def parse_poscar(file):
''' Parse Vasp's POSCAR file and return a Crys object '''
c = Crys()
junk_title = file.readline()
scaling_factor = float(file.readline().split([0]))
for i in range(3):
data = file.readline().split()
for j in range(3):
c.matrix[i][j] = float(data[j]) * scaling_factor
poscar_atomtypes = file.readline().split()
poscar_atomnumbers = file.readline().split()
for i in range(len(poscar_atomtypes)):
for j in range(int(poscar_atomnumbers[i])):
c.atom_type.append(poscar_atomtypes[i])
c.natom = len(c.atom_type)
coord_type = file.readline().split()[0]
if coord_type.lower() == 'direct':
for i in range(c.natom):
data = file.readline().split()
c.atom_fract.append(
[float(data[0]),
float(data[1]),
float(data[2])])
elif coord_type.lower() == 'cartesian':
for i in range(c.natom):
data = file.readline().split()
c.atom_xyz.append([float(data[0]), float(data[1]), float(data[2])])
return c
def parse_pdb(file):
''' Parse .pdb file and return Crys object '''
c = Crys()
while True:
line = file.readline()
data = line.split()
if line == "":
break
elif len(data) > 0 and (data[0] == 'END' or data[0] == 'ENDMDL'):
break
elif len(data) > 0 and data[0] == 'CRYST1':
c.length = [
float(line[0o6:15]),
float(line[15:24]),
float(line[24:33])
]
c.angle_deg = [
float(line[33:40]),
float(line[40:47]),
float(line[47:54])
]
elif len(data) > 0 and (data[0] == "ATOM" or data[0] == "HETATM"):
c.atom_type.append(data[2]) #maybe read to data[-1]
c.atom_xyz.append(
[float(line[30:38]),
float(line[38:46]),
float(line[46:54])])
return c
def parse_xyz_tm3(file):
''' Parse .xyz file (tailor made #3) and return Crys object '''
c = Crys()
junk = file.readline() #the first line has the filename
data = file.readline().split()
c.length = [float(data[1]), float(data[2]), float(data[3])]
ac.angle_deg = [float(data[4]), float(data[5]), float(data[6])]
c.natom = int(file.readline().split()[0])
for i in range(c.natom):
data = file.readline().split()
c.atom_type.append(data[0])
c.atom_fract.append([float(data[1]), float(data[2]), float(data[3])])
if len(data) > 4: # if not, the Qeq method crashed: no charge
charge.append(float(data[5]))
return c
def parse_cssr(file):
''' Parse .cssr file and return a Crys object '''
# File format description: http://www.chem.cmu.edu/courses/09-560/docs/msi/modenv/D_Files.html#944777
c = Crys()
data = file.readline().split()
c.length = [float(data[0]), float(data[1]), float(data[2])]
data = file.readline().split()
c.angle_deg = [float(data[0]), float(data[1]), float(data[2])]
c.natom = int(file.readline().split()[0])
junk = file.readline()
for i in range(c.natom):
data = file.readline().split()
c.atom_type.append(data[1])
c.atom_fract.append([float(data[2]), float(data[3]), float(data[4])])
if len(data) == 14:
c.atom_charge.append(float(data[13]))
return c
def parse_car(file):
''' Parse .car file and return Crys object.
TESTED just for Chongli Zhong's hCOF database.'''
c = Crys()
read_coord = False
while True:
line = file.readline()
data = line.split()
if line == "":
break
elif len(data) > 0 and data[0] == 'end':
break
elif len(data) > 0 and data[0] == 'PBC':
c.length = [float(data[1]), float(data[2]), float(data[3])]
c.angle_deg = [float(data[4]), float(data[5]), float(data[6])]
read_coord = True
elif read_coord:
c.atom_type.append(data[0])
c.atom_xyz.append([float(data[1]), float(data[2]), float(data[3])])
return c
def parse_cube(file):
''' Parse .cube file and return a Crys object '''
c = Crys()
junk = file.readline() #header1
junk = file.readline() #header2
data = file.readline().split()
c.natom = int(data[0])
for i in range(3):
data = file.readline().split()
for j in range(3):
c.matrix[i][j] = float(data[0]) * float(data[j]) / ANGS2BOHR
for i in range(c.natom):
data = file.readline().split()
# convert from atomic number to element
c.atom_type.append(ptab_atnum_inv[int(data[0])])
c.atom_xyz.append([
float(data[2]) / ANGS2BOHR,
float(data[3]) / ANGS2BOHR,
float(data[4]) / ANGS2BOHR
])
return c
def parse_axsf(file):
''' Parse .axsf and .xsf files and return a Crys object '''
c = Crys()
while True:
if file.readline().split()[0] == 'PRIMVEC':
break
for i in range(3):
data = file.readline().split()
for j in range(3):
c.matrix[i][j] = float(data[j])
