def perform_aimd(world, mm_comm, qm_comm):
me = world.Get_rank()
# receive number of atoms from the MM engine
mdi.MDI_Send_command("<NATOMS", mm_comm)
natoms = mdi.MDI_Recv(1, mdi.MDI_INT, mm_comm)
natoms = world.bcast(natoms, root=0)
# allocate arrays for coordinates and forces
coords = np.zeros(3 * natoms, dtype=np.float64)
forces = np.zeros(3 * natoms, dtype=np.float64)
# MM engine initializes a new MD simulation
mdi.MDI_Send_command("@INIT_MD", mm_comm)
# -----------------
# compute initial forces for Verlet timestepping
# and initial energy for output on step 0
# -----------------
# MM engine proceeds to @FORCES node in setup()
mdi.MDI_Send_command("@FORCES", mm_comm)
# get coords from MM engine
mdi.MDI_Send_command("<COORDS", mm_comm)
mdi.MDI_Recv(3 * natoms, mdi.MDI_DOUBLE, mm_comm, buf=coords)
world.Bcast(coords, root=0)
# send coords to QM engine
mdi.MDI_Send_command(">COORDS", qm_comm)
mdi.MDI_Send(coords, 3 * natoms, mdi.MDI_DOUBLE, qm_comm)
# get QM potential energy
mdi.MDI_Send_command("<PE", qm_comm)
qm_pe = mdi.MDI_Recv(1, mdi.MDI_DOUBLE, qm_comm)
qm_pe = world.bcast(qm_pe, root=0)
# get forces from QM engine
mdi.MDI_Send_command("<FORCES", qm_comm)
mdi.MDI_Recv(3 * natoms, mdi.MDI_DOUBLE, qm_comm, buf=forces)
world.Bcast(forces, root=0)
# send forces to MM engine
mdi.MDI_Send_command(">FORCES", mm_comm)
mdi.MDI_Send(forces, 3 * natoms, mdi.MDI_DOUBLE, mm_comm)
# get MM kinetic energy
mdi.MDI_Send_command("<KE", mm_comm)
mm_ke = mdi.MDI_Recv(1, mdi.MDI_DOUBLE, mm_comm)
mm_ke = world.bcast(mm_ke, root=0)
# output by driver
# normalize energies by atom count
if me == 0:
print("Step %d: MM energy %g, QM energy %g, Total energy %g" % \
(0,mm_ke/natoms,qm_pe/natoms,(mm_ke+qm_pe)/natoms))
# -----------------
# timestepping loop
# -----------------
for istep in range(nsteps):
# MM engine proceeds to @FORCES node
mdi.MDI_Send_command("@FORCES", mm_comm)
# get coords from MM engine
mdi.MDI_Send_command("<COORDS", mm_comm)
mdi.MDI_Recv(3 * natoms, mdi.MDI_DOUBLE, mm_comm, buf=coords)
world.Bcast(coords, root=0)
# send coords to QM engine
mdi.MDI_Send_command(">COORDS", qm_comm)
mdi.MDI_Send(coords, 3 * natoms, mdi.MDI_DOUBLE, qm_comm)
# get QM potential energy
mdi.MDI_Send_command("<PE", qm_comm)
qm_pe = mdi.MDI_Recv(1, mdi.MDI_DOUBLE, qm_comm)
qm_pe = world.bcast(qm_pe, root=0)
# get forces from QM engine
mdi.MDI_Send_command("<FORCES", qm_comm)
mdi.MDI_Recv(3 * natoms, mdi.MDI_DOUBLE, qm_comm, buf=forces)
world.Bcast(forces, root=0)
# send forces to MM engine
mdi.MDI_Send_command(">FORCES", mm_comm)
mdi.MDI_Send(forces, 3 * natoms, mdi.MDI_DOUBLE, mm_comm)
# MM engine proceeds to @ENDSTEP node
# so that KE will be for fully updated velocity
mdi.MDI_Send_command("@ENDSTEP", mm_comm)
# get MM kinetic energy
mdi.MDI_Send_command("<KE", mm_comm)
mm_ke = mdi.MDI_Recv(1, mdi.MDI_DOUBLE, mm_comm)
mm_ke = world.bcast(mm_ke, root=0)
# output by driver
# normalize energies by atom count
if me == 0:
print("Step %d: MM energy %g, QM energy %g, Total energy %g" % \
(istep+1,mm_ke/natoms,qm_pe/natoms,(mm_ke+qm_pe)/natoms))
# send EXIT to each engine
mdi.MDI_Send_command("EXIT", mm_comm)
mdi.MDI_Send_command("EXIT", qm_comm)
def perform_tasks(world, mdicomm, dummy):
me = world.Get_rank()
nprocs = world.Get_size()
# allocate vectors for per-atom types, coords, vels, forces
natoms = nx * ny * nz
atypes = np.zeros(natoms, dtype=np.int)
coords = np.zeros(3 * natoms, dtype=np.float64)
vels = np.zeros(3 * natoms, dtype=np.float64)
forces = np.zeros(3 * natoms, dtype=np.float64)
atypes[:] = 1
# initialize RN generator
random.seed(seed)
# loop over sequence of calculations
for icalc in range(ncalc):
