def __init_espresso(self,
prefix,
ik,
IBstart,
IBend,
Ecut,
Ecut0,
kptxml,
thresh=1e-4):
self.K = np.array(kptxml.find("k_point").text.split(), dtype=float)
eigen = np.array(kptxml.find("eigenvalues").text.split(), dtype=float)
self.Energy = eigen[IBstart:IBend] * Hartree_eV
try:
self.upper = eigen[IBend] * Hartree_eV
except:
self.upper = np.NaN
npw = int(kptxml.find("npw").text)
# kg= np.random.randint(100,size=(npw,3))-50
npwtot = npw * (2 if self.spinor else 1)
CG = np.zeros((IBend - IBstart, npwtot), dtype=complex)
try:
fWFC = FF("{}.save/WFC{}.dat".format(prefix, ik + 1), "r")
except FileNotFoundError:
fWFC = FF("{}.save/wfc{}.dat".format(prefix, ik + 1), "r")
rec = record_abinit(fWFC, 'i4,3f8,i4,i4,f8')[0]
# print ('rec=',rec)
ik, xk, ispin, gamma_only, scalef = rec
# xk/=bohr
# xk=xk.dot(np.linalg.inv(RecLattice))
rec = record_abinit(fWFC, '4i4')
# print ('rec=',rec)
ngw, igwx, npol, nbnd = rec
rec = record_abinit(fWFC, '(3,3)f8')
# print ('rec=',rec)
B = np.array(rec)
# print (np.mean(B/RecLattice))
self.K = xk.dot(np.linalg.inv(B))
rec = record_abinit(fWFC, '({},3)i4'.format(igwx))
# print ('rec=',rec)
kg = np.array(rec)
# print (np.mean(B/RecLattice))
# print ("k-point {0}: {1}/{2}={3}".format(ik, self.K,xk,self.K/xk))
# print ("k-point {0}: {1}".format(ik,self.K ))
for ib in range(IBend):
cg_tmp = record_abinit(fWFC, '{}f8'.format(npwtot * 2))
if ib >= IBstart:
CG[ib - IBstart] = cg_tmp[0::2] + 1.j * cg_tmp[1::2]
return self.__sortIG(kg, self.K, CG, B, Ecut0, Ecut, thresh=thresh)
def __getMat(self, suffix):
f = FF(self.seedname + "_" + suffix + "_R" +
(".dat" if self.old_format else ""))
MM_R = np.array([[
np.array(f.read_record('2f8'), dtype=float)
for m in range(self.num_wann)
] for n in range(self.num_wann)])
MM_R = MM_R[:, :, :, 0] + 1j * MM_R[:, :, :, 1]
f.close()
ncomp = MM_R.shape[2] / self.nRvec0
if ncomp == 1:
result = MM_R / self.Ndegen[None, None, :]
elif ncomp == 3:
result = MM_R.reshape(
self.num_wann, self.num_wann, 3, self.nRvec0).transpose(
0, 1, 3, 2) / self.Ndegen[None, None, :, None]
elif ncomp == 9:
result = MM_R.reshape(
self.num_wann, self.num_wann, 3, 3, self.nRvec0).transpose(
0, 1, 4, 3, 2) / self.Ndegen[None, None, :, None, None]
else:
raise RuntimeError(
"in __getMat: invalid ncomp : {0}".format(ncomp))
if self.ws_map is None:
return result
else:
return self.ws_map(result)
def read_one_cpu(output):
f = FF(output)
ncpu = f.read_ints()
ndim = f.read_ints()
npart = f.read_ints()
localseed = f.read_ints()
nstart_tot = f.read_ints()
mstar_tot = f.read_ints()
mstart_lost = f.read_ints()
nsink = f.read_ints()
x = np.zeros((ndim, npart), dtype=float)
v = np.zeros((ndim, npart), dtype=float)
m = np.zeros((npart), dtype=float)
ind = np.zeros((npart), dtype=int)
for dim in range(ndim):
x[dim] = f.read_reals()
for dim in range(ndim):
v[dim] = f.read_reals()
m = f.read_reals()
ind = f.read_ints()
lvl = f.read_ints()
try:
tp = f.read_reals()
Z = f.read_reals()
except TypeError:
tp = np.zeros((npart))
Z = np.zeros((npart))
return ind, ndim, npart, x, v, m, lvl, tp, Z
def __init__(self, normalcar='NormalCAR', wavecar='WAVECAR'):
"""
Initialize the class with supplied file name (including path)
Only the records untile projector coefficients are read for initialize
projector coefficients will only be read when explicitly invoked.