while True:
if file.readline().split()[0] == 'PRIMCOORD':
break
c.natom = int(file.readline().split()[0])
for i in range(c.natom):
data = file.readline().split()
# In this format the atom type can be given as element or atomic number
if is_number(data[0]):
# convert from atomic number to element
c.atom_type.append(ptab_atnum_inv[data[0]])
else:
c.atom_type.append(data[0])
c.atom_xyz.append([float(data[1]), float(data[2]), float(data[3])])
return c
def parse_xyz(file):
''' Parse .xyz file and return Crys object '''
c = Crys()
c.natom = int(file.readline().split()[0])
data = file.readline().split()
if len(data) >= 7 and data[0] == 'CELL:':
c.length = [float(data[1]), float(data[2]), float(data[3])]
c.angle_deg = [float(data[4]), float(data[5]), float(data[6])]
elif len(data) >= 10 and data[0] == 'cell:':
c.matrix[0] = [float(data[1]), float(data[2]), float(data[3])]
c.matrix[1] = [float(data[4]), float(data[5]), float(data[6])]
c.matrix[2] = [float(data[7]), float(data[8]), float(data[9])]
elif len(data) >= 23 and data[0] == 'jmolscript:': #Chargemol
c.matrix[0] = [float(data[10]), float(data[11]), float(data[12])]
c.matrix[1] = [float(data[15]), float(data[16]), float(data[17])]
c.matrix[2] = [float(data[20]), float(data[21]), float(data[22])]
elif len(data) >= 9 and data[0].split("\"")[0] == "Lattice=": #ASE
c.matrix[0] = [
float(data[0].split("\"")[1]),
float(data[1]),
float(data[2])
]
c.matrix[1] = [float(data[3]), float(data[4]), float(data[5])]
c.matrix[2] = [
float(data[6]),
float(data[7]),
float(data[8].split('\"')[0])
]
else:
sys.exit('WARNING: xyz file with no cell provided! EXIT.')
for i in range(c.natom):
data = file.readline().split()
c.atom_type.append(data[0])
c.atom_xyz.append([float(data[1]), float(data[2]), float(data[3])])
if len(data) == 5: # if there is an extra column read it as charge
c.atom_charge.append(float(data[4]))
return c
def parse_pwo(file):
''' Parse Quantum Espresso's .pwo and .pwi files and return Crys object '''
c = Crys()
# Parse cell:
# search for the last time the cell/coord are printed and jump to that
# line (no need to be converged). ONLY if they are not found, it reads the
# initial input cell
with file as myFile:
for num, line in enumerate(myFile, 1):
if 'CELL_PARAMETERS' in line:
cell_line = num
file.seek(0)
if 'cell_line' in locals(): #read cell in vc-relax calculation
for i in range(0, cell_line):
skip = file.readline() #title line
for i in range(3):
data = file.readline().split()
for j in range(3):
c.matrix[i][j] = float(data[j])
else: #read cell in scf or relax calculation
while True:
data = file.readline().split()
if len(data) > 0 and (data[0] == "celldm(1)="):
celldm1 = float(data[1]) / ANGS2BOHR
skip = file.readline().split()
skip = file.readline().split()
skip = file.readline().split()
for i in range(3):
data = file.readline().split()
for j in range(3):
c.matrix[i][j] = float(data[3 + j]) * celldm1
break
file.seek(0)
# Parse atomic coordinates
with file as myFile:
for num, line in enumerate(myFile, 1):
if 'ATOMIC_POSITIONS' in line:
atomicpositions_line = num
if line.split()[1] == 'angstrom' \
or line.split()[1] == '(angstrom)':
readfractional = False
elif line.split()[1] == 'crystal' \
or line.split()[1] == '(crystal)':
readfractional = True
file.seek(0)
if 'atomicpositions_line' in locals(): #read atomic in vc-relax and relax.
for i in range(0, atomicpositions_line):
skip = file.readline()
i = 0
while True:
data = file.readline().split()
if len(data) < 4: #if the coordinates are finished, break
break
else:
c.atom_type.append(data[0])
if readfractional:
c.atom_fract.append(
[float(data[1]),
float(data[2]),
float(data[3])])
else:
c.atom_xyz.append(
[float(data[1]),
float(data[2]),
float(data[3])])
else: #read atomic in scf calculation
while True:
data = file.readline().split()
if len(data) > 0 and (data[0] == "celldm(1)="):
celldm1 = float(data[1]) / ANGS2BOHR
if len(data) > 3 and (data[3] == "positions"):
while True:
data = file.readline().split()
if len(data) < 10: #if the file is finished stop
break
else:
c.atom_type.append(data[1])
c.atom_xyz.append(
[float(data[6]),
float(data[7]),
float(data[8])])
break
return c
def parse_cp2k(file):
''' Parse any CP2K input file and return a Crys object.
