Source code for calcio
# coding: utf-8
# vim: set et ts=4 sw=4 fdm=indent mouse=a cc=+1 tw=80:
"""
Module calcio
=============
"""
from datetime import datetime
import re
import numpy as np
import ase
from ase import Atom, Atoms
from ase.data import chemical_symbols
import os
from msspec.misc import UREG, LOGGER
from msspec.utils import get_atom_index
[docs]class PhagenIO(object):
def __init__(self, phagen_parameters, malloc_parameters):
self.parameters = phagen_parameters
self.malloc_parameters = malloc_parameters
self.tl = None
self.nat = None
self.nateqm = None
self.ne = None
self.ipot = None
self.lmax_mode = None
self.nlmax = None
self.energies = None
[docs] def write_input_file(self, filename='input.ms'): # noqa: C901
# in input folder
LOGGER.debug("Writing Phagen input file")
atoms = self.parameters.atoms
if not atoms.has('mt_radii'):
for a in atoms:
a.set('mt_radius', 0.)
if not atoms.has('mt_radii_scale'):
for a in atoms:
a.set('mt_radius_scale', 1.)
radii = atoms.get_array('mt_radii')
radii_scale = atoms.get_array('mt_radii_scale')
if np.all(radii == 0) and np.all(radii_scale == 1):
self.parameters.norman = 'stdcrm'
elif np.all(radii == 0) and np.any(radii_scale != 1):
self.parameters.norman = 'scaled'
radii = radii_scale
else:
self.parameters.norman = 'extrad'
radii *= radii_scale
parameters = []
for parameter in self.parameters:
name = parameter.name
if name in ('ionicity', 'atoms'):
# skip ionicity and atoms parameters as they are treated in
# other sections
continue
value = parameter.value
if isinstance(value, str) and not re.match(r'\..*\.', value):
s = ' {}=\'{:s}\''.format(name, str(parameter))
else:
s = ' {}={:s}'.format(name, str(parameter))
parameters.append(s)
header = " &job\n"
header += ',\n'.join(parameters) + "\n &end\n"
header += (' c Auto-generated file on {}\n Computes the T-matrix and '
'radial matrix elements\n\n').format(
datetime.ctime(datetime.now()))
# cluster section
try:
absorber = atoms.absorber
except AttributeError as err:
print(err)
absorber = 0
cluster_section = ''
absorber_line = ''
line_format = '{:>10s}{:4d}{:11.6f}{:14.6f}{:14.6f}{:13.4f}\n'
for iat, atom in enumerate(atoms):
symbol = atom.symbol
if symbol == 'X':
symbol = 'ES'
number = atom.number
x, y, z = atom.position
r = radii[iat]
cluster_line = line_format.format(symbol, number, x, y, z, r)
# store absober line
if atom.index == absorber:
absorber_line = cluster_line
else:
cluster_section += cluster_line
cluster_section = absorber_line + cluster_section
cluster_section += '{:10d}{:4d}{:10.0f}{:9.0f}{:9.0f}{:8.0f}\n'.format(
-1, -1, 0, 0, 0, 0)
# Ionicity section
ionicity = self.parameters.ionicity
ionicity_section = ''
ionicity_format = '{:8d}{:9.2f}\n'
numbers = np.unique(atoms.numbers)
for Z in numbers:
try:
symbol = chemical_symbols[Z]
charge = ionicity[symbol]
except KeyError:
charge = 0
ionicity_section += ionicity_format.format(Z, charge)
ionicity_section += '{:8d}\n'.format(-1)
content = header + cluster_section + ionicity_section
# Write the content to filename
try:
with open(filename, 'r') as fd:
old_content = fd.read()
except IOError:
old_content = ''
pat = re.compile(r' c .*\n')
modified = False
if pat.sub('', content) != pat.sub('', old_content):
with open(filename, 'w') as fd:
fd.write(content)
modified = True
return modified
[docs] def write_include_file(self, filename='msxas3.inc'):
# read the whole include file content
with open(filename, 'r') as fd:
content = fd.read()
# backup the content in memory
old_content = content
# replace the content
for p in self.malloc_parameters:
content = re.sub(r'({:s}\s*=\s*)\d+'.format(p.name),
r'\g<1>{:d}'.format(p.value), content)
# actually write to the file only if different from the previous file
modified = False
if content != old_content:
with open(filename, 'w') as fd:
fd.write(content)
modified = True
return modified
[docs] def load_tl_file(self, filename='tmatrix.tl'):
atom_data = []
# load all the file in the string 'content'
with open(filename, 'r') as fd:
content = fd.read()
# convert the file to a (nat x ne) array
#
# first, split the content in a list for each atom
pattern = re.compile(r'-+\s*ATOM.*-+')
lines = pattern.split(content)
# get the number of atoms (nat) and the number of energy points (ne)
nat, ne, _, ipot, lmax_mode = list(map(int,
content.split('\n')[0].split()))
self.nat = nat
self.ne = ne
self.ipot = ipot
self.lmax_mode = lmax_mode
# extract atom data
for line in lines:
numbers_str = ''.join(line.strip().split('\n')).split()
numbers = []
for n in numbers_str:
if not re.match(r'^\d+$', n):
numbers.append(float(n))
if len(numbers) > 0:
array = np.array(numbers).reshape((-1, 4))
atom_data.append(array)
# construct the data array
data = []
for i in range(nat):
data.append([])
for j in range(ne):
data[i].append(atom_data[j * nat + i])
self.tl = data
return data
[docs] def write_tl_file(self, filename='tmatrix.tl'):
def get_lmaxs(ie):
lmaxs = np.zeros(int(4 * np.ceil(self.nat / 4.)), dtype=int)
for a in range(self.nat):
lmaxs[a] = len(self.tl[a][ie]) - 1
lmaxs = lmaxs.reshape((-1, 4))
return lmaxs
def get_energies(unit='eV'):
emin = self.parameters.emin
emax = self.parameters.emax
delta = self.parameters.delta
energies = np.arange(emin, emax, delta)
if len(energies) == 0:
energies = np.array([emin])
