def load(data, pbc=(True, True, True), atom_style='atomic', units='metal'):
"""
Read a LAMMPS-style atom data file and return a System.
Argument:
data = file name, file-like object or string to read data from.
Keyword Arguments:
pbc -- list or tuple of three boolean values indicating which System directions are periodic. Default is (True, True, True).
atom_style -- LAMMPS atom_style option associated with the data file. Default is 'atomic'.
units -- LAMMPS units option associated with the data file. Default is 'metal'.
When the file is read in, the units of all property values are automatically converted to atomman's set working units.
"""
units_dict = style.unit(units)
readtime = False
count = 0
xy = 0.0
xz = 0.0
yz = 0.0
system = None
with uber_open_rmode(data) as fp:
#loop over all lines in fp
for line in fp:
terms = line.split()
if len(terms)>0:
#read atomic information if time to do so
if readtime == True:
a_id = int(terms[0]) - 1
prop_vals[a_id] = terms[1:]
count += 1
#save values to system once all atoms read in
if count == natoms:
readtime = False
count = 0
start = 0
#iterate over all atom_style properties
for name, v in props.iteritems():
if name != 'a_id':
size, dim, dtype = v
value = np.asarray(prop_vals[:, start:start+size], dtype=dtype)
start += size
#set units according to LAMMPS units style
unit = units_dict.get(dim, None)
system.atoms_prop(key=name, value=uc.set_in_units(value, unit))
#read number of atoms
elif len(terms) == 2 and terms[1] == 'atoms':
natoms = int(terms[0])
#read number of atom types
elif len(terms) == 3 and terms[1] == 'atom' and terms[2] == 'types':
natypes = int(terms[0])
#read boundary info
elif len(terms) == 4 and terms[2] == 'xlo' and terms[3] == 'xhi':
xlo = uc.set_in_units(float(terms[0]), units_dict['length'])
xhi = uc.set_in_units(float(terms[1]), units_dict['length'])
elif len(terms) == 4 and terms[2] == 'ylo' and terms[3] == 'yhi':
ylo = uc.set_in_units(float(terms[0]), units_dict['length'])
yhi = uc.set_in_units(float(terms[1]), units_dict['length'])
elif len(terms) == 4 and terms[2] == 'zlo' and terms[3] == 'zhi':
zlo = uc.set_in_units(float(terms[0]), units_dict['length'])
zhi = uc.set_in_units(float(terms[1]), units_dict['length'])
elif len(terms) == 6 and terms[3] == 'xy' and terms[4] == 'xz' and terms[5] == 'yz':
xy = uc.set_in_units(float(terms[0]), units_dict['length'])
xz = uc.set_in_units(float(terms[1]), units_dict['length'])
yz = uc.set_in_units(float(terms[2]), units_dict['length'])
#Flag when reached data and setup for reading
elif len(terms) == 1 and terms[0] in ('Atoms', 'Velocities'):
#create system if not already
if system is None:
box = am.Box(xlo=xlo, xhi=xhi,
ylo=ylo, yhi=yhi,
zlo=zlo, zhi=zhi,
xy=xy, xz=xz, yz=yz)
system = am.System(box=box, atoms=am.Atoms(natoms=natoms), pbc = pbc)
if terms[0] == 'Atoms':
props = style.atom(atom_style)
else:
props = style.velocity(atom_style)
nvals = 0
for name, v in props.iteritems():
nvals += v[0]
prop_vals = np.empty((natoms, nvals-1), dtype=float)
readtime = True
assert system.natypes == natypes, 'Number of atom types does not match!'
return system
def dump(system, fname, units='metal', atom_style='atomic'):
"""
Write a LAMMPS-style atom data file from a System.
Argument:
system -- System to write to the atom data file.
fname -- name (and location) of file to save data to.
Keyword Arguments:
atom_style -- LAMMPS atom_style option associated with the data file. Default is 'atomic'.
units -- LAMMPS units option associated with the data file. Default is 'metal'.
When the file is written, the units of all property values are automatically converted from atomman's working units to the LAMMPS style units.
