def main():
# Input
if len(sys.argv) != 3:
check_correct_insert()
if str(sys.argv[1]) != 'DFTB+' and str(sys.argv[1]) != 'GAMESS':
check_correct_insert()
if str(sys.argv[2]) != 'coll' and str(sys.argv[2]) != 'ms':
check_correct_insert()
program = str(sys.argv[1]) # GAMESS/DFTB+
mod = str(sys.argv[2]) # coll/ms
# Get parameters
if program == 'GAMESS':
parameters_list = np.loadtxt("start_input_gamess",
dtype=tuple,
usecols=[1])
mod = 'coll'
elif program == 'DFTB+':
parameters_list = np.loadtxt("start_input_dftbplus",
dtype=tuple,
usecols=[1])
else:
parameters_list = 0
print("error")
name_target = str(parameters_list[0]) # Name file target
name_bullett = str(parameters_list[1]) # Name file bullet
d = float(parameters_list[2]) # Distance [Angstrom]
limit = float(parameters_list[3]) # B_max [Angstrom]
delta_b = float(parameters_list[4]) # Delta_b[Angstrom]
numero_angoli = int(
parameters_list[5]) # Angle's number (for target rotation)
temperature_t = float(
parameters_list[6]) # Roto-vib temperature for target
temperature_p = float(parameters_list[7]) # " " " for bullet
energy_coll = float(
parameters_list[8]) # Collisional energy (in CM frame) [Kcal/mol]
dt = float(parameters_list[9]
) # Timestep for dynamic, in fs for dftbplus and s in gamess
step_to_add = int(parameters_list[10])
path_program = str(parameters_list[11])
if program == "DFTB+": # Parameters for dynamic (external programs)
path = str(parameters_list[12])
charge = int(parameters_list[13])
temp_conv = float(parameters_list[14])
spin_spaiati = int(parameters_list[15])
icharge = 0
r_oruhf = 0
mult = 0
scr_dir = 0
else:
dt = float(dt)
r_oruhf = str(parameters_list[12])
mult = int(parameters_list[13])
icharge = int(parameters_list[14])
scr_dir = str(parameters_list[15])
path = 0
charge = 0
temp_conv = 0
spin_spaiati = 0
# Variables
# Label atoms
atoms_b = np.loadtxt(name_bullett, dtype=np.str, skiprows=2, usecols=[0])
atoms_t = np.loadtxt(name_target, dtype=np.str, skiprows=2, usecols=[0])
atoms_tot = []
if atoms_b.size > 1:
for i in range(atoms_b.size):
atoms_tot.append(atoms_b[i])
else:
atoms_tot.append(str(atoms_b))
for i in range(atoms_t.size):
atoms_tot.append(atoms_t[i])
atoms_tot = np.array(atoms_tot)
# Initial coordinate
coord_target = (empty_matrix(atoms_t.size, 3))
coord_bull = (empty_matrix(atoms_b.size, 3))
count = 1
for i in range(0, int(3)):
coord_target[i] = np.loadtxt(
name_target, dtype=float, skiprows=2, usecols=[
count
]) # Matrix_coord = [[x1, x2..xn], [y1,y2..yn], [z1,z2..zn]]
coord_bull[i] = np.loadtxt(name_bullett,
dtype=float,
skiprows=2,
usecols=[count])
count += 1
# VELOCITIES
velocities_m_s, total_time_coll = get_velocities(d, program, atoms_b,
atoms_t, temperature_p,
temperature_t,
energy_coll)
if program == 'GAMESS': # dt = second
step = int(total_time_coll / dt) + step_to_add
elif program == 'DFTB+': # dt = fs > total_time_coll*1e15
step = int(total_time_coll / (dt * 1e-15)) + step_to_add
# GEOMETRY
# Shift in CM system for each molecule
if atoms_b.size > 1:
coord_bull_cm = shift_cm(coord_bull, atoms_b)
else:
coord_bull_cm = [[0], [0], [0]]
coord_target_cm = shift_cm(coord_target, atoms_t)
# Rotation in inertia axis (valid only if atoms.size > 1)
if atoms_b.size > 1:
matrix_inertia_b = inertia_matrix(coord_bull_cm, atoms_b)
coord_rotate_b = rotation_single_geom_in_inertia_axis(
matrix_inertia_b, coord_bull_cm, atoms_b.size)
else:
coord_rotate_b = [[0], [0], [0]]
matrix_inertia_t = inertia_matrix(coord_target_cm, atoms_t)
coord_rotate_t = rotation_single_geom_in_inertia_axis(
matrix_inertia_t, coord_target_cm, atoms_t.size)
b = []
if mod == 'ms':
r_temp = -limit
while r_temp < limit + delta_b:
b.append(r_temp)
r_temp += delta_b
traj_tot = geometries_output(icharge, step, 0, atoms_tot, b, d,
coord_rotate_t, coord_rotate_b, [0, 0, 0],
