Source code for abipy.abio.variable

import string
import collections
import numpy as np

__all__ = [

_SPECIAL_DATASET_INDICES = (':', '+', '?')

_DATASET_INDICES = ''.join(list(string.digits) + list(_SPECIAL_DATASET_INDICES))

_INTERNAL_DATASET_INDICES = ('__s', '__i', '__a')


_UNITS = {
    'bohr': 1.0,
    'angstrom': 1.8897261328856432,
    'hartree': 1.0,
    'Ha': 1.0,
    'eV': 0.03674932539796232,

[docs]class InputVariable(object): """ An Abinit input variable. """ def __init__(self, name, value, units='', valperline=3): self._name = name self.value = value self._units = units # Maximum number of values per line. self.valperline = valperline if name in ['bdgw']: self.valperline = 2 if (is_iter(self.value) and isinstance(self.value[-1], str) and self.value[-1] in _UNITS): self.value = list(self.value) self._units = self.value.pop(-1)
[docs] def get_value(self): """Return the value.""" if self.units: return list(self.value) + [self.units] else: return self.value
@property def name(self): return self._name @property def basename(self): """Return the name trimmed of any dataset index.""" basename = return basename.rstrip(_DATASET_INDICES) @property def dataset(self): """Return the dataset index in string form.""" return[-1] @property def units(self): """Return the units.""" return self._units def __str__(self): """Declaration of the variable in the input file.""" value = self.value if value is None or not str(value): return '' var = line = ' ' + var # By default, do not impose a number of decimal points floatdecimal = 0 # For some inputs, enforce number of decimal points... if any(inp in var for inp in ('xred', 'xcart', 'rprim', 'qpt', 'kpt')): floatdecimal = 16 # ...but not for those if any(inp in var for inp in ('ngkpt', 'kptrlatt', 'ngqpt', 'ng2qpt')): floatdecimal = 0 if isinstance(value, np.ndarray): n = 1 for i in np.shape(value): n *= i value = np.reshape(value, n) value = list(value) # values in lists if isinstance(value, (list, tuple)): # Reshape a list of lists into a single list if all(isinstance(v, (list, tuple)) for v in value): line += self.format_list2d(value, floatdecimal) else: line += self.format_list(value, floatdecimal) # scalar values else: line += ' ' + str(value) # Add units if self.units: line += ' ' + self.units return line
[docs] def format_scalar(self, val, floatdecimal=0): """ Format a single numerical value into a string with the appropriate number of decimal. """ sval = str(val) if sval.lstrip('-').lstrip('+').isdigit() and floatdecimal == 0: return sval try: fval = float(val) except Exception: return sval if fval == 0 or (abs(fval) > 1e-3 and abs(fval) < 1e4): form = 'f' addlen = 5 else: form = 'e' addlen = 8 ndec = max(len(str(fval-int(fval)))-2, floatdecimal) ndec = min(ndec, 10) sval = '{v:>{l}.{p}{f}}'.format(v=fval, l=ndec+addlen, p=ndec, f=form) sval = sval.replace('e', 'd') return sval
[docs] def format_list2d(self, values, floatdecimal=0): """Format a list of lists.""" lvals = flatten(values) # Determine the representation if all(isinstance(v, int) for v in lvals): type_all = int else: try: for v in lvals: float(v) type_all = float except Exception: type_all = str # Determine the format width = max(len(str(s)) for s in lvals) if type_all == int: formatspec = '>{0}d'.format(width) elif type_all == str: formatspec = '>{0}'.format(width) else: # Number of decimal maxdec = max(len(str(f-int(f)))-2 for f in lvals) ndec = min(max(maxdec, floatdecimal), 10) if all(f == 0 or (abs(f) > 1e-3 and abs(f) < 1e4) for f in lvals): formatspec = '>{w}.{p}f'.format(w=ndec+5, p=ndec) else: formatspec = '>{w}.{p}e'.format(w=ndec+8, p=ndec) line = '\n' for L in values: for val in L: line += ' {v:{f}}'.format(v=val, f=formatspec) line += '\n' return line.rstrip('\n')
[docs] def format_list(self, values, floatdecimal=0): """ Format a list of values into a string. The result might be spread among several lines. """ line = '' # Format the line declaring the value for i, val in enumerate(values): line += ' ' + self.format_scalar(val, floatdecimal) if self.valperline is not None and (i+1) % self.valperline == 0: line += '\n' # Add a carriage return in case of several lines if '\n' in line.rstrip('\n'): line = '\n' + line return line.rstrip('\n')
def is_iter(obj): """Return True if the argument is list-like.""" return hasattr(obj, '__iter__') def flatten(iterable): """Make an iterable flat, i.e. a 1d iterable object.""" iterator = iter(iterable) array, stack = collections.deque(), collections.deque() while True: try: value = next(iterator) except StopIteration: if not stack: return tuple(array) iterator = stack.pop() else: if not isinstance(value, str) \ and isinstance(value, stack.append(iterator) iterator = iter(value) else: array.append(value)