def toReaxLammps(system, outfile="lammps.data"):
""" output to lammps data file
"""
o = open(outfile, "w")
o.write("# \n")
o.write("\n")
o.write("%d atoms\n\n" % len(system.atoms))
o.write("%d atom types\n\n" % len(system.map))
pbc = system.pbc
if len(pbc) >= 6:
if pbc[3] == 90.0 and pbc[4] == 90 and pbc[5] == 90:
o.write(" 0.0 %12.7f xlo xhi\n" % pbc[0])
o.write(" 0.0 %12.7f ylo yhi\n" % pbc[1])
o.write(" 0.0 %12.7f zlo zhi\n" % pbc[2])
else:
xx, xy, xz, yy, yz, zz = lattice2v(pbc)
o.write(" 0.0 %12.7f xlo xhi\n" % xx)
o.write(" 0.0 %12.7f ylo yhi\n" % yy)
o.write(" 0.0 %12.7f zlo zhi\n" % zz)
o.write("%12.7f%12.7f%12.7f xy xz yz\n\n" % (xy, xz, yz))
else:
print "Warning: No box found. Using a default box 5.0 * 5.0 * 5.0"
o.write(" %12.7f %12.7f xlo xhi\n" % (-25.0, 25.0))
o.write(" %12.7f %12.7f ylo yhi\n" % (-25.0, 25.0))
o.write(" %12.7f %12.7f zlo zhi\n" % (-25.0, 25.0))
o.write("Masses\n\n")
for i in system.map:
# atom name
atn = ""
for j in i[1]:
if j.isdigit():
break
atn += j
o.write("%d %s # %s\n" % (i[0], ELEMENT2MASS[atn], atn))
o.write("\n")
o.write("Atoms\n")
o.write("\n")
counter = 1
for i in system.atoms:
line = ""
line += "%-6d" % counter
line += "%3d" % i.type1
line += "%10.6f" % i.charge
line += "%16.9f" % i.x[0]
line += "%16.9f" % i.x[1]
line += "%16.9f" % i.x[2]
line += "\n"
o.write(line)
counter += 1
o.close()
def toReaxLammps(system, outfile="lammps.data"):
""" output to lammps data file
"""
o = open(outfile, 'w')
o.write("# \n")
o.write("\n")
o.write("%d atoms\n\n" % len(system.atoms))
o.write("%d atom types\n\n" % len(system.map))
pbc = system.pbc
if len(pbc) >= 6:
if pbc[3] == 90.0 and pbc[4] == 90 and pbc[5] == 90:
o.write(" 0.0 %12.7f xlo xhi\n" % pbc[0])
o.write(" 0.0 %12.7f ylo yhi\n" % pbc[1])
o.write(" 0.0 %12.7f zlo zhi\n" % pbc[2])
else:
xx, xy, xz, yy, yz, zz = lattice2v(pbc)
o.write(" 0.0 %12.7f xlo xhi\n" % xx)
o.write(" 0.0 %12.7f ylo yhi\n" % yy)
o.write(" 0.0 %12.7f zlo zhi\n" % zz)
o.write("%12.7f%12.7f%12.7f xy xz yz\n\n" % (xy, xz, yz))
else:
print("Warning: No box found. Using a default box 5.0 * 5.0 * 5.0")
o.write(" %12.7f %12.7f xlo xhi\n" % (-25.0, 25.0))
o.write(" %12.7f %12.7f ylo yhi\n" % (-25.0, 25.0))
o.write(" %12.7f %12.7f zlo zhi\n" % (-25.0, 25.0))
o.write("Masses\n\n")
for i in system.map:
# atom name
atn = ''
for j in i[1]:
if j.isdigit():
break
atn += j
o.write("%d %s # %s\n" % (i[0], ELEMENT2MASS[atn], atn))
o.write("\n")
o.write("Atoms\n")
o.write("\n")
counter = 1
for i in system.atoms:
line = ''
line += "%-6d" % counter
line += "%3d" % i.type1
line += "%10.6f" % i.charge
line += "%16.9f" % i.x[0]
line += "%16.9f" % i.x[1]
line += "%16.9f" % i.x[2]
line += "\n"
o.write(line)
counter += 1
o.close()
def toJdft(system, outfile="coords"):
"""Output the msd file
"""
s = system
o = open(outfile, "w")
xx, xy, xz, yy, yz, zz = lattice2v(s.pbc)
xx = xx * A2Bohr
xy = xy * A2Bohr
xz = xz * A2Bohr
yy = yy * A2Bohr
yz = yz * A2Bohr
zz = zz * A2Bohr
a = [xx, xy, xz]
b = [0., yy, 0.]
