def call_read_xyz_box(dcdfile,current_frame,total_atoms,return_numpy):
# declare variables:
dcdfile,strlength = string_to_ctypes_string(dcdfile)
current_frame = int_to_ctypes_int(current_frame)
total_atoms = int_to_ctypes_int(total_atoms)
#box = (c_double*3)()
box = np.ctypeslib.as_ctypes(np.zeros(3,dtype=np.float64))
#xyz = ((c_float*total_atoms.value)*3)()
xyz = np.ctypeslib.as_ctypes(np.zeros(total_atoms.value*3,dtype=np.float32))
#current_frame = c_int(current_frame)
dcd_lib.call_dcd_traj(dcdfile,byref(strlength),byref(total_atoms),byref(current_frame),box,xyz)
if ( return_numpy ):
xyz = np.ctypeslib.as_array(xyz).reshape((total_atoms.value,3))
box = np.ctypeslib.as_array(box)
return xyz,box
else:
return xyz,box
def loadtxt(txtfile, num_lines, num_cols, skiprows, return_numpy):
txtfile, strlength = string_to_ctypes_string(txtfile)
num_selected = num_lines - skiprows
loaded_data = np.ctypeslib.as_ctypes(
np.zeros(num_selected * num_cols, dtype=np.float64))
num_lines = int_to_ctypes_int(num_lines)
num_cols = int_to_ctypes_int(num_cols)
skiprows = int_to_ctypes_int(skiprows)
txt_lib.load_txt(txtfile, byref(strlength), byref(num_lines),
byref(num_cols), byref(skiprows), loaded_data)
if (return_numpy):
return np.ctypeslib.as_array(loaded_data).reshape(
(num_cols.value, num_lines.value - skiprows.value)).T
else:
return loaded_data
def call_read_xyz_xyz_box(xyzfile,
current_frame,
total_atoms,
read_box=True,
return_numpy=True):
# declare variables:
xyzfile, strlength = string_to_ctypes_string(xyzfile)
total_atoms = int_to_ctypes_int(total_atoms)
current_frame = int_to_ctypes_int(current_frame)
# xyz = ((c_float*total_atoms.value)*3)()
xyz = np.ctypeslib.as_ctypes(
np.zeros(total_atoms.value * 3, dtype=np.float64))
# current_frame = c_int(current_frame)
# if the box is read from the xyz
if (read_box):
box = np.ctypeslib.as_ctypes(np.zeros(3, dtype=np.float64))
xyz_lib.call_read_xyz_with_box(xyzfile, byref(strlength),
byref(current_frame),
byref(total_atoms), box, xyz)
# if the xyz, box has to be returned as numpy data type
if (return_numpy):
xyz = np.ctypeslib.as_array(xyz).reshape((total_atoms.value, 3))
box = np.ctypeslib.as_array(box)
# return numpy array format of xyz,box
return xyz, box
else:
# return ctypes format of xyz,box
return xyz, box
# if the box is not read from the xyz
else:
xyz_lib.call_read_xyz_no_box(xyzfile, byref(strlength),
byref(current_frame), byref(total_atoms),
xyz)
# if the xyz has to be returned as numpy data type
if (return_numpy):
return np.ctypeslib.as_array(xyz).reshape((total_atoms.value, 3))
else:
return xyz
def get_lines_columns(txtfile):
txtfile,strlength = string_to_ctypes_string(txtfile)
num_lines = c_int()
num_columns = c_int()
txt_lib.get_txt_lines_columns(txtfile,byref(strlength),byref(num_lines),byref(num_columns))
return num_lines.value, num_columns.value
def call_read_dcd_header(dcdfile):
# declare c types varibles:
dcdfile,strlength = string_to_ctypes_string(dcdfile)
total_atoms = c_int()
total_frames = c_int()
dcd_lib.call_dcd_header(dcdfile,byref(strlength),byref(total_atoms),byref(total_frames))
return total_frames.value, total_atoms.value
def calc_ql_cluster(style,
total_atoms,
box,
xyz,
maxnb,
nnb,
l,
ql_cutoff,
cluster_cutoff,
n_bonds):
style_key, strlength = string_to_ctypes_string(style)
total_atoms = c_int(total_atoms)
maxnb = c_int(maxnb)
nnb = c_int(nnb)
l = c_int(l)
ql_cutoff_sqr = c_double(ql_cutoff * ql_cutoff)