if energies[-1] + delta / 2 < emax:
energies = np.append(energies, energies[-1] + delta)
# conversion in eV
if unit == 'eV':
energies = (energies * UREG.Ry).to('eV')
return energies
def custom_strfloat(f):
mantissa, exponent = '{:.10E}'.format(f).split('E')
m = format(float(mantissa) / 10, '.6f').replace('-0', '-')
e = format(int(exponent) + 1, '+03d')
return ' {}E{}'.format(m, e)
with open(filename, 'w') as fd:
fd.write('{:>9}{:>9}{:>9}{:>9}{:>9}\n'.format(self.nat, self.ne, 1,
self.ipot,
self.lmax_mode))
nlmax = 0
for ie in range(self.ne):
# write all lmaxs for each energy set
lmaxs = get_lmaxs(ie)
nlmax = int(max(nlmax, np.max(lmaxs)))
fmt1 = '{:>9}' * 4 + '\n'
fmt2 = '{:12.4f}{:10.4f}'
fmt3 = '{:18.6E}'
fmt_line = ' {:9.4f} {:9.4f}{:18.6E}{:18.6E}\n'
for _ in lmaxs:
fd.write(fmt1.format(*_))
for ia in range(self.nat):
# write the atom header line
fd.write('{}ATOM{:>4}{}\n'.format('-' * 26 + ' ', ia + 1,
' ' + '-' * 23))
for _a, _b, _c, _d in self.tl[ia][ie]:
# fd.write(fmt2.format(_a, _b))
# fd.write(custom_strfloat(_c))
# fd.write(custom_strfloat(_d))
#fd.write('\n')
fd.write(fmt_line.format(_a, _b, _c, _d))
self.nlmax = nlmax
self.energies = get_energies()
[docs] def load_cluster_file(self, filename='cluster.clu'):
data = np.loadtxt(filename, skiprows=1, usecols=(0, 2, 3, 4, 5, 6))
atoms = self.parameters.atoms
absorber_position = atoms[atoms.absorber].position
positions = data[:, 2:5] + absorber_position
proto_indices = []
for atom in atoms:
i = np.argmin(np.linalg.norm(positions - atom.position, axis=1))
proto_index = int(data[i, -1])
proto_indices.append(proto_index)
atoms.set_array('proto_indices', np.array(proto_indices))
self.nateqm = int(np.max([
len(np.where(data[:, -1] == i)[0]) for i in range(1, self.nat + 1)
]))
[docs] def load_prototypical_atoms(self, filename='molinpot3.out'):
with open(filename, 'r') as fd:
content = fd.readlines()
atoms = self.parameters.atoms
content = content[-len(atoms):]
proto = Atoms()
for line in content:
datatxt = np.array(re.split(r'\s+', line.strip(' \n')))
neq = int(datatxt[-1])
if neq == 0:
Z = int(datatxt[1])
xyz = (datatxt[[2, 3, 4]].astype(float) * UREG.a0).to(
'angstrom').magnitude
sym = chemical_symbols[Z]
proto += Atom(sym, position=xyz)
# now translate the cluster so that the protocluster is at the
# same origin than the original cluster
origin0 = atoms[atoms.absorber].position
origin1 = proto[0].position
proto.translate(origin0 - origin1)
# for each atom in this prototypical cluster, find the corresponding
# atom index in the original cluster
indices = []
for atom in proto:
indices.append(get_atom_index(atoms, *atom.position))
self.prototypical_atoms = atoms[indices]
return self.prototypical_atoms
[docs] def load_potential_file(self, filename='plot_vc.dat'):
a_index = 0
pot_data = []
with open(filename, 'r') as fd:
data = fd.readlines()
for d in data:
if d[1] == 'a':
a_index += 1
d = d.split()
a = {'Symbol': d[1], 'distance': float(d[4]),
'coord': np.array([float(d[7]), float(d[8]),
float(d[9])]),
'index': int(a_index), 'values': []}
pot_data.append(a)
else:
pot_data[a_index - 1]['values'].append(
tuple(float(_) for _ in d.split()))
# convert the values list to a numpy array
for _pot_data in pot_data:
v = _pot_data['values']
_pot_data['values'] = np.asarray(v)
return pot_data
[docs]class SpecIO(object):
def __init__(self, parameters, malloc_parameters, phagenio):
self.parameters = parameters
self.malloc_parameters = malloc_parameters
self.phagenio = phagenio
[docs] def write_input_file(self, filename='spec.dat'): # noqa: C901
def title(t, shift=4, width=79, center=True):
if center:
s = ('{}*{:^%ds}*\n' % (width - shift - 2)
).format(' ' * shift, t)
else:
s = ('{}*{:%ds}*\n' % (width - shift - 2)
).format(' ' * shift, t)
return s
def rule(tabs=(5, 10, 10, 10, 10), symbol='=', shift=4, width=79):
s = ' ' * shift + '*' + symbol * (width - shift - 2) + '*\n'
t = np.cumsum(tabs) + shift
sep = list(s)
for i in t:
sep[i] = '+'
return ''.join(sep)
def fillstr(a, b, index, justify='left'):
alist = list(a)
if justify == 'left':
offset = -len(b) + 1
elif justify == 'center':
offset = (-len(b) + 1) / 2
elif justify == 'decimal':
try:
offset = -(b.index('.') - 1)
except ValueError:
offset = 0
else:
offset = 0
for i, _ in enumerate(b):
alist[int(index + offset + i)] = _
return ''.join(alist)
def create_line(legend='', index=49, dots=False):
s = ' ' * 79 + '\n'
if dots:
s = fillstr(s, "..", 6, justify='right')
s = fillstr(s, "*", 4)
s = fillstr(s, "*", 78)
s = fillstr(s, legend, index, justify='right')
return s
p = self.parameters
content = rule(tabs=(), symbol='*')
content += title('spec input file')
content += rule(tabs=(), symbol='*')
content += rule(tabs=(), symbol='=')
content += title('CRYSTAL STRUCTURE :')
content += rule()
line = create_line("CRIST,CENTR,IBAS,NAT")
line = fillstr(line, "CUB", 9, 'left')
line = fillstr(line, "P", 19, 'left')
line = fillstr(line, format(0, 'd'), 29, 'left')
line = fillstr(line, str(p.get_parameter('extra_nat')), 39, 'left')
content += line
line = create_line("A,BSURA,CSURA,UNIT")
line = fillstr(line, format(1., '.4f'), 9, 'decimal')
line = fillstr(line, format(1., '.3f'), 19, 'decimal')
line = fillstr(line, format(1., '.3f'), 29, 'decimal')
line = fillstr(line, "ATU", 39, 'left')