Constraints:
- &CELL should be before &COORD
- can read both A B C (cell) and ABC ALPHA_BETA_GAMMA (CELL)
- it complains and exit if units are not [angstrom] and [deg]
- if SCALED coord, the flag should be before the fract coordinates
'''
c = Crys()
while True:
data = file.readline().split()
# Read cell: A B C
cell_dict = {"A": 0, "B": 1, "C": 2}
if len(data) > 0 and data[0] in cell_dict:
if data[1][0] != "[": # No unit specified. Default: Angstrom.
shift = 0
elif data[1].lower() == "[angstrom]":
shift = 1
else:
sys.exit("WARNING: in parsing CP2K, weird units. EXIT")
for i in range(3):
c.matrix[cell_dict[data[0]]][i] = float(data[1 + i + shift])
# Read CELL: ABC
if len(data) > 3 and data[0] == 'ABC':
if data[1][0] != "[": # No unit specified. Default: Angstrom.
shift = 0
elif data[1].lower() == "[angstrom]":
shift = 1
else:
sys.exit("WARNING: in parsing CP2K, weird units. EXIT")
c.length[0] = float(data[1 + shift])
c.length[1] = float(data[2 + shift])
c.length[2] = float(data[3 + shift])
# Read CELL: ALPHA_BETA_GAMMA
if len(data) > 3 and data[0] == 'ALPHA_BETA_GAMMA':
if data[1][0] != "[": # No unit specified. Default: deg.
shift = 0
elif data[1].lower() == "[deg]":
shift = 1
else:
sys.exit("WARNING: in parsing CP2K, weird units. EXIT")
c.angle_deg[0] = float(data[1 + shift])
c.angle_deg[1] = float(data[2 + shift])
c.angle_deg[2] = float(data[3 + shift])
if len(data) > 0 and (data[0] == "&COORD"):
break
scaled_coord = False #Default
while True:
data = file.readline().split()
if data[0] == "SCALED" \
and (len(data)==1 or data[1].lower() in ["t", "true", ".true."]):
scaled_coord = True
elif data[0] == "SCALED" \
and data[1].lower() in ["f", "false", ".false."]:
scaled_coord = False
elif data[0] == "&END": # End of &COORD section
break
elif len(data) > 0:
c.atom_type.append(data[0])
if scaled_coord:
c.atom_fract.append(
[float(data[1]),
float(data[2]),
float(data[3])])
else:
c.atom_xyz.append(
[float(data[1]),
float(data[2]),
float(data[3])])
return c
def parse_cif(file):
''' Parse .cif file and return a Crys object.
Constraints:
- only valid for P1 symmetry
- cell data can be specified before/after the atom coordinates
- it stops reading coordinates when it find a line with less than 4 columns (so no interruptions must exist)
'''
c = Crys()
reading_coord = False
while True:
line = file.readline()
data = line.split()
if line == "": #EOF
break
if len(data) > 0 \
and len(data[0].split("_")) > 1 \
and 'cell' in data[0].split("_"):
reading_coord = False
if data[0] == "_cell_length_a":
c.length[0] = parsefloat(data[1])
elif data[0] == "_cell_length_b":
c.length[1] = parsefloat(data[1])
elif data[0] == "_cell_length_c":
c.length[2] = parsefloat(data[1])
elif data[0] == "_cell_angle_alpha":
c.angle_deg[0] = parsefloat(data[1])
elif data[0] == "_cell_angle_beta":
c.angle_deg[1] = parsefloat(data[1])
elif data[0] == "_cell_angle_gamma":
c.angle_deg[2] = parsefloat(data[1])
# if the "_atom_site_***" section starts, remember the order
if len(data) > 0 \
and len(data[0].split("_")) > 1 \
and data[0].split("_")[1] == "atom":
data_order_dic = {}
order = 0
while len(data[0].split("_")) > 1 \
and data[0].split("_")[1] == "atom":
data_order_dic[data[0]] = order
line = file.readline()
data = line.split()
order += 1
reading_coord = True #entering in 'reading_coordinate MODE'
# if less than 'Atom x y z' acan not be a coordinate!
if len(data) < 4:
reading_coord = False
if reading_coord:
# looks for "type_symbol" before and, if missing for "label"
if "_atom_site_type_symbol" in data_order_dic:
c.atom_type.append(
data[data_order_dic["_atom_site_type_symbol"]])
elif "_atom_site_label" in data_order_dic:
c.atom_type.append(data[data_order_dic["_atom_site_label"]])
else:
sys.exit("EXIT: in cif missing type_symbol and label")
if "_atom_site_fract_x" in data_order_dic:
c.atom_fract.append([
float(data[data_order_dic["_atom_site_fract_x"]]),
float(data[data_order_dic["_atom_site_fract_y"]]),
float(data[data_order_dic["_atom_site_fract_z"]]),
])
elif "_atom_site_Cartn_x" in data_order_dic:
c.atom_xyz.append([
float(data[data_order_dic["_atom_site_Cartn_x"]]),
float(data[data_order_dic["_atom_site_Cartn_y"]]),
float(data[data_order_dic["_atom_site_Cartn_z"]]),
])
else:
sys.exit("EXIT: in cif missing fract_ and Cartn_ coordinates")
if "_atom_site_charge" in data_order_dic:
c.atom_charge.append(
float(data[data_order_dic["_atom_site_charge"]]))
return c