c = [0., 0., zz]
o.write("lattice \\")
o.write("\n")
for i in a:
o.write("%20.15f"%i)
o.write("\\")
o.write("\n")
for i in b:
o.write("%20.15f"%i)
o.write("\\")
o.write("\n")
for i in c:
o.write("%20.15f"%i)
o.write("\n")
o.write("\n")
o.write("coords-type lattice\n")
coords = []
coordsXr = []
natom = 0
for i in s.atoms:
coords.append(np.array(i.xFrac))
coordsXr.append(i.xr)
natom += 1
for i in range(natom):
xf = coords[i][0]
yf = coords[i][1]
zf = coords[i][2]
o.write("ion %2s %20.15f%20.15f%20.15f 0\n"%(
s.atoms[i].element, xf, yf, zf))
o.write("\n")
o.close()
def toCfg(system, outfile="out.cfg"):
"""Output the cfg file
"""
s = system
o = open(outfile, "w")
o.write("Number of particles = %d\n" % len(s.atoms))
o.write("A = 1.0 Angstrom (basic length-scale)\n")
xx, xy, xz, yy, yz, zz = lattice2v(s.pbc)
a = [xx, 0.0, 0.0]
b = [xy, yy, 0.0]
c = [xz, yz, zz]
o.write("H0(1,1) = %.4f A\n" % a[0])
o.write("H0(1,2) = %.4f A\n" % a[1])
o.write("H0(1,3) = %.4f A\n" % a[2])
o.write("H0(2,1) = %.4f A\n" % b[0])
o.write("H0(2,2) = %.4f A\n" % b[1])
o.write("H0(2,3) = %.4f A\n" % b[2])
o.write("H0(3,1) = %.4f A\n" % c[0])
o.write("H0(3,2) = %.4f A\n" % c[1])
o.write("H0(3,3) = %.4f A\n" % c[2])
o.write(".NO_VELOCITY.\n")
o.write("entry_count = 3\n")
elements = {}
elements_list = []
# sort the coordinations according to element type
for i in s.atoms:
element = i.element
if not element in elements.keys():
elements[element] = []
elements_list.append(element)
elements[element].append(i)
for i in elements_list:
o.write("%d\n" % ELEMENT2ATN[i])
o.write("%s\n" % i)
for j in elements[i]:
xf = j.xFrac[0]
yf = j.xFrac[1]
zf = j.xFrac[2]
o.write("%20.15f%20.15f%20.15f\n" % (xf, yf, zf))
o.close()
def toDump(system, outfile="output.dump"):
"""Output the dump file
"""
o = open(outfile, "w")
o.write("ITEM: TIMESTEP\n")
o.write("%d\n" % system.step)
o.write("ITEM: NUMBER OF ATOMS\n")
o.write("%d\n" % len(system.atoms))
# write the pbc
pbc = system.pbc
"""ITEM: BOX BOUNDS xy xz yz xx yy zz
xlo_bound xhi_bound xy
ylo_bound yhi_bound xz
zlo_bound zhi_bound yz
"""
if len(pbc) >= 6:
if pbc[3] == 90.0 and pbc[4] == 90 and pbc[5] == 90:
o.write("ITEM: BOX BOUNDS pp pp pp\n")
o.write(" 0.0 %9.4f 0.0\n" % pbc[0])
o.write(" 0.0 %9.4f 0.0\n" % pbc[1])