content += line
line = create_line("ALPHAD,BETAD,GAMMAD")
line = fillstr(line, format(90., '.2f'), 9, 'decimal')
line = fillstr(line, format(90., '.2f'), 19, 'decimal')
line = fillstr(line, format(90., '.2f'), 29, 'decimal')
content += line
line = create_line("H,K,I,L")
line = fillstr(line, format(0, 'd'), 9, 'left')
line = fillstr(line, format(0, 'd'), 19, 'left')
line = fillstr(line, format(0, 'd'), 29, 'left')
line = fillstr(line, format(1, 'd'), 39, 'left')
content += line
line = create_line("NIV,COUPUR,ITEST,IESURF")
line = fillstr(line, format(8, 'd'), 9, 'left')
line = fillstr(line, format(1.4, '.2f'), 19, 'decimal')
line = fillstr(line, format(0, 'd'), 29, 'left')
line = fillstr(line, format(1, 'd'), 39, 'left')
content += line
line = create_line("ATBAS,CHEM(NAT),NZAT(NAT)")
line = fillstr(line, format(0., '.6f'), 9, 'decimal')
line = fillstr(line, format(0., '.6f'), 19, 'decimal')
line = fillstr(line, format(0., '.6f'), 29, 'decimal')
line = fillstr(line, format("Mg", '>2s'), 39, 'right')
line = fillstr(line, format(12, '>2d'), 43, 'right')
content += line
line = create_line("ATBAS,CHEM(NAT),NZAT(NAT)")
line = fillstr(line, format(0., '.6f'), 9, 'decimal')
line = fillstr(line, format(0.5, '.6f'), 19, 'decimal')
line = fillstr(line, format(0., '.6f'), 29, 'decimal')
line = fillstr(line, format("O", '>2s'), 39, 'right')
line = fillstr(line, format(8, '>2d'), 43, 'right')
content += line
line = create_line("VECBAS")
line = fillstr(line, format(1., '.6f'), 9, 'decimal')
line = fillstr(line, format(0., '.6f'), 19, 'decimal')
line = fillstr(line, format(0., '.6f'), 29, 'decimal')
content += line
line = create_line("VECBAS")
line = fillstr(line, format(0., '.6f'), 9, 'decimal')
line = fillstr(line, format(1., '.6f'), 19, 'decimal')
line = fillstr(line, format(0., '.6f'), 29, 'decimal')
content += line
line = create_line("VECBAS")
line = fillstr(line, format(0., '.6f'), 9, 'decimal')
line = fillstr(line, format(0., '.6f'), 19, 'decimal')
line = fillstr(line, format(1., '.6f'), 29, 'decimal')
content += line
line = create_line("IREL,NREL,PCREL(NREL)")
line = fillstr(line, format(0, 'd'), 9, 'left')
line = fillstr(line, format(0, 'd'), 19, 'left')
line = fillstr(line, format(0., '.1f'), 29, 'decimal')
line = fillstr(line, format(0., '.1f'), 39, 'decimal')
content += line
line = create_line("OMEGA1,OMEGA2,IADS")
line = fillstr(line, format(28., '.2f'), 9, 'decimal')
line = fillstr(line, format(0., '.2f'), 19, 'decimal')
line = fillstr(line, format(1, 'd'), 29, 'left')
content += line
content += rule()
content += title('TYPE OF CALCULATION :')
content += rule()
line = create_line("SPECTRO,ISPIN,IDICHR,IPOL")
line = fillstr(line, str(p.calctype_spectro), 9, 'left')
line = fillstr(line,
str(p.get_parameter('calctype_ispin')), 19, 'left')
line = fillstr(line, str(p.calctype_idichr), 29, 'left')
line = fillstr(line, str(p.calctype_ipol), 39, 'left')
content += line
line = create_line("I_AMP")
line = fillstr(line, str(p.calctype_iamp), 9, 'left')
content += line
content += rule()
content += title('PhD EXPERIMENTAL PARAMETERS :')
content += rule()
line = create_line("LI,S-O,INITL,I_SO")
line = fillstr(line, str(p.ped_li), 9, 'left')
line = fillstr(line, str(p.ped_so), 19, 'center')
line = fillstr(line, str(p.ped_initl), 29, 'left')
line = fillstr(line, str(p.ped_iso), 39, 'left')
content += line
line = create_line("IPHI,ITHETA,IE,IFTHET")
line = fillstr(line, str(p.ped_iphi), 9, 'left')
line = fillstr(line, str(p.ped_itheta), 19, 'left')
line = fillstr(line, str(p.ped_ie), 29, 'left')
line = fillstr(line, str(p.ped_ifthet), 39, 'left')
content += line
line = create_line("NPHI,NTHETA,NE,NFTHET")
line = fillstr(line, str(p.ped_nphi), 9, 'left')
line = fillstr(line, str(p.ped_ntheta), 19, 'left')
line = fillstr(line, str(p.ped_ne), 29, 'left')
line = fillstr(line, str(p.ped_nfthet), 39, 'left')
content += line
line = create_line("PHI0,THETA0,E0,R0")
line = fillstr(line, str(p.get_parameter('ped_phi0')), 9, 'decimal')
line = fillstr(line, str(p.get_parameter('ped_theta0')), 19, 'decimal')
line = fillstr(line, str(p.get_parameter('ped_e0')), 29, 'decimal')
line = fillstr(line, str(p.get_parameter('ped_r0')), 39, 'decimal')
content += line
line = create_line("PHI1,THETA1,E1,R1")
line = fillstr(line, str(p.get_parameter('ped_phi1')), 9, 'decimal')
line = fillstr(line, str(p.get_parameter('ped_theta1')), 19, 'decimal')
line = fillstr(line, str(p.get_parameter('ped_e1')), 29, 'decimal')
line = fillstr(line, str(p.get_parameter('ped_r1')), 39, 'decimal')
content += line
line = create_line("THLUM,PHILUM,ELUM")
line = fillstr(line, str(p.get_parameter('ped_thlum')), 9, 'decimal')
line = fillstr(line, str(p.get_parameter('ped_philum')), 19, 'decimal')
line = fillstr(line, str(p.get_parameter('ped_elum')), 29, 'decimal')
content += line
line = create_line("IMOD,IMOY,ACCEPT,ICHKDIR")
line = fillstr(line, str(p.get_parameter('ped_imod')), 9, 'decimal')
line = fillstr(line, str(p.get_parameter('ped_imoy')), 19, 'decimal')
line = fillstr(line, str(p.get_parameter('ped_accept')), 29, 'decimal')
line = fillstr(line,
str(p.get_parameter('ped_ichkdir')), 39, 'decimal')
content += line
content += rule()
content += title(' ' * 22 + 'LEED EXPERIMENTAL PARAMETERS :',
center=False)
