def struct_str(struct):
"""Convert Structure object to lammps format.
The returned string can be written to a file and read in a lammps input
file by ``read_data``.
Parameters
----------
struct : Structure
Returns
-------
str : string
References
----------
ase.calculators.lammpsrun (ASE 3.8).
"""
# align cell to [[x,0,0],[xy,y,0],[xz, yz, z]] (row format, the transpose
# is what lammps uses)
st = struct.copy()
st.coords = None
st.cell = None
st.set_all()
head_str = "structure written by pwtools {0}".format(time.asctime())
info_str = '%i atoms\n%i atom types' % (st.natoms, len(st.symbols_unique))
cell_str = "0.0 {x:.14g} xlo xhi\n0.0 {y:.14g} ylo yhi\n0.0 {z:.14g} zlo zhi\n"
cell_str += "{tilts} xy xz yz\n"
cell_str = cell_str.format(x=st.cell[0, 0],
y=st.cell[1, 1],
z=st.cell[2, 2],
tilts=common.str_arr(np.array([
st.cell[1, 0], st.cell[2, 0], st.cell[2, 1]
]),
eps=1e-13,
fmt='%.14g',
delim=' '))
atoms_str = "Atoms\n\n"
for iatom in range(st.natoms):
atoms_str += "{iatom} {ispec} {xyz}".format(
iatom=iatom + 1,
ispec=st.order[st.symbols[iatom]],
xyz=common.str_arr(st.coords[iatom, :], eps=1e-13, fmt='%23.16e') +
'\n')
mass_str = "Masses\n\n"
for idx, sy in enumerate(st.symbols_unique):
mass_str += "%i %g\n" % (idx + 1, atomic_data.pt[sy]['mass'])
return head_str + '\n\n' + info_str + '\n\n' + cell_str + \
'\n' + atoms_str + '\n' + mass_str
def write_input(self, atoms, properties=None, system_changes=None):
FileIOCalculator.write_input(self, atoms, properties, system_changes)
struct = crys.atoms2struct(atoms)
self.cell = common.str_arr(struct.cell)
self.kpoints = pwscf.kpoints_str_pwin(kpts2mp(atoms, self.kpts))
if isinstance(self.pp, bytes):
pseudos = [
"%s.%s" % (sym, self.pp) for sym in struct.symbols_unique
]
else:
assert len(self.pp) == struct.ntypat
pseudos = []
for sym in struct.symbols_unique:
for ppi in self.pp:
if ppi.startswith(sym):
pseudos.append(ppi)
break
assert len(pseudos) == struct.ntypat
self.atspec = pwscf.atspec_str(symbols=struct.symbols_unique,
masses=struct.mass_unique,
pseudos=pseudos)
self.atpos = pwscf.atpos_str(symbols=struct.symbols,
coords=struct.coords_frac)
self.natoms = struct.natoms
self.ntyp = struct.ntypat
if self.backup:
for fn in [self.infile, self.outfile]:
if os.path.exists(fn):
common.backup(fn)
common.file_write(self.infile, self.fill_infile_templ())
def _fit(self):
# volume[Bohr^3] etot[Ha] for eos.x
volume = self.volume * (Ang**3.0 / Bohr**3.0)
energy = self.energy * (eV / Ha)
data = np.array([volume, energy]).T
infn_txt =\
"""
%s
%i
%i
%f, %f, %i
%i
%s
"""%(self.name,
self.natoms,
self.etype,
volume[0], volume[-1], self.npoints,
len(volume),
common.str_arr(data))
common.file_write(self.infn, infn_txt)
out = common.backtick('cd %s && %s' % (self.dir, self.app_basename))
if self.verbose:
