Commit c873cb1c authored by cmaffeo2's avatar cmaffeo2
Browse files

Added box_type=orthogonal and CUDA_DEVICE={gpu} to oxDNA input file; thanks to...

Added box_type=orthogonal and CUDA_DEVICE={gpu} to oxDNA input file; thanks to Elija Feigl for bringing the issue to our attention
parent 7cb74455
......@@ -3755,7 +3755,7 @@ proc calcforces {} {
for s in self.strands:
s.generate_oxdna_model()
def _write_oxdna_configuration(self, filename):
def _write_oxdna_configuration(self, filename, gpu=0):
_angstroms_to_oxdna = 0.11739845 ## units "AA" "8.518e-10 m"
with open(filename,'w') as fh:
......@@ -3838,7 +3838,8 @@ E = 0 0 0
verlet_skin = 0.5,
max_backbone_force = 100,
external_forces_file = None,
seq_dep_file = None
seq_dep_file = None,
gpu = 0
):
if seed is None:
......@@ -3911,6 +3912,7 @@ interaction_type = {interaction_type}
{salt_concentration}
sim_type = {sim_type}
backend = {backend}
CUDA_device = {gpu}
backend_precision = {backend_precision}
#debug = 1
seed = {seed}
......@@ -3939,6 +3941,7 @@ verlet_skin = {verlet_skin}
##############################
#### INPUT / OUTPUT ####
##############################
box_type = orthogonal
topology = {topology}
conf_file = {conf_file}
lastconf_file = {last_conf_file}
......@@ -3953,7 +3956,7 @@ print_energy_every = {print_energy_every}
time_scale = linear
""".format( **locals() ))
def simulate_oxdna(self, output_name, directory='.', output_directory='output', topology=None, configuration=None, oxDNA=None, **oxdna_args):
def simulate_oxdna(self, output_name, directory='.', output_directory='output', topology=None, configuration=None, oxDNA=None, gpu=0, **oxdna_args):
if output_directory == '': output_directory='.'
d_orig = os.getcwd()
......
......@@ -29,6 +29,7 @@ def minimize_and_simulate_oxdna( model,
num_min_steps = 5e2,
num_steps = 1e7,
output_period = None,
gpu = 0,
**oxdna_args
):
......@@ -52,6 +53,7 @@ def minimize_and_simulate_oxdna( model,
num_steps = num_min_steps,
print_conf_interval = 100,
print_energy_every = 10,
gpu = gpu,
**min_args)
top,conf = model.simulate_oxdna(output_name = "{}-oxdna".format(output_name),
......@@ -60,6 +62,7 @@ def minimize_and_simulate_oxdna( model,
num_steps = num_steps,
print_conf_interval = output_period,
print_energy_every = output_period,
gpu = gpu,
**oxdna_args)
finally:
os.chdir(d_orig)
......@@ -184,7 +187,8 @@ def multiresolution_simulation( model, output_name,
output_name = output_name,
num_min_steps = 1e3,
num_steps = oxdna_steps,
output_period = oxdna_output_period )
output_period = oxdna_output_period,
gpu = gpu)
else:
""" Atomic simulation """
model.generate_atomic_model(scale=backbone_scale)
......
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