content += rule()
line = create_line("IPHI,ITHETA,IE,IFTHET")
line = fillstr(line, str(p.get_parameter('leed_iphi')), 9, 'left')
line = fillstr(line, str(p.get_parameter('leed_itheta')), 19, 'left')
line = fillstr(line, str(p.get_parameter('leed_ie')), 29, 'left')
line = fillstr(line, str(p.get_parameter('leed_ifthet')), 39, 'left')
content += line
line = create_line("NPHI,NTHETA,NE,NFTHET")
line = fillstr(line, str(p.get_parameter('leed_nphi')), 9, 'left')
line = fillstr(line, str(p.get_parameter('leed_ntheta')), 19, 'left')
line = fillstr(line, str(p.get_parameter('leed_ne')), 29, 'left')
line = fillstr(line, str(p.get_parameter('leed_nfthet')), 39, 'left')
content += line
line = create_line("PHI0,THETA0,E0,R0")
line = fillstr(line, str(p.get_parameter('leed_phi0')), 9, 'decimal')
line = fillstr(line,
str(p.get_parameter('leed_theta0')), 19, 'decimal')
line = fillstr(line, str(p.get_parameter('leed_e0')), 29, 'decimal')
line = fillstr(line, str(p.get_parameter('leed_r0')), 39, 'decimal')
content += line
line = create_line("PHI1,THETA1,E1,R1")
line = fillstr(line, str(p.get_parameter('leed_phi1')), 9, 'decimal')
line = fillstr(line,
str(p.get_parameter('leed_theta1')), 19, 'decimal')
line = fillstr(line, str(p.get_parameter('leed_e1')), 29, 'decimal')
line = fillstr(line, str(p.get_parameter('leed_r1')), 39, 'decimal')
content += line
line = create_line("TH_INI,PHI_INI")
line = fillstr(line, str(p.get_parameter('leed_thini')), 9, 'decimal')
line = fillstr(line,
str(p.get_parameter('leed_phiini')), 19, 'decimal')
content += line
line = create_line("IMOD,IMOY,ACCEPT,ICHKDIR")
line = fillstr(line, str(p.get_parameter('leed_imod')), 9, 'decimal')
line = fillstr(line, str(p.get_parameter('leed_imoy')), 19, 'decimal')
line = fillstr(line,
str(p.get_parameter('leed_accept')), 29, 'decimal')
line = fillstr(line, str(p.get_parameter('leed_ichkdir')), 39,
'decimal')
content += line
content += rule()
content += title(' ' * 21 + 'EXAFS EXPERIMENTAL PARAMETERS :',
center=False)
content += rule()
line = create_line("EDGE,INITL,THLUM,PHILUM")
line = fillstr(line, str(p.get_parameter('exafs_edge')), 9, 'left')
line = fillstr(line, str(p.get_parameter('exafs_initl')), 19, 'left')
line = fillstr(line,
str(p.get_parameter('exafs_thlum')), 29, 'decimal')
line = fillstr(line, str(p.get_parameter('exafs_philum')), 39,
'decimal')
content += line
line = create_line("NE,EK_INI,EK_FIN,EPH_INI")
line = fillstr(line, str(p.get_parameter('exafs_ne')), 9, 'left')
line = fillstr(line,
str(p.get_parameter('exafs_ekini')), 19, 'decimal')
line = fillstr(line,
str(p.get_parameter('exafs_ekfin')), 29, 'decimal')
line = fillstr(line, str(p.get_parameter('exafs_ephini')), 39,
'decimal')
content += line
content += rule()
content += title(' ' * 22 + 'AED EXPERIMENTAL PARAMETERS :',
center=False)
content += rule()
line = create_line("EDGE_C,EDGE_I,EDGE_A")
line = fillstr(line, str(p.get_parameter('aed_edgec')), 9, 'left')
line = fillstr(line, str(p.get_parameter('aed_edgei')), 19, 'left')
line = fillstr(line, str(p.get_parameter('aed_edgea')), 29, 'left')
content += line
line = create_line("I_MULT,MULT")
line = fillstr(line, str(p.get_parameter('aed_imult')), 9, 'left')
line = fillstr(line, str(p.get_parameter('aed_mult')), 19, 'center')
content += line
line = create_line("IPHI,ITHETA,IFTHET,I_INT")
line = fillstr(line, str(p.get_parameter('aed_iphi')), 9, 'left')
line = fillstr(line, str(p.get_parameter('aed_itheta')), 19, 'left')
line = fillstr(line, str(p.get_parameter('aed_ifthet')), 29, 'left')
line = fillstr(line, str(p.get_parameter('aed_iint')), 39, 'left')
content += line
line = create_line("NPHI,NTHETA,NFTHET")
line = fillstr(line, str(p.get_parameter('aed_nphi')), 9, 'left')
line = fillstr(line, str(p.get_parameter('aed_ntheta')), 19, 'left')
line = fillstr(line, str(p.get_parameter('aed_nfthet')), 29, 'left')
content += line
line = create_line("PHI0,THETA0,R0")
line = fillstr(line, str(p.get_parameter('aed_phi0')), 9, 'decimal')
line = fillstr(line, str(p.get_parameter('aed_theta0')), 19, 'decimal')
line = fillstr(line, str(p.get_parameter('aed_r0')), 29, 'decimal')
content += line
line = create_line("PHI1,THETA1,R1")
line = fillstr(line, str(p.get_parameter('aed_phi1')), 9, 'decimal')
line = fillstr(line, str(p.get_parameter('aed_theta1')), 19, 'decimal')
line = fillstr(line, str(p.get_parameter('aed_r1')), 29, 'decimal')
content += line
line = create_line("IMOD,IMOY,ACCEPT,ICHKDIR")
line = fillstr(line, str(p.get_parameter('aed_imod')), 9, 'left')
line = fillstr(line, str(p.get_parameter('aed_imoy')), 19, 'left')
line = fillstr(line, str(p.get_parameter('aed_accept')), 29, 'decimal')
line = fillstr(line, str(p.get_parameter('aed_ichkdir')), 39, 'left')
content += line
content += rule()
content += title(' ' * 19 + 'EIGENVALUE CALCULATION PARAMETERS :',
center=False)
content += rule()
line = create_line("NE,EK_INI,EK_FIN,I_DAMP")
line = fillstr(line, str(p.get_parameter('eigval_ne')), 9, 'left')
line = fillstr(line, str(p.get_parameter('eigval_ekini')), 19,
'decimal')
line = fillstr(line, str(p.get_parameter('eigval_ekfin')), 29,
'decimal')
line = fillstr(line, str(p.get_parameter('eigval_idamp')), 39, 'left')
content += line
if p.calctype_spectro == "EIG":
nlines = int(np.ceil(p.eigval_ne / 4.))