o.write(" 0.0 %9.4f 0.0\n" % pbc[2])
else:
o.write("ITEM: BOX BOUNDS xy xz yz pp pp pp\n")
xx, xy, xz, yy, yz, zz = lattice2v(pbc)
o.write(" %9.4f %9.4f %9.4f\n" % (xz, xx, xy))
o.write(" 0.0 %9.4f %9.4f\n" % (yy, xz))
o.write(" 0.0 %9.4f %9.4f\n" % (zz, yz))
else:
print "Warning: No box found. Using a default box 5.0 * 5.0 * 5.0"
o.write(" 0.0 %9.4f xlo xhi\n" % 5.0)
o.write(" 0.0 %9.4f ylo yhi\n" % 5.0)
o.write(" 0.0 %9.4f zlo zhi\n" % 5.0)
o.write("ITEM: ATOMS id type x y z\n")
for i in system.atoms:
o.write("%-9d" % i.an)
o.write("%6d" % i.type1)
o.write("%14.6f" % i.x[0])
o.write("%14.6f" % i.x[1])
o.write("%14.6f" % i.x[2])
o.write("\n")
o.close()
def toCfg(system, outfile="out.cfg"):
"""Output the cfg file
"""
s = system
o = open(outfile, "w")
o.write("Number of particles = %d\n" % len(s.atoms))
o.write("A = 1.0 Angstrom (basic length-scale)\n")
xx, xy, xz, yy, yz, zz = lattice2v(s.pbc)
a = [xx, 0.0, 0.0]
b = [xy, yy, 0.0]
c = [xz, yz, zz]
o.write("H0(1,1) = %.4f A\n" % a[0])
o.write("H0(1,2) = %.4f A\n" % a[1])
o.write("H0(1,3) = %.4f A\n" % a[2])
o.write("H0(2,1) = %.4f A\n" % b[0])
o.write("H0(2,2) = %.4f A\n" % b[1])
o.write("H0(2,3) = %.4f A\n" % b[2])
o.write("H0(3,1) = %.4f A\n" % c[0])
o.write("H0(3,2) = %.4f A\n" % c[1])
o.write("H0(3,3) = %.4f A\n" % c[2])
o.write(".NO_VELOCITY.\n")
o.write("entry_count = 3\n")
elements = {}
elements_list = []
# sort the coordinations according to element type
for i in s.atoms:
element = i.element
if not element in elements.keys():
elements[element] = []
elements_list.append(element)
elements[element].append(i)
for i in elements_list:
o.write("%d\n" % ELEMENT2ATN[i])
o.write("%s\n" % i)
for j in elements[i]:
xf = j.xFrac[0]
yf = j.xFrac[1]
zf = j.xFrac[2]
o.write("%20.15f%20.15f%20.15f\n" % (xf, yf, zf))
o.close()
def toDump(system, outfile="output.dump"):
"""Output the dump file
"""
o = open(outfile, "w")
o.write("ITEM: TIMESTEP\n")
o.write("%d\n" % system.step)
o.write("ITEM: NUMBER OF ATOMS\n")
o.write("%d\n" % len(system.atoms))
# write the pbc
pbc = system.pbc
"""ITEM: BOX BOUNDS xy xz yz xx yy zz
xlo_bound xhi_bound xy
ylo_bound yhi_bound xz
zlo_bound zhi_bound yz
"""
if len(pbc) >= 6:
if pbc[3] == 90.0 and pbc[4] == 90 and pbc[5] == 90:
o.write("ITEM: BOX BOUNDS pp pp pp\n")