Args:
fnm (optional): NormalCAR filename (including path)
Returns:
None
Raise:
IOError if encounter problems reading NormalCAR
ValueError if inconsistent record/info read
Note:
All 'private' members or attributes (starts with single underline)
have names following the nice VASP style... with each has a
corresponding a callable getXXX() method, where XXX might be easily
understood...
"""
self._normalcar = normalcar
self._wavecar = wavecar
try:
self._fh = FF(self._normalcar, 'r')
except:
raise IOError("Failed to open NormalCAR file: {}".format(
self._fnm))
# rec 1
self._LMDIM, self._NIONS, self._NRSPINORS = FF.read_ints(self._fh)
# rec 2
self._CQIJ = FF.read_reals(self._fh)
dump = self._LMDIM * self._LMDIM * self._NIONS * self._NRSPINORS
if len(self._CQIJ) != dump:
raise ValueError(
"Inconsistent dimension for CQIJ:\n"
"\t# floats intend to read: {}\n\t# floats in this record".
format(dump, len(self._CQIJ)))
self._CQIJ = self._CQIJ.reshape(
[self._LMDIM, self._LMDIM, self._NIONS, self._NRSPINORS],
order='F')
del dump
# rec 3
self._NPROD, self._NPRO, self._NTYP = FF.read_ints(self._fh)
# rec 4 ... 3 + NTypes
self._LMMAX = []
for i in range(self._NTYP):
self._LMMAX.append(FF.read_ints(self._fh))
self._LMMAX = np.array(self._LMMAX)
self._NPROJ = np.sum(self._LMMAX[:, 0] * self._LMMAX[:, 1])
# read wavefunction stuff, number of kpts and bands
_WC = wf.WAVECAR(self._wavecar)
self._NK = _WC.getNKpts()
self._NB = _WC.getNBands()
def test_halo_particle_ids(halos):
with FF(halos._fname, mode="r") as f:
for halo_id in range(1, len(halos) + 1):
# Manually read the particle ids and make sure pynbody is reading them as it should
f._fp.seek(halos[halo_id].properties["file_offset"])
f.read_ints() # number of particles
expected_members = f.read_ints("i") # halo members
np.testing.assert_equal(expected_members,
halos[halo_id].properties["members"])
def __init_wannier(self,
NBin,
IBstart,
IBend,
Ecut,
kpt,
eigenval,
thresh=1e-4):
self.K = np.array(kpt, dtype=float)
self.Energy = eigenval[IBstart:IBend]
fname = "UNK{:05d}.{}".format(self.ik0, 'NC' if self.spinor else "1")
fUNK = FF(fname, "r")
ngx, ngy, ngz, ik, nbnd = record_abinit(fUNK, 'i4,i4,i4,i4,i4')[0]
ngtot = ngx * ngy * ngz
if ik != self.ik0:
raise RuntimeError(
"file {} contains point number {}, expected {}".format(
fname, ik, self.ik0))
if nbnd != NBin:
raise RuntimeError(
"file {} contains {} bands , expected {}".format(
fname, nbnd, NBin))
nspinor = 2 if self.spinor else 1
try:
self.upper = eigenval[IBend]
except:
self.upper = np.NaN
ig = calc_gvectors(self.K,
self.RecLattice,
Ecut,
spinor=self.spinor,
nplanemax=np.max([ngx, ngy, ngz]) // 2)
selectG = tuple(ig[0:3])
def _readWF_1(skip=False):
cg_tmp = record_abinit(fUNK, '{}f8'.format(ngtot * 2))
