def hook5(lattice):
lattice.logger.info(
"Hook5: Output water molecules as rigid rotors (Euler).")
cellmat = lattice.repcell.mat
s = ""
if cellmat[1, 0] == 0 and cellmat[2, 0] == 0 and cellmat[2, 1] == 0:
s += "@BOX3\n"
s += "{0} {1} {2}\n".format(cellmat[0, 0] * 10, cellmat[1, 1] * 10,
cellmat[2, 2] * 10)
else:
s += "@BOX9\n"
for d in range(3):
s += "{0} {1} {2}\n".format(cellmat[0, d] * 10, cellmat[1, d] * 10,
cellmat[2, d] * 10)
s += "@NX3A\n"
s += "{0}\n".format(len(lattice.reppositions))
for pos, rot in zip(lattice.reppositions, lattice.rotmatrices):
position = np.dot(pos, cellmat) * 10 #in Angstrom
euler = rigid.quat2euler(rigid.rotmat2quat(rot.transpose()))
s += "{0:9.4f} {1:9.4f} {2:9.4f} {3:9.4f} {4:9.4f} {5:9.4f}\n".format(
position[0], position[1], position[2], euler[0], euler[1],
euler[2])
s = "\n".join(lattice.doc) + "\n" + s
print(s, end="")
lattice.logger.info("Hook5: end.")
def hook5(lattice):
lattice.logger.info("Hook5: Output water molecules as rigid rotors (Quaternion).")
cellmat = lattice.repcell.mat
s = ""
if cellmat[1,0] == 0 and cellmat[2,0] == 0 and cellmat[2,1] == 0:
s += "@BOX3\n"
s += "{0} {1} {2}\n".format(cellmat[0,0]*10,cellmat[1,1]*10,cellmat[2,2]*10)
else:
s += "@BOX9\n"
for d in range(3):
s += "{0} {1} {2}\n".format(cellmat[0,d]*10,cellmat[1,d]*10,cellmat[2,d]*10)
s += "@NX4A\n"
s += "{0}\n".format(len(lattice.reppositions))
for pos,rot in zip(lattice.reppositions, lattice.rotmatrices):
position = np.dot(pos, cellmat)*10 #in Angstrom
quat = rigid.rotmat2quat(rot.transpose())
s += "{0:9.4f} {1:9.4f} {2:9.4f} {3:9.4f} {4:9.4f} {5:9.4f} {6:9.4f}\n".format(position[0],
position[1],
position[2],
quat[0],
quat[1],
quat[2],
quat[3])
s = "\n".join(lattice.doc) + "\n" + s
print(s,end="")
lattice.logger.info("Hook5: end.")
def hook5(lattice):
lattice.logger.info("Hook5: Output water molecules as rigid rotors (Quaternion).")
s = ""
if lattice.repcell[1,0] == 0 and lattice.repcell[2,0] == 0 and lattice.repcell[2,1] == 0:
s += "@BOX3\n"
s += "{0} {1} {2}\n".format(lattice.repcell[0,0]*10,lattice.repcell[1,1]*10,lattice.repcell[2,2]*10)
else:
s += "@BOX9\n"
for d in range(3):
s += "{0} {1} {2}\n".format(lattice.repcell[0,d]*10,lattice.repcell[1,d]*10,lattice.repcell[2,d]*10)
s += "@NX4A\n"
s += "{0}\n".format(len(lattice.reppositions))
for i in range(len(lattice.reppositions)):
position = np.dot(lattice.reppositions[i],lattice.repcell)*10 #in Angstrom
quat = rigid.rotmat2quat(lattice.rotmatrices[i].transpose())
s += "{0:9.4f} {1:9.4f} {2:9.4f} {3:9.4f} {4:9.4f} {5:9.4f} {6:9.4f}\n".format(position[0],
position[1],
position[2],
quat[0],
quat[1],
quat[2],
quat[3])
s = "\n".join(lattice.doc) + "\n" + s
print(s,end="")
lattice.logger.info("Hook5: end.")
def format_quaternion(positions, cell, rotmatrices, celltype):
logger = logging.getLogger()
logger.info("Output water molecules as rigid rotors (Quaternion).")
s = ""
if celltype == "rect":
s += "@BOX3\n"
s += "{0} {1} {2}\n".format(cell[0, 0] * 10, cell[1, 1] * 10,
cell[2, 2] * 10)
else:
s += "@BOX9\n"
for d in range(3):
s += "{0} {1} {2}\n".format(cell[0, d] * 10, cell[1, d] * 10,
cell[2, d] * 10)
s += "@NX4A\n"
s += "{0}\n".format(len(positions))
for i in range(len(positions)):
position = np.dot(positions[i], cell) * 10 #in Angstrom
quat = rigid.rotmat2quat(rotmatrices[i].transpose())
s += "{0:9.4f} {1:9.4f} {2:9.4f} {3:9.4f} {4:9.4f} {5:9.4f} {6:9.4f}\n".format(
position[0], position[1], position[2], quat[0], quat[1], quat[2],
quat[3])
return s