program, r_oruhf, dt, mult,
velocities_m_s)
elif mod == 'coll':
r_temp = 0
while r_temp <= limit:
if round(r_temp, 3) != round(
0, 3
): # For the head-on collision, the cross section is null. So it is negectable
b.append(r_temp)
r_temp += delta_b
theta_tot_angles = angles(numero_angoli)
theta_tot_angles_degrees = empty_matrix(3, numero_angoli)
for i in range(0, numero_angoli):
for j in range(0, 3):
theta_tot_angles_degrees[i][j] = math.degrees(
theta_tot_angles[i][j])
count_angle = 0
counting_traj = 0
while count_angle < numero_angoli:
coord_fin_targ = rotation(coord_rotate_t,
theta_tot_angles[count_angle])
counting_traj = geometries_output(
icharge, step, counting_traj, atoms_tot, b, d, coord_fin_targ,
coord_rotate_b, theta_tot_angles_degrees[count_angle], program,
r_oruhf, dt, mult, velocities_m_s)
count_angle += 1
traj_tot = len(b) * numero_angoli
# Input dftb+
if program == 'DFTB+':
input_dftb(dt, path, atoms_tot, step, temp_conv, spin_spaiati, charge)
with open("VELOC.DAT", "w") as f:
for i in range(len(atoms_tot)):
f.write("{} {} {}\n".format(velocities_m_s[0][i],
velocities_m_s[1][i],
velocities_m_s[2][i]))
system.main(mod, numero_angoli, program, scr_dir, coord_target[0].size,
coord_bull[0].size, traj_tot, path_program)
def function():
img = "sources30px/set1/b.png"
answer = system.main(img, net)
print "B recognized " + str(sum(ba) / float(len(ba)) * 100)
print "C recognized " + str(sum(ca) / float(len(ca)) * 100)
print "F recognized " + str(sum(fa) / float(len(fa)) * 100)
print "H recognized " + str(sum(ha) / float(len(ha)) * 100)
print "J recognized " + str(sum(ja) / float(len(ja)) * 100)
print "L recognized " + str(sum(la) / float(len(la)) * 100)
print "P recognized " + str(sum(pa) / float(len(pa)) * 100)
print "Q recognized " + str(sum(qa) / float(len(qa)) * 100)
print "V recognized " + str(sum(va) / float(len(va)) * 100)
print "X recognized " + str(sum(xa) / float(len(xa)) * 100)
print "Y recognized " + str(sum(ya) / float(len(ya)) * 100)
print "Z recognized " + str(sum(za) / float(len(za)) * 100)
if __name__ == "__main__":
net = sys.argv[1]
for (dir, _, files) in os.walk(sys.argv[2]):
for f in files:
if f.endswith(".png"):
path = os.path.join(dir, f)
filepath = path
expected = os.path.basename(path)
answer = system.main(filepath, net)
verify(expected, answer)
stats()
def function(): img = "sources30px/set1/b.png" answer = system.main(img, net)
print "J recognized " + str(sum(ja)/float(len(ja))*100)
print "L recognized " + str(sum(la)/float(len(la))*100)
print "P recognized " + str(sum(pa)/float(len(pa))*100)
print "Q recognized " + str(sum(qa)/float(len(qa))*100)
print "V recognized " + str(sum(va)/float(len(va))*100)
print "X recognized " + str(sum(xa)/float(len(xa))*100)
print "Y recognized " + str(sum(ya)/float(len(ya))*100)
print "Z recognized " + str(sum(za)/float(len(za))*100)
if __name__=="__main__":
net = sys.argv[1]
for (dir, _, files) in os.walk(sys.argv[2]):
for f in files:
if f.endswith(".png"):
path = os.path.join(dir,f)
filepath = path
expected = os.path.basename(path)
answer = system.main(filepath, net)
verify(expected, answer)
stats()
# ---------------------------------------------------------------------------
# run the program
try:
import system.main
system.main.main(g_py_path, log_folder)
except:
logging.exception("")
# print some closing lines
ts = t
t = time.time()
utc = time.gmtime(t)
total_time = t - ts
log.info("")
log.info("------------------------------------------------------------------------------")
log.info("utc : " + time.asctime( utc ))
log.info("local time : " + time.asctime( time.localtime(t) ))
log.info("total time : %i days %i hours %i minutes %i seconds",
total_time // (60*60*24), total_time // (60*60) % 24,
total_time // 60 % 60, total_time % 60)
if __name__ == "__main__":
main()
