def read_cp2k_qm_kind(fh):
"""
Read a file in cp2k_input.qmmm_qm_kind
This is the format produced by the QUIP cp2k_driver.
Returns a list of tuples (qm_kind, atom_indices).
"""
filename, lines = read_text_file(fh)
qm_kinds = []
current_qm_kind = None
current_indices = []
for line in lines:
line = line.strip()
if line.startswith('&QM_KIND'):
current_qm_kind = line.split()[1]
current_indices = []
elif line.startswith('&END QM_KIND'):
qm_kinds.append((current_qm_kind, current_indices))
elif line.startswith('MM_INDEX'):
index = int(line.split()[1])
current_indices.append(index)
else:
raise ValueError('Unexpected line %r' % line)
return qm_kinds
def read(self, filename):
filename, lines = read_text_file(filename)
for line in lines:
dummy, key, value = line.split()
self[key] = value
def CP2KDirectoryReader(run_dir,
at_ref=None,
proj='quip',
calc_qm_charges=None,
calc_virial=False,
out_i=None,
qm_vacuum=6.0,
run_suffix='_extended',
format=None):
if at_ref is None:
filepot_xyz = os.path.join(run_dir, 'filepot.xyz')
if not os.path.exists(filepot_xyz):
# try looking up one level
filepot_xyz = os.path.join(run_dir, '../filepot.xyz')
if os.path.exists(filepot_xyz):
at_ref = Atoms(filepot_xyz)
else:
at_ref = Atoms(os.path.join(run_dir, 'cp2k_output.out'),
format='cp2k_output')
at = at_ref.copy()
cp2k_output_filename, cp2k_output = read_text_file(
os.path.join(run_dir, 'cp2k_output.out'))
cp2k_params = CP2KInputHeader(
os.path.join(run_dir, 'cp2k_input.inp.header'))
at.params.update(cp2k_params)
run_type = cp2k_run_type(cp2k_output=cp2k_output,
cp2k_input_header=cp2k_params)
try:
cluster_mark = getattr(at, 'cluster_mark' + run_suffix)
qm_list_a = ((cluster_mark != HYBRID_NO_MARK).nonzero()[0]).astype(
np.int32)
except AttributeError:
qm_list_a = fzeros(0, dtype=np.int32)
if calc_qm_charges is None:
calc_qm_charges = ''
try:
cur_qmmm_qm_abc = [
float(cp2k_params['QMMM_ABC_X']),
float(cp2k_params['QMMM_ABC_Y']),
float(cp2k_params['QMMM_ABC_Z'])
]
except KeyError:
if 'QM_cell' + run_suffix in at.params:
cur_qmmm_qm_abc = at.params['QM_cell' + run_suffix]
else:
cur_qmmm_qm_abc = qmmm_qm_abc(at, qm_list_a, qm_vacuum)
quip_cp2k_at = Atoms(os.path.join(run_dir, 'quip_cp2k.xyz'))
rev_sort_index_file = os.path.join(run_dir, '../quip_rev_sort_index')
fields = [int(x) for x in open(rev_sort_index_file).read().split()]
rev_sort_index = farray(fields, dtype=np.int32)
#verbosity_push(PRINT_SILENT)
cp2k_energy, cp2k_force = read_output(quip_cp2k_at, qm_list_a,
cur_qmmm_qm_abc, run_dir, proj,
calc_qm_charges, calc_virial, True,
3, at.n, out_i)
#verbosity_pop()
qm_list = None
if os.path.exists(os.path.join(run_dir, 'cp2k_input.qmmm_qm_kind')):
qm_kind_grep_cmd = "grep MM_INDEX %s/cp2k_input.qmmm_qm_kind | awk '{print $2}'" % run_dir
qm_list = [int(i) for i in os.popen(qm_kind_grep_cmd).read().split()]
if qm_list is not None:
if run_type == 'QMMM':
reordering_index = getattr(at, 'reordering_index', None)
at.add_property('qm', False, overwrite=True)
if reordering_index is not None:
qm_list = reordering_index[qm_list]
at.qm[qm_list] = True
elif run_type == 'QS':
at.add_property('qm_orig_index', 0, overwrite=True)
for i, qm_at in fenumerate(qm_list):
at.qm_orig_index[i] = sort_index[qm_at]
at.add_property('force', cp2k_force, overwrite=True)
at.params['energy'] = cp2k_energy
yield at
def CP2KOutputReader(fh,
module=None,
type_map=None,
kind_map=None,
format=None):
# mapping from run type to (default module index, list of available module)
run_types = {
'QS': ['QUICKSTEP'],
'QMMM': ['FIST', 'QM/MM', 'QUICKSTEP'],
'MM': ['FIST']
}
filename, lines = read_text_file(fh)
run_type = cp2k_run_type(cp2k_output=lines)
if type_map is None:
type_map = {}
if kind_map is None:
kind_map = {}
try:
available_modules = run_types[run_type]
except KeyError:
raise ValueError('Unknown CP2K run type %s' % run_type)
if module is None:
module = available_modules[0]
try:
cell_index = available_modules.index(module)
except ValueError:
raise ValueError("Don't know how to read module %s from file %s" %
(module, filename))
cell_lines = [
i for i, line in enumerate(lines) if line.startswith(" CELL| Vector a")
]
if cell_lines == []:
raise ValueError("Cannot find cell in file %s" % filename)
try:
cell_line = cell_lines[cell_index]
except IndexError:
raise ValueError(
"Cannot find cell with index %d in file %s for module %s" %
(cell_index, filename, module))
lattice = fzeros((3, 3))
for i in [0, 1, 2]:
lattice[:,
i + 1] = [float(c) for c in lines[cell_line + i].split()[4:7]]
try:
start_line = lines.index(
" MODULE %s: ATOMIC COORDINATES IN angstrom\n" % module)
except ValueError:
raise ValueError(
"Cannot find atomic positions for module %s in file %s" %
(module, filename))
kinds = []
species = []
Zs = []
pos = []
masses = []
Zeffs = []
types = []
qeffs = []
for line in lines[start_line + 4:]:
if line.strip() == '':
break
if module == 'FIST':
atom, kind, typ, x, y, z, qeff, mass = line.split()
types.append(typ)
Z = type_map.get(typ, 0)
kind = int(kind)
if Z == 0:
Z = kind_map.get(kind, 0)
Zs.append(Z)
qeffs.append(float(qeff))
else:
atom, kind, sp, Z, x, y, z, Zeff, mass = line.split()
species.append(sp)
Zs.append(int(Z))
Zeffs.append(float(Zeff))
kinds.append(int(kind))
pos.append([float(x), float(y), float(z)])
masses.append(float(mass))
at = Atoms(n=len(kinds), lattice=lattice)
at.pos[...] = farray(pos).T
at.set_atoms(Zs)
at.add_property('mass', farray(masses) * MASSCONVERT)
at.add_property('kind', kinds)
if module == 'FIST':
at.add_property('type', ' ' * TABLE_STRING_LENGTH)
at.add_property('qm', False)
at.qm[:] = (at.type.stripstrings()
== '_QM_') | (at.type.stripstrings() == '_LNK')
at.type[...] = s2a(types, TABLE_STRING_LENGTH)
at.add_property('qeff', qeffs)
else:
at.species[...] = s2a(species, TABLE_STRING_LENGTH)
at.add_property('zeff', Zeffs)
yield at