esm = Protocol(clone_settings=False)
# Create simulations and add them to the protocol
for step, numsteps in zip(Esmacs.steps, Esmacs.numsteps):
sim = Simulation()
sim.engine = 'namd_openmp_cuda'
sim.cutoff = 10.0
sim.switchingdist = 8.0
sim.pairlistdist = 11.5
sim.water_model = 'tip4'
# This is present in step 3 only.
sim.numsmallsteps = 20000
sim.numsteps = numsteps
sim.add_input_file(step, is_executable_argument=True)
sim.add_ensemble('replica', range(25))
sim.add_ensemble('system', systems)
esm.append(sim)
# Create runner and assign protocol to it
ht = Runner(resource='titan_orte',
comm_server=('csc190specfem.marble.ccs.ornl.gov', 30672))
ht.add_protocol(esm)
# define step 0:
s0 = Simulation(name='stage-0')
s0.engine = 'namd'
s0.processes = 32
s0.threads_per_process = 1
s0.add_ensemble('replica', range(25))
s0.add_input_file(
"default_configs/esmacs/esmacs-pde2-4d08-l1/esmacs-stage-0.conf",
is_executable_argument=True)
s0.system = system
s0.cutoff = 12.0
s0.switchdist = 10.0
s0.pairlistdist = 13.5
s0.numsteps = 1000
s0.numsmallsteps = 100
s0.constraint_column = "B"
# append step 0 to protocol:
p.append(s0)
# define step 1:
s1 = Simulation(name='stage-1')
s1.engine = 'namd'
s1.processes = 32
s1.threads_per_process = 1
s1.add_ensemble('replica', range(25))
s1.add_input_file(
"default_configs/esmacs/esmacs-pde2-4d08-l1/esmacs-stage-1.conf",
is_executable_argument=True)
s1.system = system