print(out)
print((open(os.path.join(self.dir, 'PARAM.OUT')).read()))
# Remove normalization on natoms. See .../eos/output.f90:
# fitev: [volume [Bohr^3] / natoms, energy [Ha] / natoms]
# fitpv: [volume [Bohr^3] / natoms, pressure [GPa]]
fitev = np.loadtxt(os.path.join(self.dir, 'EVPAI.OUT')) * self.natoms
# convert energy back to [Ang^3, eV]
fitev[:, 0] *= (Bohr**3 / Ang**3)
fitev[:, 1] *= (Ha / eV)
self.ev = fitev
fitpv = np.loadtxt(os.path.join(self.dir, 'PVPAI.OUT'))
fitpv[:, 0] *= (self.natoms * Bohr**3 / Ang**3)
self.pv = fitpv
def _fit(self):
# volume[Bohr^3] etot[Ha] for eos.x
volume = self.volume*(Ang**3.0 / Bohr**3.0)
energy = self.energy*(eV / Ha)
data = np.array([volume, energy]).T
infn_txt =\
"""
%s
%i
%i
%f, %f, %i
%i
%s
"""%(self.name,
self.natoms,
self.etype,
volume[0], volume[-1], self.npoints,
len(volume),
common.str_arr(data))
common.file_write(self.infn, infn_txt)
out = common.backtick('cd %s && %s' %(self.dir, self.app_basename))
if self.verbose:
print out
print(open(os.path.join(self.dir,'PARAM.OUT')).read())
# Remove normalization on natoms. See .../eos/output.f90:
# fitev: [volume [Bohr^3] / natoms, energy [Ha] / natoms]
# fitpv: [volume [Bohr^3] / natoms, pressure [GPa]]
fitev = np.loadtxt(os.path.join(self.dir,'EVPAI.OUT')) * self.natoms
# convert energy back to [Ang^3, eV]
fitev[:,0] *= (Bohr**3 / Ang**3)
fitev[:,1] *= (Ha / eV)
self.ev = fitev
fitpv = np.loadtxt(os.path.join(self.dir,'PVPAI.OUT'))
fitpv[:,0] *= (self.natoms * Bohr**3 / Ang**3)
self.pv = fitpv
def write_input(self, atoms, properties=None, system_changes=None):
FileIOCalculator.write_input(self, atoms, properties,
system_changes)
struct = crys.atoms2struct(atoms)
self.cell = common.str_arr(struct.cell)
self.kpoints = pwscf.kpoints_str_pwin(kpts2mp(atoms, self.kpts))
if isinstance(self.pp, types.StringType):
pseudos = ["%s.%s" %(sym, self.pp) for sym in struct.symbols_unique]
else:
assert len(self.pp) == struct.ntypat
pseudos = []
for sym in struct.symbols_unique:
for ppi in self.pp:
if ppi.startswith(sym):
pseudos.append(ppi)
break
assert len(pseudos) == struct.ntypat
self.atspec = pwscf.atspec_str(symbols=struct.symbols_unique,
masses=struct.mass_unique,
pseudos=pseudos)
self.atpos = pwscf.atpos_str(symbols=struct.symbols,
coords=struct.coords_frac)
self.natoms = struct.natoms
self.ntyp = struct.ntypat
if self.backup:
for fn in [self.infile, self.outfile]:
if os.path.exists(fn):
common.backup(fn)
common.file_write(self.infile, self.fill_infile_templ())
def struct_str(struct):
"""Convert Structure object to lammps format.
The returned string can be written to a file and read in a lammps input
file by ``read_data``.
Parameters
----------
struct : Structure
Returns
-------
str : string
References
----------
ase.calculators.lammpsrun (ASE 3.8).
