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

mrdna/segmentmodel.py

@@ -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()

mrdna/simulate.py

@@ -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)