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 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 compute_static_sf(file_lst, R_ranges, Q_ranges, num_bins_q):
corrected = True
num_bins_q = int_to_ctypes_int(num_bins_q)
ssf_or_pair = "structure_factor"
r_or_Q, pair_correl_or_ssf = compute_pair_correl_from_hist_file(
file_lst, ssf_or_pair, corrected, R_ranges, Q_ranges)
return r_or_Q[0], pair_correl_or_ssf[0]
def compute_q_tetra(total_atoms, xyz, box):
sorted_q_indx = np.ctypeslib.as_ctypes(
np.zeros(total_atoms, dtype=np.int32))
q_tetra = np.ctypeslib.as_ctypes(np.zeros(total_atoms, dtype=np.float64))
total_atoms = int_to_ctypes_int(total_atoms)
maxnb = c_int(35)
nnb = c_int(4)
cutoff_sqr = c_double(5.8 * 5.8)
bt_lib.call_label_high_q_low_q(byref(total_atoms),
byref(maxnb), byref(nnb), xyz, box,
byref(cutoff_sqr), sorted_q_indx, q_tetra)
return np.ctypeslib.as_array(sorted_q_indx), q_tetra
def compute_Bhatia_Thornton_ssf(file_lst, R_ranges, Q_ranges, num_bins_q,
x_H_frac, x_L_frac):
corrected = True
ssf_or_pair = "structure_factor"
x_H_frac = c_double(x_H_frac)
x_L_frac = c_double(x_L_frac)
SNN = np.ctypeslib.as_ctypes(np.zeros(num_bins_q, dtype=np.float64))
SCC = np.ctypeslib.as_ctypes(np.zeros(num_bins_q, dtype=np.float64))
SNC = np.ctypeslib.as_ctypes(np.zeros(num_bins_q, dtype=np.float64))
theta = np.ctypeslib.as_ctypes(np.zeros(num_bins_q, dtype=np.float64))
SA = np.ctypeslib.as_ctypes(np.zeros(num_bins_q, dtype=np.float64))
num_bins_q = int_to_ctypes_int(num_bins_q)
S0_fs_lst, r_or_Q, pair_correl_or_ssf = compute_pair_correl_from_hist_file(
file_lst, ssf_or_pair, corrected, R_ranges, Q_ranges, num_bins_q)
SHH, SLL, SHL = pair_correl_or_ssf
SHH = np.ctypeslib.as_ctypes(SHH)
SLL = np.ctypeslib.as_ctypes(SLL)
SHL = np.ctypeslib.as_ctypes(SHL)
ssf_lib.call_Bhatia_Thornton(byref(num_bins_q), byref(x_H_frac),
byref(x_L_frac), SHH, SLL, SHL, SNN, SCC, SNC,
theta, SA)
return (np.ctypeslib.as_array(r_or_Q[0]), np.ctypeslib.as_array(SNN),
np.ctypeslib.as_array(SCC), np.ctypeslib.as_array(SNC),
np.ctypeslib.as_array(theta), np.ctypeslib.as_array(SA))
def compute_pair_correl_ssf(keyword, corrected, partial, same_species, N1N2,
x_spec_1_2, N, R_ranges, Q_ranges, num_bins_q,
num_bins_gr, rho, r_mid, gr):
corrected = c_bool(corrected)
partial = c_bool(partial)
same_species = c_bool(same_species)
N1N2 = double_to_ctypes_double(N1N2)
x_spec_1_2 = double_to_ctypes_double(x_spec_1_2)
N = double_to_ctypes_double(N)
R_size = int_to_ctypes_int(R_ranges.size)
R_ranges = np_to_ctypes_array(R_ranges.astype(np.float64))
Q_ranges = np_to_ctypes_array(Q_ranges.astype(np.float64))
num_bins_q = int_to_ctypes_int(num_bins_q)
num_bins_gr = int_to_ctypes_int(num_bins_gr)
rho = double_to_ctypes_double(rho)
r_mid = np_to_ctypes_array(r_mid)
gr = np_to_ctypes_array(gr)
if (keyword == "pair_correl"):
r2hr = np.ctypeslib.as_ctypes(
np.zeros(num_bins_gr.value, dtype=np.float64))
ssf_lib.call_hr_fs_correct(byref(corrected), byref(partial),
byref(same_species), byref(N1N2),
byref(x_spec_1_2), byref(N),
byref(R_size), R_ranges, Q_ranges,
byref(num_bins_q), byref(num_bins_gr),
byref(rho), r_mid, gr, r2hr)
return np.ctypeslib.as_array(r_mid), np.ctypeslib.as_array(r2hr)
elif (keyword == "structure_factor"):
SQ = np.ctypeslib.as_ctypes(
np.zeros(num_bins_q.value, dtype=np.float64))
Q_mid = np.ctypeslib.as_ctypes(
np.zeros(num_bins_q.value, dtype=np.float64))
S0_fs = c_double()
ssf_lib.call_ssf_fs_correct(byref(corrected), byref(partial),
byref(same_species), byref(x_spec_1_2),
byref(N), byref(R_size), R_ranges,
Q_ranges, byref(num_bins_q),
byref(num_bins_gr), byref(rho), r_mid, gr,
byref(S0_fs), Q_mid, SQ)
return S0_fs.value, np.ctypeslib.as_array(
Q_mid), np.ctypeslib.as_array(SQ)
