mirror of https://github.com/QMCPACK/qmcpack.git
nexus: eshdf split write_nk() out from kinetic()
This commit is contained in:
Yubo "Paul" Yang
parent
1ebca7c53b
commit
fa38f3f52f
168
nexus/bin/eshdf
168
nexus/bin/eshdf
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@ -159,9 +159,53 @@ def read_eshdf_nofk_data(filename,Ef,ncore=0,nval=-1):
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#end def read_eshdf_nofk_data
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def first_eshdf_file(args):
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# check files provided
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eshdf_files = list(sorted(args[1:]))
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if len(eshdf_files)!=1:
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user_error('exactly one ESHDF file is allowed as input.\nYou provided: {}'.format(eshdf_files))
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#end if
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eshdf_filepath = eshdf_files[0]
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if not os.path.exists(eshdf_filepath):
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user_error('ESHDF file does not exist.\nPlease check the path provided:\n {}'.format(eshdf_filepath))
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elif not eshdf_filepath.endswith('.h5'):
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user_error('file provided is not an HDF5 file.\nAn ESHDF file must have a .h5 extension.\nPlease check the path provided:\n {}'.format(eshdf_filepath))
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#end if
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return eshdf_filepath
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#end def first_eshdf_file
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def interpret_nk_options(parser):
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options,args = parser.parse_args()
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opt.transfer_from(options.__dict__)
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for k,v in opt.items():
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if v=='None':
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opt[k] = None
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#end if
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#end for
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eshdf_files = list(sorted(args[1:]))
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if opt.help or len(eshdf_files)==0:
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print('\n'+parser.format_help().strip()+'\n')
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exit()
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#end if
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# check Fermi energy
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if opt.E_fermi is None:
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user_error('please provide the Fermi energy via the --Ef option.')
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else:
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try:
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opt.E_fermi = float(opt.E_fermi)
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except:
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user_error('value provided for Fermi energy is not a real number.\nYou provided: {}'.format(opt.E_fermi))
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#end try
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#end if
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# set active space
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opt.ncore = int(opt.ncore)
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opt.nval = int(opt.nval)
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return opt, args
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#end def interpret_nk_options
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def kinetic():
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# read command line inputs
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usage = '''usage: %prog kinetic [options] [eshdf_file]'''
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parser = OptionParser(usage=usage,add_help_option=False,version='%prog {}.{}.{}'.format(*nexus_version))
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@ -186,59 +230,16 @@ def kinetic():
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action='store_true',default=False,
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help='Print per orbital kinetic energies (default=%default).'
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)
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parser.add_option('--ispin',dest='ispin',default=0,
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help='spin channel (default=%default).'
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)
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parser.add_option('--ncore',dest='ncore',default=0,
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help='number of core states to exclude (default=%default).'
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)
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parser.add_option('--nval',dest='nval',default=-1,
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help='number of valence states to include (default=%default, i.e. all).'
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)
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parser.add_option('--fnk3d',dest='fnk3d',
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default=None,
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help='Output 3D momentum distribution'
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)
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options,args = parser.parse_args()
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eshdf_files = list(sorted(args[1:]))
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opt.transfer_from(options.__dict__)
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for k,v in opt.items():
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if v=='None':
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opt[k] = None
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#end if
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#end for
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if opt.help or len(eshdf_files)==0:
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print('\n'+parser.format_help().strip()+'\n')
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exit()
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#end if
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# check files provided
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if len(eshdf_files)!=1:
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user_error('exactly one ESHDF file is allowed as input.\nYou provided: {}'.format(eshdf_files))
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#end if
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eshdf_filepath = eshdf_files[0]
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if not os.path.exists(eshdf_filepath):
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user_error('ESHDF file does not exist.\nPlease check the path provided:\n {}'.format(eshdf_filepath))
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elif not eshdf_filepath.endswith('.h5'):
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user_error('file provided is not an HDF5 file.\nAn ESHDF file must have a .h5 extension.\nPlease check the path provided:\n {}'.format(eshdf_filepath))
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#end if
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# check Fermi energy
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if opt.E_fermi is None:
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user_error('please provide the Fermi energy via the --Ef option.')