o.write(" 0.0 %9.4f 0.0\n" % pbc[0])
o.write(" 0.0 %9.4f 0.0\n" % pbc[1])
o.write(" 0.0 %9.4f 0.0\n" % pbc[2])
else:
o.write("ITEM: BOX BOUNDS xy xz yz pp pp pp\n")
xx, xy, xz, yy, yz, zz = lattice2v(pbc)
o.write(" %9.4f %9.4f %9.4f\n" % (xz, xx, xy))
o.write(" 0.0 %9.4f %9.4f\n" % (yy, xz))
o.write(" 0.0 %9.4f %9.4f\n" % (zz, yz))
else:
print("Warning: No box found. Using a default box 5.0 * 5.0 * 5.0")
o.write(" 0.0 %9.4f xlo xhi\n" % 5.0)
o.write(" 0.0 %9.4f ylo yhi\n" % 5.0)
o.write(" 0.0 %9.4f zlo zhi\n" % 5.0)
o.write("ITEM: ATOMS id type x y z\n")
for i in system.atoms:
o.write("%-9d" % i.an)
o.write("%6d" % i.type1)
o.write("%14.6f" % i.x[0])
o.write("%14.6f" % i.x[1])
o.write("%14.6f" % i.x[2])
o.write("\n")
o.close()
def gen_scan(s, args):
start = 0.7
end = 1.3
start = np.power(start, 1/3.0)
end = np.power(end, 1/3.0)
n = 11
x = np.linspace(start, end, n)
for i in range(n):
folder = "scan_%02d"%i
if not os.path.exists(folder):
os.mkdir(folder)
os.chdir(folder)
shutil.copy("../INCAR", ".")
shutil.copy("../POTCAR", ".")
shutil.copy("../KPOINTS", ".")
if os.path.exists('../pbs'):
shutil.copy("../pbs", ".")
s_new = copy.copy(s)
xx, xy, xz, yy, yz, zz = lattice2v(s.pbc)
a = np.array([xx, 0.0, 0.0])
b = np.array([xy, yy, 0.0])
c = np.array([xz, yz, zz])
if args.xyz:
tmp = args.xyz[0]
if tmp == "xy":
a = a * x[i]
b = b * x[i]
elif tmp == "z":
c = c * x[i]
else:
a = a * x[i]
b = b * x[i]
c = c * x[i]
pbc = v2lattice(a, b, c)
s_new.pbc = pbc
toPoscar(s_new, "POSCAR")
os.chdir("..")
def gen_scan(s, args):
start = 0.8
end = 1.2
start = np.power(start, 1/3.0)
end = np.power(end, 1/3.0)
n = 11
x = np.linspace(start, end, n)
for i in range(n):
folder = "scan_%02d"%i
if not os.path.exists(folder):
os.mkdir(folder)
os.chdir(folder)
shutil.copy("../INCAR", ".")
shutil.copy("../POTCAR", ".")
shutil.copy("../KPOINTS", ".")
shutil.copy("../pbs", ".")
s_new = copy.copy(s)
xx, xy, xz, yy, yz, zz = lattice2v(s.pbc)
a = np.array([xx, 0.0, 0.0])
b = np.array([xy, yy, 0.0])
c = np.array([xz, yz, zz])
if args.xyz:
tmp = args.xyz[0]
if tmp == "xy":
a = a * x[i]
b = b * x[i]
elif tmp == "z":
c = c * x[i]
else:
a = a * x[i]
b = b * x[i]
c = c * x[i]
pbc = v2lattice(a, b, c)
s_new.pbc = pbc
toPoscar(s_new, "POSCAR")
os.chdir("..")