else:
nlines = 1
table = np.chararray((nlines, 4), unicode=True)
table[:] = str(p.get_parameter('eigval_ispectrum_ne').value)
for i in range(nlines):
line = create_line("I_SPECTRUM(NE)")
for j, o in enumerate((9, 19, 29, 39)):
line = fillstr(line, table[i, j], o, 'left')
content += line
line = create_line("I_PWM,METHOD,ACC,EXPO")
line = fillstr(line, str(p.get_parameter('eigval_ipwm')), 9, 'left')
line = fillstr(line, str(p.get_parameter('eigval_method')), 19, 'left')
line = fillstr(line, str(p.get_parameter('eigval_acc')), 29, 'decimal')
line = fillstr(line,
str(p.get_parameter('eigval_expo')), 39, 'decimal')
content += line
line = create_line("N_MAX,N_ITER,N_TABLE,SHIFT")
line = fillstr(line, str(p.get_parameter('eigval_nmax')), 9, 'left')
line = fillstr(line, str(p.get_parameter('eigval_niter')), 19, 'left')
line = fillstr(line, str(p.get_parameter('eigval_ntable')), 29, 'left')
line = fillstr(line, str(p.get_parameter('eigval_shift')), 39,
'decimal')
content += line
line = create_line("I_XN,I_VA,I_GN,I_WN")
line = fillstr(line, str(p.get_parameter('eigval_ixn')), 9, 'left')
line = fillstr(line, str(p.get_parameter('eigval_iva')), 19, 'left')
line = fillstr(line, str(p.get_parameter('eigval_ign')), 29, 'left')
line = fillstr(line, str(p.get_parameter('eigval_iwn')), 39, 'left')
content += line
line = create_line("L,ALPHA,BETA")
line = fillstr(line, str(p.get_parameter('eigval_l')), 9, 'left')
line = fillstr(line, str(p.get_parameter('eigval_alpha')), 19,
'decimal')
line = fillstr(line, str(p.get_parameter('eigval_beta')), 29,
'decimal')
content += line
content += rule()
content += title(' ' * 24 + 'CALCULATION PARAMETERS :', center=False)
content += rule()
line = create_line("NO,NDIF,ISPHER,I_GR")
line = fillstr(line, str(p.get_parameter('calc_no')), 9, 'left')
line = fillstr(line, str(p.get_parameter('calc_ndif')), 19, 'left')
line = fillstr(line, str(p.get_parameter('calc_ispher')), 29, 'left')
line = fillstr(line, str(p.get_parameter('calc_igr')), 39, 'left')
content += line
line = create_line("I_REN,N_REN,REN_R,REN_I")
line = fillstr(line, str(p.get_parameter('calc_iren')), 9, 'left')
line = fillstr(line, str(p.get_parameter('calc_nren')), 19, 'left')
line = fillstr(line, str(p.get_parameter('calc_renr')), 29, 'decimal')
line = fillstr(line, str(p.get_parameter('calc_reni')), 39, 'decimal')
content += line
line = create_line("ISFLIP,IR_DIA,ITRTL,I_TEST")
line = fillstr(line, str(p.get_parameter('calc_isflip')), 9, 'left')
line = fillstr(line, str(p.get_parameter('calc_irdia')), 19, 'left')
line = fillstr(line, str(p.get_parameter('calc_itrtl')), 29, 'left')
line = fillstr(line, str(p.get_parameter('calc_itest')), 39, 'left')
content += line
line = create_line("NEMET,IEMET(NEMET)")
line = fillstr(line, format(1, 'd'), 9, 'left')
line = fillstr(line, format(1, 'd'), 19, 'left')
line = fillstr(line, format(0, 'd'), 29, 'left')
line = fillstr(line, format(0, 'd'), 39, 'left')
content += line
line = create_line("ISOM,NONVOL,NPATH,VINT")
line = fillstr(line, str(p.get_parameter('calc_isom')), 9, 'left')
line = fillstr(line, str(p.get_parameter('calc_nonvol')), 19, 'left')
line = fillstr(line, str(p.get_parameter('calc_npath')), 29, 'left')
line = fillstr(line, str(p.get_parameter('calc_vint')), 39, 'decimal')
content += line
line = create_line("IFWD,NTHOUT,I_NO,I_RA")
line = fillstr(line, str(p.get_parameter('calc_ifwd')), 9, 'left')
line = fillstr(line, str(p.get_parameter('calc_nthout')), 19, 'left')
line = fillstr(line, str(p.get_parameter('calc_ino')), 29, 'left')
line = fillstr(line, str(p.get_parameter('calc_ira')), 39, 'left')
content += line
nat = p.extra_nat
nra_arr = np.ones((nat), dtype=np.int)
thfwd_arr = np.ones((nat))
path_filtering = p.extra_parameters['calculation'].get_parameter(
'path_filtering').value
if (path_filtering is not None and
'backward_scattering' in path_filtering):
ibwd_arr = np.ones((nat), dtype=np.int)
else:
ibwd_arr = np.zeros((nat), dtype=np.int)
thbwd_arr = np.ones((nat))
for at in p.extra_atoms:
i = at.get('proto_index') - 1
thfwd_arr[i] = at.get('forward_angle')
thbwd_arr[i] = at.get('backward_angle')
nra_arr[i] = at.get('RA_cut_off')
for i in range(p.extra_nat):
line = create_line("N_RA,THFWD,IBWD,THBWD(NAT)", dots=True)
line = fillstr(line, format(nra_arr[i], 'd'), 9, 'left')
line = fillstr(line, format(thfwd_arr[i], '.2f'), 19, 'decimal')
line = fillstr(line, format(ibwd_arr[i], 'd'), 29, 'left')
line = fillstr(line, format(thbwd_arr[i], '.2f'), 39, 'decimal')
content += line
line = create_line("IPW,NCUT,PCTINT,IPP")
line = fillstr(line, str(p.get_parameter('calc_ipw')), 9, 'left')
line = fillstr(line, str(p.get_parameter('calc_ncut')), 19, 'left')
line = fillstr(line,
str(p.get_parameter('calc_pctint')), 29, 'decimal')
line = fillstr(line, str(p.get_parameter('calc_ipp')), 39, 'left')
content += line
line = create_line("ILENGTH,RLENGTH,UNLENGTH")
line = fillstr(line, str(p.get_parameter('calc_ilength')), 9, 'left')
line = fillstr(line, str(p.get_parameter('calc_rlength')), 19,
'decimal')
line = fillstr(line, str(p.get_parameter('calc_unlength')), 29, 'left')
content += line
line = create_line("IDWSPH,ISPEED,IATT,IPRINT")
# Here, if 'vibrational_damping' is None, use the 'debye_waller'
# approach and the debye model for the mean square displacements
# and set the temeprature to 0K and the Debye temeparture to 500K.
calc_param = p.extra_parameters['calculation']
if calc_param.vibrational_damping is None:
idwsph = format(0, 'd')
idcm = format(2, 'd')
temp = format(0., '.2f')
td = format(500., '.2f')
LOGGER.warning('Vibrational damping is disabled for this '
'calculation.')
else:
idwsph = str(p.get_parameter('calc_idwsph'))
idcm = str(p.get_parameter('calc_idcm'))
temp = str(p.get_parameter('calc_t'))
td = str(p.get_parameter('calc_td'))
ispeed = str(p.get_parameter('calc_ispeed'))
line = fillstr(line, idwsph, 9, 'left')
line = fillstr(line, ispeed, 19, 'left')
line = fillstr(line, str(p.get_parameter('calc_iatt')), 29, 'left')
line = fillstr(line, str(p.get_parameter('calc_iprint')), 39, 'left')
content += line
line = create_line("IDCM,TD,T,RSJ")
line = fillstr(line, idcm, 9, 'left')
line = fillstr(line, td, 19, 'decimal')
line = fillstr(line, temp, 29, 'decimal')
line = fillstr(line, str(p.get_parameter('calc_rsj')), 39, 'decimal')
content += line
line = create_line("ILPM,XLPM0")
line = fillstr(line, str(p.get_parameter('calc_ilpm')), 9, 'left')
line = fillstr(line, str(p.get_parameter('calc_xlpm0')), 19, 'decimal')
content += line
nat = p.extra_nat
nlines = int(np.ceil(nat / 4.))