"""
# align cell to [[x,0,0],[xy,y,0],[xz, yz, z]] (row format, the transpose
# is what lammps uses)
st = struct.copy()
st.coords = None
st.cell = None
st.set_all()
head_str = "structure written by pwtools {0}".format(time.asctime())
info_str = '%i atoms\n%i atom types' %(st.natoms, len(st.symbols_unique))
cell_str = "0.0 {x:.14g} xlo xhi\n0.0 {y:.14g} ylo yhi\n0.0 {z:.14g} zlo zhi\n"
cell_str += "{tilts} xy xz yz\n"
cell_str = cell_str.format(x=st.cell[0,0],
y=st.cell[1,1],
z=st.cell[2,2],
tilts=common.str_arr(np.array([st.cell[1,0],
st.cell[2,0],
st.cell[2,1]]),
eps=1e-13, fmt='%.14g',
delim=' '))
atoms_str = "Atoms\n\n"
for iatom in range(st.natoms):
atoms_str += "{iatom} {ispec} {xyz}".format(
iatom=iatom+1,
ispec=st.order[st.symbols[iatom]],
xyz=common.str_arr(st.coords[iatom,:], eps=1e-13, fmt='%23.16e') + '\n')
mass_str = "Masses\n\n"
for idx,sy in enumerate(st.symbols_unique):
mass_str += "%i %g\n" %(idx+1, atomic_data.pt[sy]['mass'])
return head_str + '\n\n' + info_str + '\n\n' + cell_str + \
'\n' + atoms_str + '\n' + mass_str
def write_axsf(filename, obj):
"""Write animated XSF file for Structure (only 1 step) or Trajectory.
Note that forces are converted eV / Ang -> Ha / Ang.
length: Angstrom
forces: Ha / Angstrom
Parameters
----------
filename : target file name
obj : Structure or Trajectory
References
----------
[XSF] http://www.xcrysden.org/doc/XSF.html
"""
# Notes
# -----
# XSF: The XSF spec [XSF] is a little fuzzy about what PRIMCOORD actually
# is (fractional or cartesian Angstrom). Only the latter case results
# in a correctly displayed structure in xcrsyden. So we use that.
#
# Speed: The only time-consuming step is calling atpos_str*() in the loop
# b/c that transforms *every* single float to a string, which
# effectively is a double loop over `ccf`. No way to get faster w/ pure
# Python.
#
traj = crys.struct2traj(obj)
# ccf = cartesian coords + forces (6 columns)
if traj.is_set_attr('forces'):
ccf = np.concatenate((traj.coords, traj.forces*eV/Ha), axis=-1)
else:
ccf = traj.coords
axsf_str = "ANIMSTEPS %i\nCRYSTAL" %traj.nstep
for istep in range(traj.nstep):
axsf_str += "\nPRIMVEC %i\n%s" %(istep+1,
common.str_arr(traj.cell[istep,...]))
axsf_str += "\nPRIMCOORD %i\n%i 1\n%s" %(istep+1,
traj.natoms,
pwscf.atpos_str_fast(traj.symbols,
ccf[istep,...]))
common.file_write(filename, axsf_str)
def write_axsf(filename, obj):
"""Write animated XSF file for Structure (only 1 step) or Trajectory.
Note that forces are converted eV / Ang -> Ha / Ang.
length: Angstrom
forces: Ha / Angstrom
Parameters
----------
filename : target file name
obj : Structure or Trajectory
References
----------
[XSF] http://www.xcrysden.org/doc/XSF.html
"""
# Notes
# -----
# XSF: The XSF spec [XSF] is a little fuzzy about what PRIMCOORD actually
# is (fractional or cartesian Angstrom). Only the latter case results
# in a correctly displayed structure in xcrsyden. So we use that.
#
# Speed: The only time-consuming step is calling atpos_str*() in the loop
# b/c that transforms *every* single float to a string, which
# effectively is a double loop over `ccf`. No way to get faster w/ pure
# Python.
#
traj = crys.struct2traj(obj)
# ccf = cartesian coords + forces (6 columns)
if traj.is_set_attr('forces'):
ccf = np.concatenate((traj.coords, traj.forces * eV / Ha), axis=-1)
else:
ccf = traj.coords
axsf_str = "ANIMSTEPS %i\nCRYSTAL" % traj.nstep
for istep in range(traj.nstep):
axsf_str += "\nPRIMVEC %i\n%s" % (
istep + 1, common.str_arr(traj.cell[istep, ...]))
axsf_str += "\nPRIMCOORD %i\n%i 1\n%s" % (
istep + 1, traj.natoms,
pwscf.atpos_str_fast(traj.symbols, ccf[istep, ...]))
common.file_write(filename, axsf_str)
def atpos_str(symbols, coords, fmt="%.16e", zero_eps=None, eps=EPS, delim=4*' '):
"""Convenience function to make a string for the ATOMIC_POSITIONS section
of a pw.x input file.