def toFullLammps(system, outfile="output.data"):
""" output to lammps data file in full format
"""
s = system
o = open(outfile, "w")
o.write("# \n")
o.write("\n")
o.write("%d atoms\n" % s.n_atoms)
o.write("%d bonds\n" % s.n_bonds)
o.write("%d angles\n" % s.n_angles)
o.write("%d dihedrals\n" % s.n_dihedrals)
o.write("%d impropers\n\n" % s.n_impropers)
o.write("%d atom types\n" % s.n_atomtypes)
o.write("%d bond types\n" % s.n_bondtypes)
o.write("%d angle types\n" % s.n_angletypes)
o.write("%d dihedral types\n" % s.n_dihedraltypes)
o.write("%d improper types\n\n" % s.n_impropertypes)
pbc = s.pbc
if len(pbc) >= 6:
if pbc[3] == 90.0 and pbc[4] == 90 and pbc[5] == 90:
o.write(" %12.4f %12.4f xlo xhi\n" % (0.0, pbc[0]))
o.write(" %12.4f %12.4f ylo yhi\n" % (0.0, pbc[1]))
o.write(" %12.4f %12.4f zlo zhi\n" % (0.0, pbc[2]))
else:
xx, xy, xz, yy, yz, zz = lattice2v(pbc)
o.write(" %12.4 %12.4f xlo xhi\n" % (0.0, xx))
o.write(" %12.4 %12.4f ylo yhi\n" % (0.0, yy))
o.write(" %12.4 %12.4f zlo zhi\n" % (0.0, zz))
o.write("%12.4f%12.4f%12.4f xy xz yz\n\n" % (xy, xz, yz))
else:
print "Warning: No box found. Using a default box 5.0 * 5.0 * 5.0"
o.write(" %9.4f %9.4f xlo xhi\n" % (-25.0, 25.0))
o.write(" %9.4f %9.4f ylo yhi\n" % (-25.0, 25.0))
o.write(" %9.4f %9.4f zlo zhi\n" % (-25.0, 25.0))
o.write("\nMasses\n\n")
counter = 1
for i in s.atomtypes:
# atom name
na = counter
ele = s.atomtypes[na - 1]
o.write("%12d %12s # %s\n" % (na, ELEMENT2MASS[ele], ele))
counter += 1
o.write("\n")
o.write("Atoms\n")
o.write("\n")
counter = 1
for i in s.atoms:
line = ""
line += "%12d" % counter
line += "%12d" % i.resn
line += "%6d" % i.type2
line += "%12.6f" % i.charge
line += "%12.6f" % i.x[0]
line += "%12.6f" % i.x[1]
line += "%12.6f" % i.x[2]
line += " # "
line += "%6s" % i.name
line += "\n"
o.write(line)
counter += 1
counter = 1
if s.n_bonds > 0:
o.write("\nBonds\n\n")
for i in s.bonds:
o.write("%12d" % counter)
o.write("%12d" % i[1])
o.write("%12d" % i[2])
o.write("%12d" % i[3])
o.write("\n")
counter += 1
counter = 1
if s.n_angles > 0:
o.write("\nAngles\n\n")
for i in s.angles:
o.write("%12d" % counter)
o.write("%12d" % i[1])
o.write("%12d" % i[2])
o.write("%12d" % i[3])
o.write("%12d" % i[4])
o.write("\n")
counter += 1
counter = 1
if s.n_dihedrals > 0:
o.write("\nDihedrals\n\n")
for i in s.dihedrals:
o.write("%12d" % counter)
o.write("%12d" % i[1])
o.write("%12d" % i[2])
o.write("%12d" % i[3])
o.write("%12d" % i[4])
o.write("%12d" % i[5])
o.write("\n")
counter += 1
if len(s.ffparams) > 0:
o.write("\n")
for i in s.ffparams:
o.write(i)
o.write("\n")
o.close()
def toPoscar(system, outfile="POSCAR"):