uj2_array = np.zeros((4 * nlines))
# Now, for each atom in the cluster, get the mean_square_vibration and
# store it in the index corresponding to the prototypical index
for at in p.extra_atoms:
i = at.get('proto_index') - 1
msq_vib = at.get('mean_square_vibration')
uj2_array[i] = msq_vib
uj2_array = uj2_array.reshape((nlines, 4))
for i in range(nlines):
line = create_line("UJ2(NAT)", dots=True)
for j, o in enumerate((9, 19, 29, 39)):
line = fillstr(line, format(uj2_array[i, j], '.5f'), o,
'decimal')
content += line
content += rule()
content += title(' ' * 17 + 'INPUT FILES (PHD, EXAFS, LEED, AED, '
'APECS) :', center=False)
content += rule(tabs=(), symbol='-')
content += title(
' ' * 8 + 'NAME' + ' ' * 20 + 'UNIT' + ' ' * 16 + 'TYPE',
center=False)
content += rule(tabs=(5, 23, 7, 10))
line = create_line("DATA FILE,UNIT")
line = fillstr(line, str(p.get_parameter('input_data')), 9, 'right')
line = fillstr(line, str(p.get_parameter('input_unit00')), 39, 'left')
content += line
line = create_line("PHASE SHIFTS/TL FILE,UNIT")
line = fillstr(line, str(p.get_parameter('input_tl')), 9, 'right')
line = fillstr(line, str(p.get_parameter('input_unit01')), 39, 'left')
content += line
line = create_line("RADIAL MATRIX ELTS FILE,UNIT")
line = fillstr(line, str(p.get_parameter('input_rad')), 9, 'right')
line = fillstr(line, str(p.get_parameter('input_unit02')), 39, 'left')
content += line
line = create_line("CLUSTER FILE,UNIT")
line = fillstr(line, str(p.get_parameter('input_cluster')), 9, 'right')
line = fillstr(line, str(p.get_parameter('input_unit03')), 39, 'left')
content += line
line = create_line("ADSORBATE FILE,UNIT")
line = fillstr(line, str(p.get_parameter('input_adsorbate')), 9,
'right')
line = fillstr(line, str(p.get_parameter('input_unit04')), 39, 'left')
content += line
line = create_line("K DIRECTIONS FILE,UNIT")
line = fillstr(line, str(p.get_parameter('input_kdirs')), 9, 'right')
line = fillstr(line, str(p.get_parameter('input_unit05')), 39, 'left')
content += line
content += rule(tabs=(5, 23, 7, 10))
content += title(' ' * 21 + 'ADDITIONAL INPUT FILES (APECS) :',
center=False)
content += title(' ' * 28 + '(AUGER ELECTRON)', center=False)
content += rule(tabs=(), symbol='-')
content += title(
' ' * 8 + 'NAME' + ' ' * 20 + 'UNIT' + ' ' * 16 + 'TYPE',
center=False)
content += rule(tabs=(5, 23, 7, 10))
line = create_line("PHASE SHIFTS/TL FILE,UNIT")
line = fillstr(line, str(p.get_parameter('input2_tl')), 9, 'right')
line = fillstr(line, str(p.get_parameter('input2_unit06')), 39, 'left')
content += line
line = create_line("RADIAL MATRIX ELTS FILE,UNIT")
line = fillstr(line, str(p.get_parameter('input2_rad')), 9, 'right')
line = fillstr(line, str(p.get_parameter('input2_unit07')), 39, 'left')
content += line
line = create_line("K DIRECTIONS FILE,UNIT")
line = fillstr(line, str(p.get_parameter('input2_kdirs')), 9, 'right')
line = fillstr(line, str(p.get_parameter('input2_unit08')), 39, 'left')
content += line
content += rule(tabs=(5, 23, 7, 10))
content += title(' ' * 29 + 'OUTPUT FILES :', center=False)
content += rule(tabs=(), symbol='-')
content += title(
' ' * 8 + 'NAME' + ' ' * 20 + 'UNIT' + ' ' * 16 + 'TYPE',
center=False)
content += rule(tabs=(5, 23, 7, 10))
line = create_line("CONTROL FILE,UNIT")
line = fillstr(line, str(p.get_parameter('output_log')), 9, 'right')
line = fillstr(line, str(p.get_parameter('output_unit09')), 39, 'left')
content += line
line = create_line("RESULT FILE,UNIT")
line = fillstr(line, str(p.get_parameter('output_res')), 9, 'right')
line = fillstr(line, str(p.get_parameter('output_unit10')), 39, 'left')
content += line
line = create_line("SCATTERING FACTOR FILE,UNIT")
line = fillstr(line, str(p.get_parameter('output_sf')), 9, 'right')
line = fillstr(line, str(p.get_parameter('output_unit11')), 39, 'left')
content += line
line = create_line("AUGMENTED CLUSTER FILE,UNIT")
line = fillstr(line,
str(p.get_parameter('output_augclus')), 9, 'right')
line = fillstr(line, str(p.get_parameter('output_unit12')), 39, 'left')
content += line
content += rule(tabs=(5, 23, 7, 10))
content += title(' ' * 26 + 'END OF THE DATA FILE', center=False)
content += rule(tabs=())
content += rule(tabs=(), symbol='*')
try:
with open(filename, 'r') as fd:
old_content = fd.read()
except IOError:
old_content = ''
modified = False
if content != old_content:
with open(filename, 'w') as fd:
fd.write(content)
LOGGER.debug(f"Writing Spec input file written in {filename}")
modified = True
return modified
[docs] def write_include_file(self, filename='spec.inc'):
def get_li(level):
orbitals = 'spdfghi'
m = re.match(r'\d(?P<l>[%s])(\d/2)?' % orbitals, level)
return orbitals.index(m.group('l'))
requirements = {
'NATP_M': self.phagenio.nat,
'NATCLU_M': len(self.parameters.extra_atoms),
'NAT_EQ_M': self.phagenio.nateqm,
'N_CL_L_M': 0,
'NE_M': self.phagenio.ne,
'NL_M': self.phagenio.nlmax + 1,
'LI_M': get_li(self.parameters.extra_level) + 1,
'NEMET_M': 1,
'NO_ST_M': self.parameters.calc_no,
}
# read the include file
with open(filename, 'r') as fd:
content = fd.read()
# backup the content in memory
old_content = content
# for key in ('NATP_M', 'NATCLU_M', 'NE_M', 'NEMET_M', 'LI_M', 'NL_M',
# 'NO_ST_M'):
# required = requirements[key]
# limit = self.malloc_parameters.get_parameter(key).value
# value = required if required > limit else limit
# content = re.sub(r'({:s}\s*=\s*)\d+'.format(key),
# r'\g<1>{:d}'.format(value), content)
for key in ('NAT_EQ_M', 'N_CL_N_M', 'NDIF_M', 'NSO_M', 'NTEMP_M',
'NODES_EX_M', 'NSPIN_M', 'NTH_M', 'NPH_M', 'NDIM_M',
'N_TILT_M', 'N_ORD_M', 'NPATH_M', 'NGR_M'):
value = self.malloc_parameters.get_parameter(key).value
content = re.sub(r'({:s}\s*=\s*)\d+'.format(key),
r'\g<1>{:d}'.format(value), content)
for key, value in list(requirements.items()):
content = re.sub(r'({:s}\s*=\s*)\d+'.format(key),
r'\g<1>{:d}'.format(value), content)
modified = False
if content != old_content:
with open(filename, 'w') as fd:
fd.write(content)
modified = True
return modified
[docs] def write_kdirs_file(self, filename='kdirs.dat'):
fwhm = 1.
