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Add multielement support for SPRKKR potential

This commit is contained in:
Sylvain Tricot 2020-07-07 17:27:26 +02:00
parent 47e35b3b7f
commit 8e79e90fb5
7 changed files with 161 additions and 55 deletions
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1
src/msspec/__init__.py
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@ -35,6 +35,7 @@ def init_msspec():
ase.atom.names['forward_angle'] = ('forward_angles', 20.)
ase.atom.names['backward_angle'] = ('backward_angles', 20.)
ase.atom.names['RA_cut_off'] = ('RA_cuts_off', 1)
ase.atom.names['atom_type'] = ('atom_types', None)
ase.atoms.Atoms.absorber = None
init_msspec()

33
src/msspec/calcio.py
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@ -15,6 +15,7 @@ from ase import Atom, Atoms
from ase.data import chemical_symbols
from msspec.misc import UREG, LOGGER
from msspec.utils import get_atom_index
class PhagenIO(object):
@ -107,15 +108,14 @@ class PhagenIO(object):
ionicity = self.parameters.ionicity
ionicity_section = ''
ionicity_format = '{:8d}{:9.2f}\n'
symbols = set(atoms.get_chemical_symbols())
for symbol in symbols:
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(
ase.data.atomic_numbers[symbol],
charge)
charge = 0
ionicity_section += ionicity_format.format(Z, charge)
ionicity_section += '{:8d}\n'.format(-1)
content = header + cluster_section + ionicity_section
@ -279,8 +279,9 @@ class PhagenIO(object):
with open(filename, 'r') as fd:
content = fd.readlines()
content = content[-len(self.parameters.atoms):]
cluster = Atoms()
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])
@ -289,9 +290,19 @@ class PhagenIO(object):
xyz = (datatxt[[2, 3, 4]].astype(float) * UREG.a0).to(
'angstrom').magnitude
sym = chemical_symbols[Z]
cluster += Atom(sym, position=xyz)
self.prototypical_atoms = cluster
return cluster
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
def load_potential_file(self, filename='plot_vc.dat'):
a_index = 0

9
src/msspec/calculator.py
View File

@ -314,14 +314,16 @@ class _MSCALCULATOR(Calculator):
shutil.copy(inpot_fname, dest)
# Run if input files changed
os.chdir(os.path.join(self.tmp_folder, 'output'))
modified = True
if modified:
# Run phagen
os.chdir(os.path.join(self.tmp_folder, 'output'))
do_phagen()
# Copy some output files to be more explicit
shutil.copy('clus/clus.out', 'cluster.clu')
shutil.copy('fort.35', 'tmatrix.tl')
shutil.copy('fort.55', 'tmatrix.rad')
# Load data
self.phagenio.load_tl_file('tmatrix.tl')
self.phagenio.load_cluster_file('cluster.clu')
@ -353,6 +355,7 @@ class _MSCALCULATOR(Calculator):
#self._make('compute')
#t1 = time.time()
#self.resources['spec_time'] = t1 - t0
self.modified = True
if self.modified:
#self.get_tmatrix()
t0 = time.time()
@ -479,7 +482,9 @@ class _MSCALCULATOR(Calculator):
max_tl = self.tmatrix_parameters.get_parameter('max_tl').value
cluster = self.phagen_parameters.get_parameter('atoms').value
proto_indices = cluster.get_array('proto_indices')
#proto_indices = cluster.get_array('proto_indices')
proto_indices = np.array(
[atom.get('proto_index') for atom in self.atoms])
if max_tl != None:
LOGGER.debug(" applying max_tl: %s", max_tl)

7
src/msspec/parameters.py
View File

@ -201,6 +201,9 @@ class Parameter(object):
value = args[-1]
self.value = value
def reset(self):
self.value = self.default
def __str__(self):
fmt = '{:' + self.fmt + '}'
try:
@ -358,6 +361,8 @@ class PhagenParameters(BaseParameters):
Parameter('l2h', types=(int,), fmt='d', default=4),
Parameter('ionicity', types=dict, default={}),
Parameter('noproto', allowed_values=('.true.', '.false.'),
types=(str,), fmt='>7s', default='.true.'),
#Parameter('absorber', types=(int,), limits=(1, None), fmt='d', default=1),
#Parameter('nosym', types=(str,), allowed_values=('.true.', '.false.'), fmt='s', default='.true.'),
#Parameter('outersph', types=(str,), allowed_values=('.true.', '.false.'), fmt='s', default='.false.'),
@ -625,7 +630,7 @@ class SpecParameters(BaseParameters):
fmt='d'),
Parameter('calc_npath', types=int, limits=[0, None], default=100,
fmt='d'),
Parameter('calc_vint', types=float, default=0., fmt='.2f'),
Parameter('calc_vint', types=(float,int), default=0., fmt='.2f'),
Parameter('calc_ifwd', types=int, limits=[0, 1], default=0,
fmt='d'),
Parameter('calc_nthout', types=int, limits=[0, None], default=1,