"""Output the POSCAR file
"""
s = system
o = open(outfile, "w")
o.write("%s\n" % s.name)
o.write("%20.15f\n" % s.scaleFactor)
xx, xy, xz, yy, yz, zz = lattice2v(s.pbc)
a = [xx, 0.0, 0.0]
b = [xy, yy, 0.0]
c = [xz, yz, zz]
# write the cells
for i in a:
o.write("%20.15f" % i)
o.write("\n")
for i in b:
o.write("%20.15f" % i)
o.write("\n")
for i in c:
o.write("%20.15f" % i)
o.write("\n")
elements = {}
elements_list = []
# sort the coordinations according to element type
for i in s.atoms:
element = i.element
if not element in elements.keys():
elements[element] = []
elements_list.append(element)
elements[element].append(i)
for i in elements_list:
o.write("%6s" % i)
o.write("\n")
for i in elements_list:
o.write("%6d" % len(elements[i]))
o.write("\n")
o.write("Selective dynamics\n")
o.write("Direct\n")
coords = []
coordsXr = []
natom = 0
for i in elements_list:
for j in elements[i]:
coords.append(np.array(j.xFrac))
coordsXr.append(j.xr)
natom += 1
for i in range(natom):
xf = coords[i][0]
yf = coords[i][1]
zf = coords[i][2]
o.write("%20.15f%20.15f%20.15f" % (xf, yf, zf))
xr = "T"
yr = "T"
zr = "T"
if coordsXr[i][0] == 1:
xr = "F"
if coordsXr[i][1] == 1:
yr = "F"
if coordsXr[i][2] == 1:
zr = "F"
o.write("%4s%4s%4s\n" % (xr, yr, zr))
o.write("\n")
o.close()
def toPoscar(system, outfile="POSCAR"):
"""Output the msd file
"""
s = system
o = open(outfile, "w")
o.write("%s\n"%s.name)
o.write("%20.15f\n"%s.scaleFactor)
xx, xy, xz, yy, yz, zz = lattice2v(s.pbc)
a = [xx, 0.0, 0.0]
b = [xy, yy, 0.0]
c = [xz, yz, zz]
"""
latvecs = np.array([a, b, c], dtype=float)
invlatvecs = np.linalg.inv(latvecs)
[xf, yf, zf] = np.dot(coords[i], invlatvecs)
"""
# write the cells
for i in a:
o.write("%20.15f"%i)
o.write("\n")
for i in b:
o.write("%20.15f"%i)
o.write("\n")
for i in c:
o.write("%20.15f"%i)
o.write("\n")
for i in s.atomtypes:
o.write("%6s"%i)
o.write("\n")
for i in s.natoms:
o.write("%6d"%i)
o.write("\n")
o.write("Selective dynamics\n")
o.write("Direct\n")
coords = []
coordsXr = []
natom = 0
for i in s.atoms:
coords.append(np.array(i.xFrac))
coordsXr.append(i.xr)
natom += 1
for i in range(natom):
xf = coords[i][0]
yf = coords[i][1]
zf = coords[i][2]
o.write("%20.15f%20.15f%20.15f"%(xf, yf, zf))
xr = "T"
yr = "T"
zr = "T"
if coordsXr[i][0] == 1:
xr = "F"
if coordsXr[i][1] == 1:
yr = "F"
if coordsXr[i][2] == 1:
zr = "F"
o.write("%4s%4s%4s\n"%(xr, yr, zr))
o.write("\n")
o.close()
def toFullLammps(system, outfile="output.data"):
""" output to lammps data file in full format
"""
s = system
o = open(outfile, 'w')
o.write("# \n")
o.write("\n")
o.write("%d atoms\n" % s.n_atoms)
o.write("%d bonds\n" % s.n_bonds)