all_theta = self.parameters.extra_parameters['scan'].theta
all_phi = self.parameters.extra_parameters['scan'].phi
f = '{:7}{:4}{:6}\n'
old_content = None
try:
with open(filename, 'r') as fd:
old_content = fd.read()
except IOError:
pass
content = ''
content += f.format(2, 1, len(all_theta) * len(all_phi))
content += f.format(1, len(all_phi), len(all_theta))
for iphi, phi in enumerate(all_phi):
for itheta, theta in enumerate(all_theta):
s = '{:5}{:5}{:13.3f}{:11.3f}{:15e}\n'
s = s.format(iphi + 1, itheta + 1, theta, phi, fwhm)
content += s
modified = False
if content != old_content:
with open(filename, 'w') as fd:
fd.write(content)
modified = True
return modified
[docs] def load_results(self, filename='results.dat'):
rows2skip = {
'PED': 27,
'AED': 27,
'EXAFS': 27,
'LEED': 26,
'EIG': 0
}
spectro = self.parameters.extra_parameters['global'].spectroscopy
skip = rows2skip[spectro]
data = np.loadtxt(filename, skiprows=skip, unpack=True)
if len(data.shape) <= 1:
data = data.reshape((2, -1))
return data
[docs] def load_facdif(self, filename='facdif1.dat'):
data = np.loadtxt(filename, skiprows=1)
return data
[docs] def load_log(self, filename='spec.log'):
pat = re.compile(r'ORDER\s+(\d+)\s+TOTAL NUMBER OF PATHS\s+:\s+(\d+)')
with open(filename, 'r') as fd:
content = fd.read()
return pat.findall(content)
[docs]class CompCurveIO(object):
def __init__(self, parameters):
self.parameters = parameters
[docs] def write_input_file(self, filename='comp_curve.dat'):
def title(t, shift=4, width=78, center=True):
if center:
s = ('{}*{:^%ds}*\n' % (width - shift - 2)
).format(' ' * shift, t)
else:
s = ('{}*{:%ds}*\n' % (width - shift - 2)
).format(' ' * shift, t)
return s
def rule(tabs=(5, 10, 10, 10, 10), symbol='=', shift=4, width=78):
s = ' ' * shift + '*' + symbol * (width - shift - 2) + '*\n'
t = np.cumsum(tabs) + shift
sep = list(s)
for i in t:
sep[i] = '+'
return ''.join(sep)
def fillstr(a, b, index, justify='left'):
alist = list(a)
if justify == 'left':
offset = -len(b) + 1
elif justify == 'center':
offset = (-len(b) + 1) / 2
elif justify == 'decimal':
try:
offset = -(b.index('.') - 1)
except ValueError:
offset = 0
else:
offset = 0
for i, _ in enumerate(b):
alist[int(index + offset + i)] = _
return ''.join(alist)
def create_line(legend='', index=49, dots=False):
s = ' ' * 78 + '\n'
if dots:
s = fillstr(s, "..", 6, justify='right')
s = fillstr(s, "*", 4)
s = fillstr(s, "*", 77)
s = fillstr(s, legend, index, justify='right')
return s
p = self.parameters
content = rule(tabs=(), symbol='*')
content += title('R-FACTOR, SIMILARITY INDEX, DISTANCE, GOODNESS OF FIT')
content += title('KERNEL DISTANCE AND SHAPE ANALYSIS')
content += rule(tabs=(), symbol='*')
content += rule(tabs=(5,10,10,10,10))
content += create_line('CALCULATION PARAMETERS : GENERAL', index=29)
content += rule(tabs=(5,10,10,10,10))
line = create_line("N_PAR,NORM,I_SCALE,I_NORM")
line = fillstr(line, str(p.get_parameter('general_npar')), 9, 'left')
line = fillstr(line, str(p.get_parameter('general_norm')), 19, 'left')
line = fillstr(line, str(p.get_parameter('general_iscale')), 29, 'left')
line = fillstr(line, str(p.get_parameter('general_inorm')), 39, 'left')
content += line
line = create_line("I_SYM,SYM,I_POSI")
line = fillstr(line, str(p.get_parameter('general_isym')), 9, 'left')
line = fillstr(line, str(p.get_parameter('general_sym')), 19, 'decimal')
line = fillstr(line, str(p.get_parameter('general_iposi')), 29, 'left')
content += line
line = create_line("I_DIST,I_CUR,I_SA,I_PRINT")
line = fillstr(line, str(p.get_parameter('general_idist')), 9, 'left')
line = fillstr(line, str(p.get_parameter('general_icur')), 19, 'left')
line = fillstr(line, str(p.get_parameter('general_isa')), 29, 'left')
line = fillstr(line, str(p.get_parameter('general_iprint')), 39, 'left')
content += line
content += rule(tabs=(5,10,10,10,10))
content += create_line('CALCULATION PARAMETERS : WEIGHTS', index=29)
content += rule(tabs=(5,10,10,10,10))
line = create_line("I_WEIGHT,ALPHA,BETA,SIGMA")
line = fillstr(line, str(p.get_parameter('weights_iweight')), 9, 'left')
line = fillstr(line, str(p.get_parameter('weights_alpha')), 19, 'decimal')
line = fillstr(line, str(p.get_parameter('weights_beta')), 29, 'decimal')
line = fillstr(line, str(p.get_parameter('weights_sigma')), 39, 'decimal')
content += line
line = create_line("I_SHIFT,MAXW")
line = fillstr(line, str(p.get_parameter('weights_ishift')), 9, 'left')
line = fillstr(line, str(p.get_parameter('weights_maxw')), 19, 'decimal')
content += line
content += rule(tabs=(5,10,10,10,10))
content += create_line('CALCULATION PARAMETERS : R-FACTORS', index=29)
content += rule(tabs=(5,10,10,10,10))
line = create_line("V_I")
line = fillstr(line, str(p.get_parameter('rfc_vi')), 9, 'decimal')
content += line
content += rule(tabs=(5,10,10,10,10))
content += create_line('CALCULATION PARAMETERS : SIMILARITY INDICES', index=29)
content += rule(tabs=(5,10,10,10,10))
line = create_line("ALHPAS,BETAS,N_BINS")
line = fillstr(line, str(p.get_parameter('sim_alphas')), 9, 'decimal')
line = fillstr(line, str(p.get_parameter('sim_betas')), 19, 'decimal')
line = fillstr(line, str(p.get_parameter('sim_nbins')), 29, 'left')
content += line
content += rule(tabs=(5,10,10,10,10))
content += create_line('CALCULATION PARAMETERS : DISTANCES', index=29)