cluster_cutoff = c_double(cluster_cutoff)
n_bonds = c_int(n_bonds)
nxtl = c_int()
lcl = c_int()
HMC_lib.call_calc_ql_cluster(style_key,
byref(strlength),
byref(total_atoms),
box,
xyz,
byref(maxnb),
byref(nnb),
byref(l),
byref(ql_cutoff_sqr),
byref(cluster_cutoff),
byref(n_bonds),
byref(nxtl),
byref(lcl))
return nxtl.value, lcl.value
def call_read_xyz_header(xyzfile):
if (not IO.check_file.status_is_ok(xyzfile)):
sys.exit("Errors in reading file: %s; The file "
"does not exist or is empty " % xyzfile)
xyzfile, strlength = string_to_ctypes_string(xyzfile)
total_atoms = c_int()
total_frames = c_int()
xyz_lib.call_read_xyz_header(xyzfile, byref(strlength), byref(total_atoms),
byref(total_frames))
return total_atoms.value, total_frames.value
def get_lines_columns(txtfile):
if (not IO.check_file.status_is_ok(txtfile)):
sys.exit("Errors in reading file: %s; The file "
"does not exist or is empty " % txtfile)
txtfile, strlength = string_to_ctypes_string(txtfile)
num_lines = c_int()
num_columns = c_int()
txt_lib.get_txt_lines_columns(txtfile, byref(strlength), byref(num_lines),
byref(num_columns))
return num_lines.value, num_columns.value
def call_read_dcd_header(dcdfile):
if (not IO.check_file.status_is_ok(dcdfile)):
sys.exit("Errors in reading file: %s; The file "
"does not exist or is empty " % dcdfile)
# declare c types varibles:
dcdfile, strlength = string_to_ctypes_string(dcdfile)
total_atoms = c_int()
total_frames = c_int()
dcd_lib.call_dcd_header(dcdfile, byref(strlength), byref(total_atoms),
byref(total_frames))
return total_atoms.value, total_frames.value
def call_read_dcd_xyz_box_in_chunk(dcdfile, start_at, num_configs, total_atoms,
return_numpy):
# declare variables:
dcdfile, strlength = string_to_ctypes_string(dcdfile)
num_configs = int_to_ctypes_int(num_configs)
start_at = int_to_ctypes_int(start_at)
total_atoms = int_to_ctypes_int(total_atoms)
# box = ((c_double*3)*num_configs)()
box = np.ctypeslib.as_ctypes(
np.zeros(3 * num_configs.value, dtype=np.float64))
# xyz = (((c_float*total_atoms.value)*3)*num_configs.value)()
xyz = np.ctypeslib.as_ctypes(
np.zeros(3 * num_configs.value * total_atoms.value, dtype=np.float32))
dcd_lib.call_dcd_traj_chunk(dcdfile, byref(strlength), byref(start_at),
byref(num_configs), byref(total_atoms), box,
xyz)
if (return_numpy):
xyz = np.ctypeslib.as_array(xyz).reshape(
(num_configs.value, total_atoms.value, 3))
box = np.ctypeslib.as_array(box).reshape((num_configs.value, 3))
return xyz, box
else:
# convert to double precision
xyz = np.ctypeslib.as_ctypes(
np.ctypeslib.as_array(xyz).astype(np.float64))
return xyz, box
def call_CHILL(keyword, sph_const, Plm_const, total_atoms, l, xyz, box, maxnb, nnb, cutoff_sqr):
CHILL_keyword, strlength = string_to_ctypes_string(keyword)
cij = np.ctypeslib.as_ctypes(np.zeros(nnb*total_atoms, dtype=np.float64))
cij_hist = np.ctypeslib.as_ctypes(np.zeros(20, dtype=np.float64))
chill_ID_list = np.ctypeslib.as_ctypes(np.zeros(total_atoms, dtype=np.int32))
cutoff_sqr = c_double(cutoff_sqr)
l = c_int(l)
total_atoms = c_int(total_atoms)
maxnb = c_int(maxnb)
nnb = c_int(nnb)
num_ice = c_int()
CHILL_lib.call_CHILL(sph_const,
Plm_const,
CHILL_keyword,
byref(strlength),
byref(total_atoms),
byref(maxnb),
byref(nnb),
byref(l),
byref(cutoff_sqr),
box,
xyz,
cij,
cij_hist,
chill_ID_list,
byref(num_ice))
return np.ctypeslib.as_array(cij_hist), np.ctypeslib.as_array(chill_ID_list)
