atoms_pole_numbers, from_fragment = index_fragments(fragment_list, ipoles)
elapsed = time.time() - start
print(F'Bookkeeping:\t {elapsed}')
###########################################################################
#
# Send Probe Information to Tinker
#
###########################################################################
start = time.time()
# Inform Tinker of the probe atoms
for comm in engine_comm:
mdi.MDI_Send_Command(">NPROBES", comm)
mdi.MDI_Send(len(probes), 1, mdi.MDI_INT, comm)
mdi.MDI_Send_Command(">PROBES", comm)
mdi.MDI_Send(probe_pole_indices, len(probes), mdi.MDI_INT, comm)
angstrom_to_bohr = mdi.MDI_Conversion_Factor("angstrom",
"atomic_unit_of_length")
elapsed - time.time() - start
print(F'Sending info to tinker:\t {elapsed}')
###########################################################################
#
# Engine and Trajectory File Compatibility Check.
#
###########################################################################
# Check that engine and trajectory are compatible.
ds_dr = colvar.GetGradient()
# Apply restraints
if colvar_val > upper_restraint:
dVg_ds = k_restraint * (colvar_val - upper_restraint)
# Compute the updated forces
mdi.MDI_Send_Command("<FORCES", comm)
forces = mdi.MDI_Recv(3 * natoms, mdi.MDI_DOUBLE, comm)
for idx_atom in range(2):
for idx_dir in range(3):
iatom = colvar.GetAtoms()[idx_atom]
forces[3 * iatom +
idx_dir] -= dVg_ds * ds_dr[idx_atom][idx_dir]
# Send the new forces to the engine
mdi.MDI_Send_Command(">FORCES", comm)
mdi.MDI_Send(forces, 3 * natoms, mdi.MDI_DOUBLE, comm)
print(" Colvar_val: " + str(colvar_val / angstrom_to_atomic))
# Send the "EXIT" command to each of the engines
mdi.MDI_Send_Command("EXIT", comm)
# Print the data to an output file
output = open("s_of_t.out", "w")
for i in range(len(s_of_t)):
output.write(str(i) + " " + str(s_of_t[i]) + "\n")
my_plot.finalize()