content += rule(tabs=(5,10,10,10,10))
line = create_line("ALHPAD,I_BETA,L,SIGMAD")
line = fillstr(line, str(p.get_parameter('dist_alphad')), 9, 'decimal')
line = fillstr(line, str(p.get_parameter('dist_ibeta')), 19, 'left')
line = fillstr(line, str(p.get_parameter('dist_l')), 29, 'left')
line = fillstr(line, str(p.get_parameter('dist_sigmad')), 39, 'decimal')
content += line
content += rule(tabs=(5,10,10,10,10))
content += create_line('CALCULATION PARAMETERS : GOODNESS OF FIT', index=29)
content += rule(tabs=(5,10,10,10,10))
line = create_line("N_BING,ALPHAG")
line = fillstr(line, str(p.get_parameter('gof_nbing')), 9, 'left')
line = fillstr(line, str(p.get_parameter('gof_alphag')), 19, 'decimal')
content += line
content += rule(tabs=(5,10,10,10,10))
content += create_line('CALCULATION PARAMETERS : KERNEL DISTANCES', index=29)
content += rule(tabs=(5,10,10,10,10))
line = create_line("ALPHAK,L,SIGMAK")
line = fillstr(line, str(p.get_parameter('kdist_alphak')), 9, 'decimal')
line = fillstr(line, str(p.get_parameter('kdist_l')), 19, 'left')
line = fillstr(line, str(p.get_parameter('kdist_sigmak')), 29, 'decimal')
content += line
content += rule(tabs=(5,10,10,10,10))
content += create_line('CALCULATION PARAMETERS : MOMENTS', index=29)
content += rule(tabs=(5,10,10,10,10))
line = create_line("N_GRID,N_MOM,BASIS")
line = fillstr(line, str(p.get_parameter('mom_ngrid')), 9, 'left')
line = fillstr(line, str(p.get_parameter('mom_nmom')), 19, 'left')
line = fillstr(line, str(p.get_parameter('mom_basis')), 29, 'left')
content += line
line = create_line("I_ALG,MU,NU")
line = fillstr(line, str(p.get_parameter('mom_ialg')), 9, 'left')
line = fillstr(line, str(p.get_parameter('mom_mu')), 19, 'decimal')
line = fillstr(line, str(p.get_parameter('mom_nu')), 29, 'decimal')
content += line
content += rule(tabs=(5,10,10,10,10))
content += create_line('CALCULATION PARAMETERS : CHORDS', index=29)
content += rule(tabs=(5,10,10,10,10))
line = create_line("I_CHORD,METHOD,VALUE,N_BINC")
line = fillstr(line, str(p.get_parameter('chords_ichord')), 9, 'left')
line = fillstr(line, str(p.get_parameter('chords_method')), 19, 'left')
line = fillstr(line, str(p.get_parameter('chords_value')), 29, 'left')
line = fillstr(line, str(p.get_parameter('chords_nbinc')), 39, 'left')
content += line
content += rule(tabs=(5,10,10,10,10))
content += create_line('CALCULATION PARAMETERS : CHAIN CODES', index=29)
content += rule(tabs=(5,10,10,10,10))
line = create_line("N_CONNECT,SCALEC")
line = fillstr(line, str(p.get_parameter('codes_nconnect')), 9, 'left')
line = fillstr(line, str(p.get_parameter('codes_scalec')), 19, 'decimal')
content += line
content += rule(tabs=(5,10,10,10,10))
content += create_line('CALCULATION PARAMETERS : CONTOUR', index=29)
content += rule(tabs=(5,10,10,10,10))
line = create_line("NBIN,N_LEN,SH_AN,I_FOU")
line = fillstr(line, str(p.get_parameter('cont_nbin')), 9, 'left')
line = fillstr(line, str(p.get_parameter('cont_nlen')), 19, 'left')
line = fillstr(line, str(p.get_parameter('cont_shan')), 29, 'left')
line = fillstr(line, str(p.get_parameter('cont_ifou')), 39, 'left')
content += line
line = create_line("I_NORM")
line = fillstr(line, str(p.get_parameter('cont_ifou')), 9, 'left')
content += line
content += rule(tabs=(5,10,10,10,10))
content += create_line('EXPERIMENTAL INPUT FILE :', index=29)
content += rule(tabs=(), symbol='-')
line = create_line('')
line = fillstr(line, 'NAME', 14, 'right')
line = fillstr(line, 'TYPE', 58, 'right')
content += line
content += rule(tabs=(5,40))
line = create_line('EXPERIMENT', index=49)
line = fillstr(line, str(p.get_parameter('exp_filename')), 9, 'right')
content += line
content += rule(tabs=(5,40))
content += create_line('CALCULATED INPUT FILE :', index=29)
content += rule(tabs=(), symbol='-')
line = create_line('')
line = fillstr(line, 'NAME', 14, 'right')
line = fillstr(line, 'PARAMETER 1', 49, 'right')
line = fillstr(line, 'PARAMETER 2', 63, 'right')
content += line
content += rule(tabs=(5,40,7,7,7))
calc_fnames = p.get_parameter('calc_filename').value
for fname in calc_fnames:
line = create_line('')
line = fillstr(line, fname, 9, 'right')
line = fillstr(line, str(p.get_parameter('calc_param1')), 56, 'decimal')
line = fillstr(line, str(p.get_parameter('calc_param2')), 70, 'decimal')
content += line
content += rule(tabs=(5,40,7,7,7))
content += create_line('END OF DATA FILE', index=31)
content += rule(tabs=())
content += rule(tabs=(),symbol='*')
# Write the content to filename
try:
with open(filename, 'r') as fd:
old_content = fd.read()
except IOError:
old_content = ''
modified = False
if content != old_content:
with open(filename, 'w') as fd:
fd.write(content)
modified = True
return modified
[docs] def load_results(self, index=0, prefix='rfc/experiment_rf'):
data = []
for i in range(1, 13):
#data.append(np.loadtxt(prefix + f'{i:02d}' + '.txt')[-1])
results = np.loadtxt(prefix + f'{i:02d}' + '.txt')
results = results.reshape((-1, 2))
data.append(results[index,1])
suffix = 'ren'
exp = {'int': None, 'ren': None, 'chi': None, 'cdf': None}
exp_ren = np.loadtxt(os.path.join('exp', 'div',
f'experiment_{suffix}.txt'))
calc_ren = np.loadtxt(os.path.join('calc', 'div',
f'calculation{index:d}_{suffix}.txt'))
return data, exp_ren, calc_ren