def setUp(self):
h2_xyz_file = 'tmp.xyz'
with open(h2_xyz_file, 'w') as ftemp:
ftemp.write(" %d\n" % 2)
ftemp.write(" \n")
ftemp.write("H 0.0 0.0 0.0\n")
ftemp.write("H 0.0 0.0 0.7\n")
mopac_inst = mopac.Mopac(h2_xyz_file)
mopac_inst.prepare_input(keyword="PM7")
def make_monomers(self, mers_list):
n_of_molecules = len(mers_list)
energy_list = []
for i in range(n_of_molecules):
mer_i = "mer_" + str(i) + ".xyz"
with open(mer_i, 'w') as fp:
fp.write(" %d\n" % len(mers_list[i]))
fp.write("xyz for cooperativity\n")
for j in mers_list[i]:
fp.write("%s %f %f %f\n" % (j[0], j[1], j[2], j[3]))
mopac_inst = mopac.Mopac(mer_i)
prepare_input_status = mopac_inst.prepare_input(keyword="PM7 1SCF")
optimize = mopac_inst.optimize()
energy = mopac_inst.get_energy()
energy_list.append([mer_i, energy])
return energy_list
def run_cluster(fragment_1_all_set, fragment_2_all_set, tabu_file, xyz_file_adder, no_of_orientation, aggregates, atoms_name,\
translational_vector_range, tvector_dimension, rvector_dimension):
print "Running the Cluster calculation"
tot_atoms = len(atoms_name)
dict_struct_energy = {}
for orientation in range(no_of_orientation):
xaxis = [translational_vector_range[0], translational_vector_range[1], 1]
yaxis = [translational_vector_range[0], translational_vector_range[1], 1]
zaxis = [translational_vector_range[0], translational_vector_range[1], 1]
all_trans = [xaxis, yaxis, zaxis]
all_rot = [[0, 360, 12], [0, 180, 6], [0, 360, 12]]
start_xyz_file_name = "start_"+str(aggregates)+"_"+xyz_file_adder+"_"+str(orientation)+".xyz"
vectors = vector_generator.vector_generator(tvector_dimension, rvector_dimension)
tvectors, rvectors = vectors.trans_rot_vector_generator(tabu_file, all_trans, all_rot, 0.1, 30.0)
new_rot_coords_of_frag_2 = species.rotate_euler(fragment_2_all_set, rvectors[:])
final_coords_of_frag_2 = species.translate(atoms_name, fragment_1_all_set, new_rot_coords_of_frag_2[:], tvectors[:])
all_coords = np.concatenate((fragment_1_all_set, final_coords_of_frag_2), axis=0)
fstart = open(start_xyz_file_name, 'w')
fstart.write("%d\n" % tot_atoms)
fstart.write(" \n")
for n in range(len(all_coords)):
fstart.write("%-5s %17.10f %17.10f %17.10f \n" % (atoms_name[n], all_coords[n][0], all_coords[n][1], all_coords[n][2]))
fstart.close()
mopac_inst = mopac.Mopac(start_xyz_file_name)
xyz_file_result_name = "result_"+str(aggregates)+"_"+xyz_file_adder+"_"+str(orientation)
prepare_input_status = mopac_inst.prepare_input(keyword="PM7 PRECISE SINGLET LET DDMIN=0.0 CYCLES=10000 THREADS=8")
optimize_status = mopac_inst.optimize()
if optimize_status != 0:
print "optimize status: ", optimize_status
print "The optimization for geometry:", start_xyz_file_name, "has failed."
print "New geometry will be optimized and it will be discarded."
continue
#if files_dirs.file_exists_check_with_return_status("start_"+str(aggregates)+"_"+str(orientation)+".arc"):
# energies = mopac_inst.get_energy()
#else:
# continue
energies = mopac_inst.get_energy()
en_kcal = energies[0]
en_kj = energies[1]
print "xyz_file_result_name is: ", xyz_file_result_name
mopac_inst.extract_xyz(xyz_file_result_name+".xyz")
dict_struct_energy[xyz_file_result_name] = en_kcal
pprint.pprint(dict_struct_energy)
return
def make_dimers(self, mers_list):
n_of_molecules = len(mers_list)
no_of_atoms_in_each_mer = len(mers_list[0])
energy_list = []
for i in range(n_of_molecules - 1):
for j in range(i + 1, n_of_molecules):
mer_ij = "mer_" + str(i) + "_" + str(j) + ".xyz"
with open(mer_ij, 'w') as fp:
fp.write(" %d\n" % (2 * no_of_atoms_in_each_mer))
fp.write("xyz for cooperativity\n")
for k in mers_list[i]:
fp.write("%s %f %f %f\n" % (k[0], k[1], k[2], k[3]))
for l in mers_list[j]:
fp.write("%s %f %f %f\n" % (l[0], l[1], l[2], l[3]))
mopac_inst = mopac.Mopac(mer_ij)
prepare_input_status = mopac_inst.prepare_input(
keyword="PM7 1SCF")
optimize = mopac_inst.optimize()
energy = mopac_inst.get_energy()
energy_list.append([mer_ij, energy])
return energy_list
def test_return_status(self):
mopac_inst = mopac.Mopac(self.h2_xyz_file)
status = mopac_inst.prepare_input(keyword="PM7")
self.assertEqual(status, 0)
def single_point_nmer(self, xyz_file):
mopac_inst = mopac.Mopac(xyz_file)
prepare_input_status = mopac_inst.prepare_input(keyword="PM7 1SCF")
optimize_status = mopac_inst.optimize()
energy = mopac_inst.get_energy()
return energy