32
src/msspec/phagen/fortran/phagen_scf_2.1_dp.f
View File

@ -335,6 +335,9 @@ CST Phagen to python shared object modification <==
C
complex*16 eelsme,p1,p2,p3,ramfsr1,ramfsr2,ramfsr3
complex*16 p3irreg,p2irreg
CST
logical noproto
CST
C
C.....................................................................
C
@ -347,6 +350,9 @@ C
5 lmxels(3,ua_),p3irreg(rdx_,7),p2irreg(rdx_,7)
common /typot/ ipot
common /v_type/ version
CST
common /misc/ noproto
CST
C
C.....................................................................
C
@ -354,7 +360,11 @@ C
1 emin,emax,delta,gamma,eftri,cip,vc0,rs0,vinput,
2 eikappr,rsh,db,lmaxt,ovlpfac,ionzst,charelx,
3 calctype,potgen,lmax_mode,relc,einc,esct,scangl,
4 optrsh,enunit,lambda,expmode,nosym,version
4 optrsh,enunit,lambda,expmode,nosym,version,
CST ==> Phagen to python shared object modification
CST I added an option to control the number of prototypical atoms
5 noproto
CST Phagen to python shared object modification <==
C
C.....................................................................
C
@ -385,6 +395,11 @@ C
enunit='Ryd' ! energy unit
C
version='2.0' ! MsSpec version number
CST ==> Phagen to python shared object modification
noproto = .false.
CST Phagen to python shared object modification
C
vc0 = -0.7d0
rs0 = 3.d0
@ -2391,11 +2406,24 @@ c
common/charge_center/cc_dif(3,1),z_shift,i_z_shift,shift_cc
common/transform/trans
logical shift_cc
CST
common /misc/ noproto
logical noproto
CST
c
data zero,thr/0.0d0,0.001d0/ !if thr is negative, all cluster atoms are considered prototypical
CST ==> Phagen to python shared object modification
CST data zero,thr/0.0d0,0.001d0/ !if thr is negative, all cluster atoms are considered prototypical
data zero/0.0d0/
CST Phagen to python shared object modification <==
c
data jtape/21/
data lunout/7/
CST ==> Phagen to python shared object modification
CST
thr=0.001d0
if (noproto) thr=-1*thr
CST Phagen to python shared object modification
c
c-----------------------------------------------------------------------
c find the center of charge of the nuclear framework and