if skip:
return np.array([0], dtype=complex)
cg_tmp = (cg_tmp[0::2] + 1.j * cg_tmp[1::2]).reshape(
(ngx, ngy, ngz), order='F')
cg_tmp = np.fft.fftn(cg_tmp)
return cg_tmp[selectG]
def _readWF(skip=False):
return np.hstack([_readWF_1(skip) for i in range(nspinor)])
for ib in range(IBstart):
_readWF(skip=True)
WF = np.array([_readWF(skip=False) for ib in range(IBend - IBstart)])
return WF, ig
def write_mock_clus(vx, vy, vz, it, digits=5, path=''):
with FF(os.path.join(path, masclet.read_masclet.filename(it, 'b', digits)),
'w') as clus:
clus.write_record(np.array([it, 0, 0, 0]).astype('i4')) #first line
# base level
clus.write_record(np.array([0]).astype('i4'))
clus.write_record(vx[0].T.astype('f4'))
clus.write_record(vy[0].T.astype('f4'))
clus.write_record(vz[0].T.astype('f4'))
for i in range(6):
clus.write_record(np.array([0]).astype('i4'))
# refinement levels
for vxi, vyi, vzi in zip(vx[1:], vy[1:], vz[1:]):
clus.write_record(np.array([0]).astype('i4'))
clus.write_record(vxi.T.astype('f4'))
clus.write_record(vyi.T.astype('f4'))
clus.write_record(vzi.T.astype('f4'))
for i in range(7):
clus.write_record(np.array([0]).astype('i4'))
def read(fname: PathType) -> IOResult:
"""Read a grafic file.
Parameters
----------
fname : str, filename
"""
try:
aexp = float(fname.split("-")[-1].replace(".dat", ""))
except ValueError:
aexp = 1
with FF(fname, "r") as f:
N1, N2, N3, qq, Xc1, Xc2, Xc3, Omega_m, Omega_c, Omega_l, H = f.read_record(
*["i"] * 3, *["f"] * 8
)
Lbox = qq * Xc1 * H / 100
Lbox /= 1000 # Gpc
Lbox = float(Lbox)
N1, N2, N3 = (int(_) for _ in (N1, N2, N3))
Xc = np.stack((Xc1, Xc2, Xc3)).flatten()
dens = np.zeros((N1, N2, N3), dtype="f")
for i in range(N1):
dens[i] = f.read_reals("f").reshape(N2, N3)
return IOResult(
data=dict(rho=dens),
metadata=dict(
Lbox=Lbox,
Omega_m=Omega_m,
Omega_c=Omega_c,
Omega_l=Omega_l,
Xc=Xc,
aexp=aexp,
N=N1,
),
)
def __init__(self, fname):
self.fWFK = FF(fname, "r")
fWFK = self.fWFK
record = fWFK.read_record('a6,2i4')
# print (record)
stdout.flush()
codsvn = record[0][0].decode('ascii')
headform, fform = record[0][1]
defversion = '8.6.3 '
if not (codsvn == defversion):
print("WARNING, the version {0} of abinit is not {1}".format(
codsvn, defversion))
if headform < 80:
raise ValueError(
"Head form {0}<80 is not supported".format(headform))
record = fWFK.read_record('18i4,19f8,4i4')[0]
# write(unit=header) codvsn,headform,fform
# write(unit=header) bantot,date,intxc,ixc,natom,ngfft(1:3),&
# & nkpt,nspden,nspinor,nsppol,nsym,npsp,ntypat,occopt,pertcase,usepaw,&
# & ecut,ecutdg,ecutsm,ecut_eff,qptn(1:3),rprimd(1:3,1:3),stmbias,tphysel,tsmear,usewvl,
#hdr%nshiftk_orig, hdr%nshiftk, hdr%mband
# print (record)
self.rprimd = record[1][7:16].reshape((3, 3))