# define simulation box
onerho = rho + (random.random() - 0.5) * rhodelta
sigma = pow(1.0 / onerho, 1.0 / 3.0)
xlo = ylo = zlo = 0.0
xhi = nx * sigma
yhi = ny * sigma
zhi = nz * sigma
# send simulation box to engine
vec = [xhi - xlo, 0.0, 0.0] + [0.0, yhi - ylo, 0.0
] + [0.0, 0.0, zhi - zlo]
mdi.MDI_Send_command(">CELL", mdicomm)
mdi.MDI_Send(vec, 9, mdi.MDI_DOUBLE, mdicomm)
# create atoms on perfect lattice
m = 0
for k in range(nz):
for j in range(ny):
for i in range(nx):
coords[m] = i * sigma
coords[m + 1] = j * sigma
coords[m + 2] = k * sigma
m += 3
# perturb lattice
for m in range(3 * natoms):
coords[m] += 2.0 * random.random() * delta - delta
# define initial velocities
for m in range(3 * natoms):
vels[m] = random.random() - 0.5
tcurrent = 0.0
for m in range(3 * natoms):
tcurrent += vels[m] * vels[m]
tcurrent /= 3 * (natoms - 1)
factor = math.sqrt(tinitial / tcurrent)
for m in range(3 * natoms):
vels[m] *= factor
# send atoms and their properties to engine
mdi.MDI_Send_command(">NATOMS", mdicomm)
mdi.MDI_Send(natoms, 1, mdi.MDI_INT, mdicomm)
mdi.MDI_Send_command(">TYPES", mdicomm)
mdi.MDI_Send(atypes, natoms, mdi.MDI_INT, mdicomm)
mdi.MDI_Send_command(">COORDS", mdicomm)
mdi.MDI_Send(coords, 3 * natoms, mdi.MDI_DOUBLE, mdicomm)
mdi.MDI_Send_command(">VELOCITIES", mdicomm)
mdi.MDI_Send(vels, 3 * natoms, mdi.MDI_DOUBLE, mdicomm)
# eval or run or minimize
if mode == "eval":
pass
elif mode == "run":
mdi.MDI_Send_command(">NSTEPS", mdicomm)
mdi.MDI_Send(nsteps, 1, mdi.MDI_INT, mdicomm)
mdi.MDI_Send_command("MD", mdicomm)
elif mode == "min":
mdi.MDI_Send_command(">TOLERANCE", mdicomm)
params = [tol, tol, 1000.0, 1000.0]
mdi.MDI_Send(params, 4, mdi.MDI_DOUBLE, mdicomm)
mdi.MDI_Send_command("OPTG", mdicomm)
# request potential energy
mdi.MDI_Send_command("<PE", mdicomm)
pe = mdi.MDI_Recv(1, mdi.MDI_DOUBLE, mdicomm)
pe = world.bcast(pe, root=0)
# request virial tensor
mdi.MDI_Send_command("<STRESS", mdicomm)
virial = mdi.MDI_Recv(9, mdi.MDI_DOUBLE, mdicomm)
virial = world.bcast(virial, root=0)
# request forces
mdi.MDI_Send_command("<FORCES", mdicomm)
mdi.MDI_Recv(3 * natoms, mdi.MDI_DOUBLE, mdicomm, buf=forces)
world.Bcast(forces, root=0)
# final output from each calculation
# pressure = trace of virial tensor, no kinetic component
aveeng = pe / natoms
pressure = (virial[0] + virial[4] + virial[8]) / 3.0
m = 0
fx = fy = fz = 0.0
for i in range(natoms):
fx += forces[m]
fy += forces[m + 1]
fz += forces[m + 2]
m += 3
fx /= natoms
fy /= natoms
fz /= natoms
line = "Calc %d: eng %7.5g pressure %7.5g aveForce %7.5g %7.5g %7.5g" % \
(icalc+1,aveeng,pressure,fx,fy,fz)
if me == 0: print(line)
# send EXIT command to engine
# in plugin mode, removes the plugin library
mdi.MDI_Send_command("EXIT", mdicomm)
# return needed for plugin mode
return 0
if not mdiarg: error()
# LAMMPS engines are stand-alone codes
# world = MPI communicator for just this driver
# invoke perform_tasks() directly
if not plugin:
mdi.MDI_Init(mdiarg)
world = mdi.MDI_MPI_get_world_comm()
# connect to 2 engines, determine which is MM vs QM
mdicomm1 = mdi.MDI_Accept_Communicator()
mdicomm2 = mdi.MDI_Accept_Communicator()
mdi.MDI_Send_command("<NAME", mdicomm1)
name1 = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH, mdi.MDI_CHAR, mdicomm1)
name1 = world.bcast(name1, root=0)
mdi.MDI_Send_command("<NAME", mdicomm2)
name2 = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH, mdi.MDI_CHAR, mdicomm2)
name2 = world.bcast(name2, root=0)
if name1 == "MM" and name2 == "QM":
mm_comm = mdicomm1
qm_comm = mdicomm2
elif name1 == "QM" and name2 == "MM":
mm_comm = mdicomm2
qm_comm = mdicomm1
else:
error("Two engines have invalid names")