Parameters
----------
symbols : sequence
strings with atom symbols, (natoms,), must match with the
rows of coords
coords : array (natoms, 3)
with atomic coords, can also be (natoms, >3) to add constraints on
atomic forces in PWscf
eps : float
Print values as 0.0 where abs(coords[i,j]) < eps. If eps < 0.0, then
disable this.
delim : str
delimiter between columns
Returns
-------
string
Examples
--------
>>> print atpos_str(['Al', 'N'], array([[0,0,0], [0,0,1.]]))
Al 0.0000000000 0.0000000000 0.0000000000
N 0.0000000000 0.0000000000 1.0000000000
"""
if zero_eps is not None:
warnings.warn("`zero_eps` is deprecated, use `eps` > 0 instead",
DeprecationWarning)
coords = np.asarray(coords)
assert len(symbols) == coords.shape[0], "len(symbols) != coords.shape[0]"
txt = '\n'.join("%s%s%s" %(symbols[i], delim, str_arr(row, fmt=fmt, eps=eps,
delim=delim)) \
for i,row in enumerate(coords))
return txt
def atpos_str(symbols, coords, fmt="%.16e", zero_eps=None, eps=EPS, delim=4*' '):
"""Convenience function to make a string for the ATOMIC_POSITIONS section
of a pw.x input file.
Parameters
----------
symbols : sequence
strings with atom symbols, (natoms,), must match with the
rows of coords
coords : array (natoms, 3)
with atomic coords, can also be (natoms, >3) to add constraints on
atomic forces in PWscf
eps : float
Print values as 0.0 where abs(coords[i,j]) < eps. If eps < 0.0, then
disable this.
delim : str
delimiter between columns
Returns
-------
string
Examples
--------
>>> print atpos_str(['Al', 'N'], array([[0,0,0], [0,0,1.]]))
Al 0.0000000000 0.0000000000 0.0000000000
N 0.0000000000 0.0000000000 1.0000000000
"""
if zero_eps is not None:
warnings.warn("`zero_eps` is deprecated, use `eps` > 0 instead",
DeprecationWarning)
coords = np.asarray(coords)
assert len(symbols) == coords.shape[0], "len(symbols) != coords.shape[0]"
txt = '\n'.join("%s%s%s" %(symbols[i], delim, str_arr(row, fmt=fmt, eps=eps,
delim=delim)) \
for i,row in enumerate(coords))
return txt
scratch='/scratch/schmerler',
filename='calc.templ/job.pbs.theo',
home='/home/schmerler')
templates = [batch.FileTemplate(basename='pw.in')]
# rs-AlN
st = crys.Structure(coords_frac=np.array([[0.0]*3, [0.5]*3]),
symbols=['Al','N'],
cryst_const=np.array([2.76]*3 + [60]*3))
params_lst = []
for ecutwfc in np.linspace(30,100,8):
params_lst.append([sql.SQLEntry(key='ecutwfc', sqlval=ecutwfc),
sql.SQLEntry(key='ecutrho', sqlval=4.0*ecutwfc),
sql.SQLEntry(key='cell', sqlval=common.str_arr(st.cell)),
sql.SQLEntry(key='natoms', sqlval=st.natoms),
sql.SQLEntry(key='atpos',
sqlval=pwscf.atpos_str(st.symbols,
st.coords_frac)),
])
calc = batch.ParameterStudy(machines=theo,
templates=templates,
params_lst=params_lst,
study_name='convergence_test_cutoff',
)
calc.write_input(sleep=0, backup=False, mode='w')
if not os.path.exists('calc'):
os.symlink('calc_theo', 'calc')