o.write("%d angles\n" % s.n_angles)
o.write("%d dihedrals\n" % s.n_dihedrals)
o.write("%d impropers\n\n" % s.n_impropers)
o.write("%d atom types\n" % s.n_atomtypes)
o.write("%d bond types\n" % s.n_bondtypes)
o.write("%d angle types\n" % s.n_angletypes)
o.write("%d dihedral types\n" % s.n_dihedraltypes)
o.write("%d improper types\n\n" % s.n_impropertypes)
pbc = s.pbc
if len(pbc) >= 6:
if pbc[3] == 90.0 and pbc[4] == 90 and pbc[5] == 90:
o.write(" %12.4f %12.4f xlo xhi\n" % (0.0, pbc[0]))
o.write(" %12.4f %12.4f ylo yhi\n" % (0.0, pbc[1]))
o.write(" %12.4f %12.4f zlo zhi\n" % (0.0, pbc[2]))
else:
xx, xy, xz, yy, yz, zz = lattice2v(pbc)
o.write(" %12.4 %12.4f xlo xhi\n" % (0.0, xx))
o.write(" %12.4 %12.4f ylo yhi\n" % (0.0, yy))
o.write(" %12.4 %12.4f zlo zhi\n" % (0.0, zz))
o.write("%12.4f%12.4f%12.4f xy xz yz\n\n" % (xy, xz, yz))
else:
print("Warning: No box found. Using a default box 5.0 * 5.0 * 5.0")
o.write(" %9.4f %9.4f xlo xhi\n" % (-25.0, 25.0))
o.write(" %9.4f %9.4f ylo yhi\n" % (-25.0, 25.0))
o.write(" %9.4f %9.4f zlo zhi\n" % (-25.0, 25.0))
o.write("\nMasses\n\n")
counter = 1
for i in s.atomtypes:
# atom name
na = counter
ele = s.atomtypes[na - 1]
o.write("%12d %12s # %s\n" % (na, ELEMENT2MASS[ele], ele))
counter += 1
o.write("\n")
o.write("Atoms\n")
o.write("\n")
counter = 1
for i in s.atoms:
line = ''
line += "%12d" % counter
line += "%12d" % i.resn
line += "%6d" % i.type2
line += "%12.6f" % i.charge
line += "%12.6f" % i.x[0]
line += "%12.6f" % i.x[1]
line += "%12.6f" % i.x[2]
line += " # "
line += "%6s" % i.name
line += "\n"
o.write(line)
counter += 1
counter = 1
if s.n_bonds > 0:
o.write("\nBonds\n\n")
for i in s.bonds:
o.write("%12d" % counter)
o.write("%12d" % i[1])
o.write("%12d" % i[2])
o.write("%12d" % i[3])
o.write("\n")
counter += 1
counter = 1
if s.n_angles > 0:
o.write("\nAngles\n\n")
for i in s.angles:
o.write("%12d" % counter)
o.write("%12d" % i[1])
o.write("%12d" % i[2])
o.write("%12d" % i[3])
o.write("%12d" % i[4])
o.write("\n")
counter += 1
counter = 1
if s.n_dihedrals > 0:
o.write("\nDihedrals\n\n")
for i in s.dihedrals:
o.write("%12d" % counter)
o.write("%12d" % i[1])
o.write("%12d" % i[2])
o.write("%12d" % i[3])
o.write("%12d" % i[4])
o.write("%12d" % i[5])
o.write("\n")
counter += 1
if len(s.ffparams) > 0:
o.write("\n")
for i in s.ffparams:
o.write(i)
o.write("\n")
o.close()
def toJdft(system, outfile="coords"):
"""Output the Jdft file
"""
s = system
o = open(outfile, "w")
xx, xy, xz, yy, yz, zz = lattice2v(s.pbc)
xx = xx * A2Bohr
xy = xy * A2Bohr
xz = xz * A2Bohr
yy = yy * A2Bohr
yz = yz * A2Bohr
zz = zz * A2Bohr
a = [xx, xy, xz]
b = [0., yy, 0.]