"""
#wrap atoms because LAMMPS hates atoms out of bounds in atom data files
system.wrap()
#get unit information according to the units style
units_dict = style.unit(units)
length = units_dict['length']
#open file
with open(fname,'w') as f:
#header info
f.write('\n%i atoms\n' % system.natoms)
f.write('%i atom types\n' % system.natypes)
#f.write('%f %f xlo xhi\n' % (uc.get_in_units(system.box.xlo, length), uc.get_in_units(system.box.xhi, length)))
#f.write('%f %f ylo yhi\n' % (uc.get_in_units(system.box.ylo, length), uc.get_in_units(system.box.yhi, length)))
#f.write('%f %f zlo zhi\n' % (uc.get_in_units(system.box.zlo, length), uc.get_in_units(system.box.zhi, length)))
f.write('%s %s xlo xhi\n' % (repr(uc.get_in_units(system.box.xlo, length)), repr(uc.get_in_units(system.box.xhi, length))))
f.write('%s %s ylo yhi\n' % (repr(uc.get_in_units(system.box.ylo, length)), repr(uc.get_in_units(system.box.yhi, length))))
f.write('%s %s zlo zhi\n' % (repr(uc.get_in_units(system.box.zlo, length)), repr(uc.get_in_units(system.box.zhi, length))))
#add tilts if tilt values not equal to zero
if system.box.xy == 0.0 and system.box.xz == 0.0 and system.box.yz == 0.0:
pass
else:
#f.write('%f %f %f xy xz yz\n' % (uc.get_in_units(system.box.xy, length), uc.get_in_units(system.box.xz, length), uc.get_in_units(system.box.yz, length)))
f.write('%s %s %s xy xz yz\n' % (repr(uc.get_in_units(system.box.xy, length)), repr(uc.get_in_units(system.box.xz, length)), repr(uc.get_in_units(system.box.yz, length))))
#Write atom info
f.write('\nAtoms\n\n')
props = style.atom(atom_style)
#Count how many terms are being printed
all_size = 0
for v in props.itervalues():
all_size += v[0]
outarray = np.empty((system.natoms, all_size))
start = 0
print_string = ''
#iterate over all properties and set values for printing
for name, v in props.iteritems():
size, dim, dtype = v
try:
unit = units_dict[dim]
except:
unit = None
if np.issubdtype(dtype, 'int64'):
for i in xrange(size):
print_string += ' %i'
else:
for i in xrange(size):
print_string += ' %.13e'
if name == 'a_id':
outarray[:, start:start+size] = np.arange(1, system.natoms+1).reshape((system.natoms, size))
else:
outarray[:, start:start+size] = uc.get_in_units(system.atoms_prop(key=name), unit).reshape((system.natoms, size))
start += size
print_string = print_string.strip() + '\n'
#iterate over all atoms
for i in xrange(system.natoms):
f.write(print_string % tuple(outarray[i]))
#Test for velocity info
v_test = system.atoms_prop(a_id=0, key='velocity')
if v_test is not None:
#Write velocity info
f.write('\nVelocities\n\n')
props = style.velocity(atom_style)
#Count how many terms are being printed
all_size = 0
for v in props.itervalues():
all_size += v[0]
outarray = np.empty((system.natoms, all_size))
start = 0
print_string = ''
#iterate over all properties and set values for printing
for name, v in props.iteritems():
size, dim, dtype = v
try:
unit = units_dict[dim]
except:
unit = None
if np.issubdtype(dtype, 'int64'):
for i in xrange(size):
print_string += ' %i'
else:
for i in xrange(size):
print_string += ' %.13e'
if name == 'a_id':
outarray[:, start:start+size] = np.arange(1, system.natoms+1).reshape((system.natoms, size))
else:
outarray[:, start:start+size] = uc.get_in_units(system.atoms_prop(key=name), unit).reshape((system.natoms, size))
start += size
print_string = print_string.strip() + '\n'
#iterate over all atoms
for i in xrange(system.natoms):
f.write(print_string % tuple(outarray[i]))
#return appropriate unts, atom_style, boundary, and read_data LAMMPS commands
boundary = ''
for i in xrange(3):
if system.pbc[i]:
boundary += 'p '
else:
boundary += 'm '
newline = '\n'
script = newline.join(['#Script and atom data file prepared by AtomMan package',
'',
'units ' + units,
'atom_style ' + atom_style,
''
'boundary ' + boundary,
'read_data ' + fname])
return script