#!/usr/bin/python
# Create a PWscf MD "trajectory" where the CELL_PARAMETERS unit changes. This
# is for testing if the parser can handle that. The output file consists only
# of CELL_PARAMETERS blocks, which is enough for PwVCMDOutputFile.get_gell() .
#
# usage
# ------
# ./make-vc-md-cell.py > ../files/pw.vc-md.cell.out
import numpy as np
from pwtools import common
cell = np.arange(1,10).reshape((3,3))
alat_lst = [2.0, 4.0]
for ialat,alat in enumerate(alat_lst):
for ii in range(5):
cell_str = common.str_arr((cell + 0.02*ii + ialat)/alat)
print "CELL_PARAMETERS (alat= %.5f)\n%s" %(alat, cell_str)
&input
asr='crystal',
XXXMASS
flfrc='q2r.fc',
flfrq='XXXFNFREQ'
/
XXXNKS
XXXKS
"""
matdyn_in_fn = 'matdyn.disp.in'
matdyn_freq_fn = 'matdyn.freq.disp'
mass_str = '\n'.join("amass(%i)=%e" %(ii+1,m) for ii,m in \
enumerate(st.mass_unique))
rules = {
'XXXNKS': ks_path.shape[0],
'XXXKS': common.str_arr(ks_path),
'XXXMASS': mass_str,
'XXXFNFREQ': matdyn_freq_fn,
}
txt = common.template_replace(templ_txt, rules, conv=True, mode='txt')
common.file_write(matdyn_in_fn, txt)
common.system("gunzip q2r.fc.gz; matdyn.x < %s; gzip q2r.fc" % matdyn_in_fn)
# parse matdyn output and plot
# define special points path, used in plot_dis() to plot lines at special
# points and make x-labels
sp = kpath.SpecialPointsPath(ks=sp_points,
ks_frac=sp_points_frac,
symbols=sp_symbols)
# test/test_read_matdyn.py .
import numpy as np
from pwtools.common import str_arr
natoms = 2
qpoints = np.array([[0, 0, 0.0], [0, 0, 0.5]])
nqpoints = len(qpoints)
nmodes = 3 * natoms
freqs = np.empty((nqpoints, nmodes))
vecs = np.empty((nqpoints, nmodes, natoms, 3))
num = 0
for iqpoint in range(nqpoints):
print " diagonalizing the dynamical matrix ...\n"
print " q = %s" % str_arr(qpoints[iqpoint], fmt="%f")
print "*" * 79
for imode in range(nmodes):
freqs[iqpoint, imode] = num
print " omega(%i) = %f [THz] = %f [cm-1]" % (imode + 1, num * 0.1, num)
num += 1
for iatom in range(natoms):
vec_str = " ("
for icoord in range(3):
vecs[iqpoint, imode, iatom, icoord] = num
vec_str += " %f %f " % (num, 0.03 * num)
num += 1
vec_str += ")"
