring+'.*\n?', '', string) | ||
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| full_string = remove_substring('None', full_string) | ||
| file = open(filename, 'w+') | ||
| file.write(full_string) | ||
| file.close() | ||
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