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else:
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try:
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opt.E_fermi = float(opt.E_fermi)
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except:
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user_error('value provided for Fermi energy is not a real number.\nYou provided: {}'.format(opt.E_fermi))
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#end try
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#end if
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opt.ncore = int(opt.ncore)
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opt.nval = int(opt.nval)
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opt, args = interpret_nk_options(parser)
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eshdf_filepath = first_eshdf_file(args)
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d = read_eshdf_nofk_data(eshdf_filepath,opt.E_fermi,ncore=opt.ncore,nval=opt.nval)
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@ -315,34 +316,65 @@ def kinetic():
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#end for
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#end for
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#end if
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if opt.fnk3d is not None:
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ispin0 = int(opt.ispin)
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log('Writing n(k) to HDF5 {}'.format(opt.fnk3d))
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import tables
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klist = []
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nklist = []
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for key, val in d.data.items():
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ik, ispin = key
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if ispin != ispin0: continue
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klist.append(val.k)
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nklist.append(val.nk)
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kvecs = np.concatenate(klist, axis=0)
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nk = np.concatenate(nklist, axis=0)
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data = np.c_[kvecs, nk]
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filters = tables.Filters(complevel=5, complib='zlib')
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fp = tables.open_file(opt.fnk3d, mode='w', filter=filters)
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atom = tables.Atom.from_dtype(data.dtype)
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ca = fp.create_carray(fp.root, 'data', atom, data.shape)
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ca[:] = data
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fp.close()
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#end if
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#end def kinetic
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def write_nk():
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# read command line inputs
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usage = '''usage: %prog write_nk [options] [eshdf_file]'''
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parser = OptionParser(usage=usage,add_help_option=False,version='%prog {}.{}.{}'.format(*nexus_version))
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parser.add_option('-h','--help',dest='help',
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action='store_true',default=False,
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help='Print help information and exit (default=%default).'
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)
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parser.add_option('--Ef',dest='E_fermi',
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default='None',
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help='Fermi energy in eV (default=%default).'
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)
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parser.add_option('--ncore',dest='ncore',default=0,
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help='number of core states to exclude (default=%default).'
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)
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parser.add_option('--nval',dest='nval',default=-1,
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help='number of valence states to include (default=%default, i.e. all).'
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)
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parser.add_option('--ispin',dest='ispin',default=0,
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help='spin channel (default=%default).'
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)
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parser.add_option('--outfile',dest='outfile',
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default=None,
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help='Output 3D momentum distribution'
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)
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opt, args = interpret_nk_options(parser)
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eshdf_filepath = first_eshdf_file(args)
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d = read_eshdf_nofk_data(eshdf_filepath,opt.E_fermi,ncore=opt.ncore,nval=opt.nval)
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ispin0 = int(opt.ispin)
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log('Writing n(k) to HDF5 {}'.format(opt.outfile))
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import tables
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klist = []
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nklist = []
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for key, val in d.data.items():
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ik, ispin = key
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if ispin != ispin0: continue
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klist.append(val.k)
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nklist.append(val.nk)
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kvecs = np.concatenate(klist, axis=0)
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nk = np.concatenate(nklist, axis=0)
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data = np.c_[kvecs, nk]
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filters = tables.Filters(complevel=5, complib='zlib')
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fp = tables.open_file(opt.outfile, mode='w', filter=filters)
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atom = tables.Atom.from_dtype(data.dtype)
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ca = fp.create_carray(fp.root, 'data', atom, data.shape)
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ca[:] = data
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fp.close()
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#end def write_nk
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operations = obj(
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kinetic = kinetic,
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write_nk = write_nk,
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)
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