115
src/msspec/utils.py
View File

@ -30,9 +30,11 @@ Module utils
"""
import os
import re
import numpy as np
import ase.atom
from ase import Atom
from ase import Atoms
@ -51,6 +53,7 @@ class ForeignPotential(object):
# 'RHOint' : <float>,
# 'types': [
# {
# 'atom_type': <int>,
# 'Z' : <int>,
# 'RWS' : <float>,
# 'data' : <np.array(..., 4, dtype=float)>
@ -65,7 +68,7 @@ class ForeignPotential(object):
def write(self, filename, prototypical_atoms):
LOGGER.debug(f"Writing Phagen input potential file: {filename}")
def append_atom_potential(atom):
def DEPRECATEDappend_atom_potential(atom):
Z = atom.number
# Find the right type (Z) in the phagen_data
itypes = []
@ -85,6 +88,18 @@ class ForeignPotential(object):
s += line_fmt.format(*row)
return s
def append_atom_potential(atom):
line_fmt = "{:+1.8e} " * 4 + "\n"
atom_type = atom.get('atom_type')
assert atom_type != None, f"Unable get the atom type!"
for t in self.phagen_data['types']:
if t['atom_type'] == atom_type:
s = "{:<7d}{:<10d}{:1.4f}\n".format(
t['Z'], len(t['data']), t['RWS'])
for row in t['data']:
s += line_fmt.format(*row)
return s
content = ""
# Start by writing the header line
content += "{:.2f} {:.4f} {:.2f}\n".format(
@ -115,7 +130,43 @@ class ForeignPotential(object):
class SPRKKRPotential(ForeignPotential):
def __init__(self, atoms, potfile, *exported_files):
super().__init__()
"""
self.atoms = atoms
self.potfile = potfile
self.load_sprkkr_atom_types()
for f in exported_files:
LOGGER.info(f"Loading file {f}...")
# get the IT from the filename
m=re.match('SPRKKR-IT_(?P<IT>\d+)-PHAGEN.*', os.path.basename(f))
it = int(m.group('IT'))
# load the content of the header (2 lines)
with open(f, 'r') as fd:
first_line, second_line = [fd.readline().strip()
for _ in range(2)]
# load Coulomb and Total interstitial potential
pattern = (r'#\s*VMTZ_TOTAL\s*=\s*(?P<TOTAL>.*?)\s+'
r'VMTZ_Coulomb\s*=\s*(?P<COULOMB>.*?)\s+.*$')
m = re.match(pattern, first_line)
self.phagen_data.update(VintCoulomb=float(m.group('COULOMB')),
VintTotal=float(m.group('TOTAL')),
RHOint=0.)
# load Z, Wigner-Seitz radius from 2nd line of header
type_data = {}
_ = re.split(r'\s+', second_line.strip("# "))
type_data.update(atom_type=int(it), Z=int(_[0]), RWS=float(_[3]))
# load the data
data = np.loadtxt(f, comments='#')
type_data.update(data=data)
self.phagen_data['types'].append(type_data)
# store the sprkkr type number in the sprkkr_info property of each
# atom in the provided self.atoms
def load_sprkkr_atom_types(self):
def read(content, pattern, types):
# compile the pattern for regex matching
pat = re.compile(pattern, re.MULTILINE)
@ -137,7 +188,8 @@ class SPRKKRPotential(ForeignPotential):
return data
# load info in *.pot file
with open(potfile, 'r') as fd:
LOGGER.info(f"Loading SPRKKR *.pot file {self.potfile}...")
with open(self.potfile, 'r') as fd:
content = fd.read()
self.sites_data = read(content,
@ -152,35 +204,33 @@ class SPRKKRPotential(ForeignPotential):
(r'^\s*OCCUPATION\s*\n(\s*(?P<KEYS>IQ.*)\n'
r'(?P<DATA>(.*\n)+?))\*+'),
[int] * 5 + [float])
"""
for f in exported_files:
# get the IT from the filename
# m=re.match('SPRKKR-IT_(?P<IT>\d+)-PHAGEN.*', os.path.basename(f))
# it = int(m.group('IT'))
# load the content of the header (2 lines)
with open(f, 'r') as fd:
first_line = fd.readline().strip('\n')
second_line = fd.readline().strip('\n')
LOGGER.debug("SITES:")
for _ in self.sites_data:
LOGGER.debug(_)
# load Coulomb and Total interstitial potential
pattern = (r'#\s*VMTZ_TOTAL\s*=\s*(?P<TOTAL>.*?)\s+'
r'VMTZ_Coulomb\s*=\s*(?P<COULOMB>.*?)\s+.*$')
m = re.match(pattern, first_line)
self.phagen_data.update(VintCoulomb=float(m.group('COULOMB')),
VintTotal=float(m.group('TOTAL')),
RHOint=0.)
LOGGER.debug("TYPES:")
for _ in self.types_data:
LOGGER.debug(_)
# load Z, Wigner-Seitz radius from 2nd line of header
type_data = {}
_ = re.split(r'\s+', second_line.strip("# "))
type_data.update(Z=int(_[0]), RWS=float(_[3]))
LOGGER.debug("OCCUPATION:")
for _ in self.occ_data:
LOGGER.debug(_)
# load the data
data = np.loadtxt(f, comments='#')
type_data.update(data=data)
for site in self.sites_data:
IQ = site['IQ']
# Get the Atom at x, y, z
x = site['QBAS(X)']
y = site['QBAS(Y)']
z = site['QBAS(Z)']
i = get_atom_index(self.atoms, x, y, z, scaled=True)
for occupation in self.occ_data:
if occupation['IQ'] == IQ:
IT = occupation['ITOQ']
atom = self.atoms[i]
atom.set('atom_type', IT)
LOGGER.debug(f"Site #{IQ} is type #{IT}, atom {atom}")
self.phagen_data['types'].append(type_data)
class EmptySphere(Atom):
@ -189,7 +239,7 @@ class EmptySphere(Atom):
self.symbol = 'X'
def get_atom_index(atoms, x, y, z):
def get_atom_index(atoms, x, y, z, scaled=False):
""" Return the index of the atom that is the closest to the coordiantes
given as parameters.
@ -197,15 +247,20 @@ def get_atom_index(atoms, x, y, z):
:param float x: the x position in angstroms
:param float y: the y position in angstroms
:param float z: the z position in angstroms
:param bool scaled: whether the x,y,z coordinates are scaled
:return: the index of the atom as an integer
:rtype: int
"""
# get all distances
d = np.linalg.norm(atoms.get_positions() - np.array([x, y, z]), axis=1)
if scaled:
positions = atoms.get_scaled_positions()
else:
positions = atoms.get_positions()
d = np.linalg.norm(positions - np.array([x, y, z]), axis=1)
# get the index of the min distance
i = np.argmin(d)
# return the index and the corresponding distance
# return the index
return i

1
tests/sprkkr/copper/Cu.py
View File

@ -67,6 +67,7 @@ if 'msspec' in sys.argv:
pot = SPRKKRPotential(Cu, "Cu/Cu.pot", *glob.glob("Cu/*PHAGEN.pot"))
calc.tmatrix_parameters.potential = pot
calc.phagen_parameters.noproto = '.true.'
data = calc.get_theta_scan(level='2p3/2')
data.view()