# print (self.rprimd)
self.ecut = record[1][0] * Hartree_eV
print("ecut={0} eV".format(self.ecut))
stdout.flush()
bandtot, self.natom, self.nkpt, nsym, npsp, nsppol, ntypat, self.usepaw, nspinor = np.array(
record[0])[[0, 4, 8, 12, 13, 11, 14, 17, 10]]
if nsppol != 1:
raise RuntimeError(
"Only nsppol=1 is supported. found {0}".format(nsppol))
if nspinor == 2:
self.spinor = True
elif nspinor == 1:
self.spinor = False
else:
raise RuntimeError(
"Unexpected value nspinor = {0}".format(nspinor))
#if usepaw==1: raise ValueError("usepaw==1 not implemented")
nshiftk_orig = record[2][1]
nshiftk = record[2][2]
#print (bandtot,natom,nkpt,nsym,npsp,nsppol,ntypat)
record = fWFK.read_record(
'{nkpt}i4,{n2}i4,{nkpt}i4,{npsp}i4,{nsym}i4,({nsym},3,3)i4,{natom}i4,({nkpt},3)f8,{bandtot}f8,({nsym},3)f8,{ntypat}f8,{nkpt}f8'
.format(nkpt=self.nkpt,
n2=self.nkpt * nsppol,
npsp=npsp,
nsym=nsym,
natom=self.natom,
bandtot=bandtot,
ntypat=ntypat))[0]
#print (record)
# write(unit=header) istwfk(1:nkpt),nband(1:nkpt*nsppol),&
# & npwarr(1:nkpt),so_psp(1:npsp),symafm(1:nsym),symrel(1:3,1:3,1:nsym),typat(1:natom),&
# & kpt(1:3,1:nkpt),occ(1:bantot),tnons(1:3,1:nsym),znucltypat(1:ntypat),wtk(1:nkpt)
# wtk=record[11]
self.npwarr = record[2]
istwfk = record[0]
if set(istwfk) != {1}:
raise ValueError(
"istwfk should be 1 for all kpoints. found {0}".format(istwfk))
self.typat = record[6]
self.kpt = record[7]
self.nband = record[1]
assert (np.sum(self.nband) == bandtot)
#print (kpt,nband)
record = fWFK.read_record('f8,({natom},3)f8,f8,f8,{ntypat}f8'.format(
natom=self.natom, ntypat=ntypat))[0]
self.xred = record[1]
self.efermi = record[3]
# write(unit,err=10, iomsg=errmsg) hdr%residm, hdr%xred(:,:), hdr%etot, hdr%fermie, hdr%amu(:)
#print (record)
record = fWFK.read_record(
"i4,i4,f8,f8,i4,(3,3)i4,(3,3)i4,({nshiftkorig},3)f8,({nshiftk},3)f8"
.format(nshiftkorig=nshiftk_orig, nshiftk=nshiftk))[0]
#record=fWFK.read_record("i4,i4,f8,f8,i4,i4,(3,3)f8,5f8,i4".format(nshiftkorig=nshiftk_orig,nshiftk=nshiftk) )[0]
##record=fWFK.read_record("i4,i4,f8,f8,i4,9i4,9i4,6f8".format(nshiftkorig=nshiftk_orig,nshiftk=nshiftk) )[0]
# write(unit,err=10, iomsg=errmsg) &
# hdr%kptopt, hdr%pawcpxocc, hdr%nelect, hdr%charge, hdr%icoulomb,&
# hdr%kptrlatt,hdr%kptrlatt_orig, hdr%shiftk_orig(:,1:hdr%nshiftk_orig),hdr%shiftk(:,1:hdr%nshiftk)
#print (record)
for ipsp in range(npsp):
record = fWFK.read_record("a132,f8,f8,5i4,a32")[0]
# read(unit, err=10, iomsg=errmsg) &
# & hdr%title(ipsp), hdr%znuclpsp(ipsp), hdr%zionpsp(ipsp), hdr%pspso(ipsp), hdr%pspdat(ipsp), &
# & hdr%pspcod(ipsp), hdr%pspxc(ipsp), hdr%lmn_size(ipsp), hdr%md5_pseudos(ipsp)
# print (record)
if self.usepaw == 1:
record = fWFK.read_record('i4')
# print(record)
record = fWFK.read_record('f8')