print vec_str
print "*" * 79
#!/usr/bin/python
# Create a PWscf MD "trajectory" where the CELL_PARAMETERS unit changes. This
# is for testing if the parser can handle that. The output file consists only
# of CELL_PARAMETERS blocks, which is enough for PwVCMDOutputFile.get_gell() .
#
# usage
# ------
# ./make-vc-md-cell.py > ../files/pw.vc-md.cell.out
import numpy as np
from pwtools import common
if __name__ == '__main__':
cell = np.arange(1, 10).reshape((3, 3))
alat_lst = [2.0, 4.0]
for ialat, alat in enumerate(alat_lst):
for ii in range(5):
cell_str = common.str_arr((cell + 0.02 * ii + ialat) / alat)
print("CELL_PARAMETERS (alat= %.5f)\n%s" % (alat, cell_str))
templ_txt = """
&input
asr='crystal',
XXXMASS
flfrc='q2r.fc',
flfrq='XXXFNFREQ'
/
XXXNKS
XXXKS
"""
matdyn_in_fn = 'matdyn.disp.in'
matdyn_freq_fn = 'matdyn.freq.disp'
mass_str = '\n'.join("amass(%i)=%e" %(ii+1,m) for ii,m in \
enumerate(st.mass_unique))
rules = {'XXXNKS': ks_path.shape[0],
'XXXKS': common.str_arr(ks_path),
'XXXMASS': mass_str,
'XXXFNFREQ': matdyn_freq_fn,
}
txt = common.template_replace(templ_txt,
rules,
conv=True,
mode='txt')
common.file_write(matdyn_in_fn, txt)
common.system("gunzip q2r.fc.gz; matdyn.x < %s; gzip q2r.fc" %matdyn_in_fn)
# parse matdyn output and plot
# define special points path, used in plot_dis() to plot lines at special
# points and make x-labels
sp = kpath.SpecialPointsPath(ks=sp_points, ks_frac=sp_points_frac,
/
CELL_PARAMETERS angstrom
{cp_ang}
CELL_PARAMETERS bohr
{cp_bohr}
ATOMIC_SPECIES
{atspec}
ATOMIC_POSITIONS crystal
{atpos_frac}
"""
rules = {'bar': bar,
'nat': struct.natoms,
'ntyp': struct.ntypat,
'cp_alat': str_arr(struct.cell / struct.cryst_const[0]),
'cp_bohr': str_arr(struct.cell),
'cp_ang': str_arr(struct.cell * Bohr / Angstrom),
'atspec': atspec,
'atpos_frac': atpos_frac,
}
for ii, cd in enumerate(celldm):
rules['cd%i' %(ii+1,)] = cd
print out.format(**rules)
#-------------------------------------------------------------------------------
# ABINIT
#-------------------------------------------------------------------------------
print "\n"
print bar
import numpy as np
from pwtools.common import str_arr
if __name__ == '__main__':
natoms = 2
qpoints = np.array([[0, 0, 0.], [0, 0, 0.5]])
nqpoints = len(qpoints)
nmodes = 3 * natoms
freqs = np.empty((nqpoints, nmodes))
vecs = np.empty((nqpoints, nmodes, natoms, 3))
num = 0
for iqpoint in range(nqpoints):
print(" diagonalizing the dynamical matrix ...\n")
print(" q = %s" % str_arr(qpoints[iqpoint], fmt='%f'))
print("*" * 79)
for imode in range(nmodes):
freqs[iqpoint, imode] = num
print(" omega(%i) = %f [THz] = %f [cm-1]" %
(imode + 1, num * 0.1, num))
num += 1
for iatom in range(natoms):
vec_str = " ("
for icoord in range(3):
vecs[iqpoint, imode, iatom, icoord] = num
vec_str += " %f %f " % (num, 0.03 * num)
num += 1
vec_str += ")"
print(vec_str)
print("*" * 79)
CELL_PARAMETERS angstrom
{cp_ang}
CELL_PARAMETERS bohr
{cp_bohr}
ATOMIC_SPECIES
{atspec}
ATOMIC_POSITIONS crystal
{atpos_frac}
"""
rules = {
'bar': bar,
'nat': struct.natoms,
'ntyp': struct.ntypat,
'cp_alat': str_arr(struct.cell / struct.cryst_const[0]),
'cp_bohr': str_arr(struct.cell),
'cp_ang': str_arr(struct.cell * Bohr / Angstrom),
'atspec': atspec,
'atpos_frac': atpos_frac,
}
for ii, cd in enumerate(celldm):
rules['cd%i' % (ii + 1, )] = cd
print(out.format(**rules))
#-------------------------------------------------------------------------------
# ABINIT
#-------------------------------------------------------------------------------
print("\n")
print(bar)