c = [0., 0., zz]
o.write("lattice \\")
o.write("\n")
for i in a:
o.write("%20.15f" % i)
o.write("\\")
o.write("\n")
for i in b:
o.write("%20.15f" % i)
o.write("\\")
o.write("\n")
for i in c:
o.write("%20.15f" % i)
o.write("\n")
o.write("\n")
o.write("coords-type lattice\n")
coords = []
coordsXr = []
natom = 0
for i in s.atoms:
coords.append(np.array(i.xFrac))
coordsXr.append(i.xr)
natom += 1
for i in range(natom):
xf = coords[i][0]
yf = coords[i][1]
zf = coords[i][2]
o.write("ion %2s %20.15f%20.15f%20.15f 0\n" %
(s.atoms[i].element, xf, yf, zf))
o.write("\n")
o.close()
o = open(outfile + "_cartesian", "w")
o.write("lattice \\")
o.write("\n")
for i in a:
o.write("%20.15f" % i)
o.write("\\")
o.write("\n")
for i in b:
o.write("%20.15f" % i)
o.write("\\")
o.write("\n")
for i in c:
o.write("%20.15f" % i)
o.write("\n")
o.write("\n")
o.write("coords-type cartesian\n")
coords = []
coordsXr = []
natom = 0
for i in s.atoms:
coords.append(np.array(i.x))
coordsXr.append(i.xr)
natom += 1
for i in range(natom):
x = coords[i][0] * A2Bohr
y = coords[i][1] * A2Bohr
z = coords[i][2] * A2Bohr
o.write("ion %2s %20.15f%20.15f%20.15f 0\n" %
(s.atoms[i].element, x, y, z))
o.write("\n")
o.close()
def toPoscar(system, outfile="POSCAR"):
"""Output the POSCAR file
"""
ndxfile = 'index.ndx'
s = system
o = open(outfile, "w")
ndx = open(ndxfile, 'w')
ndx.write('# original-id new-id\n')
o.write("%s\n" % s.name)
o.write("%20.15f\n" % s.scaleFactor)
xx, xy, xz, yy, yz, zz = lattice2v(s.pbc)
a = [xx, 0.0, 0.0]
b = [xy, yy, 0.0]
c = [xz, yz, zz]
# write the cells
for i in a:
o.write("%20.15f" % i)
o.write("\n")
for i in b:
o.write("%20.15f" % i)
o.write("\n")
for i in c:
o.write("%20.15f" % i)
o.write("\n")
elements = {}
elements_list = []
# sort the coordinations according to element type
for i in s.atoms:
element = i.element
if not element in elements.keys():
elements[element] = []
elements_list.append(element)
elements[element].append(i)
for i in elements_list:
o.write("%6s" % i)
o.write("\n")
for i in elements_list:
o.write("%6d" % len(elements[i]))
o.write("\n")
o.write("Selective dynamics\n")
o.write("Direct\n")
coords = []
coordsXr = []
id_numbers = []
natom = 0
for i in elements_list:
for j in elements[i]:
coords.append(np.array(j.xFrac))
coordsXr.append(j.xr)
id_numbers.append(j.number)
natom += 1
for i in range(natom):
ndx.write('%d %d\n' % (i + 1, id_numbers[i]))
xf = coords[i][0]
yf = coords[i][1]
zf = coords[i][2]
o.write("%20.15f%20.15f%20.15f" % (xf, yf, zf))
xr = "T"
yr = "T"
zr = "T"
if coordsXr[i][0] == 1:
xr = "F"
if coordsXr[i][1] == 1:
yr = "F"
if coordsXr[i][2] == 1:
zr = "F"
o.write("%4s%4s%4s\n" % (xr, yr, zr))
o.write("\n")
ndx.close()
o.close()
1
2
improper
0
"""
if len(sys.argv) > 2:
nmol = int(sys.argv[2])
a = Pdb(sys.argv[1])
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
toTowheecoords(b)
rcut = 3.5
xx, xy, xz, yy, yz, zz = lattice2v(b.pbc)
la = [xx, 0.0, 0.0]
lb = [xy, yy, 0.0]
lc = [xz, yz, zz]
print la
print lb
print lc
o = open("towhee_input", "w")
o.write("inputformat\n")
o.write("'Towhee'\n")
o.write("ensemble\n")
o.write("'uvt'\n")
o.write("temperature\n")
o.write("256.0d0\n")
o.write("nmolty\n")