From 47848822279ff05f0b1ba50f99a80c76c31482ed Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 18 Feb 2020 17:51:28 -0600
Subject: [PATCH] Added origin parameter to ArbdModel; made
ArbdModel.atomic_simulate() call NAMD
---
arbdmodel/__init__.py | 58 ++++++++++++++++++++++++++++++++++++++++---
1 file changed, 54 insertions(+), 4 deletions(-)
diff --git a/arbdmodel/__init__.py b/arbdmodel/__init__.py
index b48e179..1708211 100644
--- a/arbdmodel/__init__.py
+++ b/arbdmodel/__init__.py
@@ -674,11 +674,13 @@ class PdbModel(Transformable, Parent):
class ArbdModel(PdbModel):
- def __init__(self, children, dimensions=(1000,1000,1000), temperature=291,
- timestep=50e-6, particle_integrator = 'Brown',
+ def __init__(self, children, origin=None, dimensions=(1000,1000,1000), temperature=291, timestep=50e-6,
+ particle_integrator = 'Brown',
cutoff=50, decomp_period=1000, pairlist_distance=None, nonbonded_resolution=0.1,
remove_duplicate_bonded_terms=True, extra_bd_file_lines=""):
+
PdbModel.__init__(self, children, dimensions, remove_duplicate_bonded_terms)
+ self.origin = origin
self.temperature = temperature
self.timestep = timestep
@@ -935,8 +937,14 @@ class ArbdModel(PdbModel):
params['outputPeriod'] = outputPeriod
for k,v in zip('XYZ', self.dimensions):
- params['origin'+k] = -v*0.5
params['dim'+k] = v
+
+ if self.origin is None:
+ for k,v in zip('XYZ', self.dimensions):
+ params['origin'+k] = -v*0.5
+ else:
+ for k,v in zip('XYZ', self.origin):
+ params['origin'+k] = v
params['pairlist_distance'] -= params['cutoff']
@@ -1316,7 +1324,7 @@ if {{$nLast == 0}} {{
run {num_steps:d}
""".format(**format_data))
- def atomic_simulate(self, output_name, output_directory='output'):
+ def atomic_simulate(self, output_name, output_directory='output', dry_run = False, namd2=None, log_file=None, num_procs=None, gpu=None):
if self.cacheUpToDate == False: # TODO: remove cache?
self._countParticleTypes()
self._updateParticleOrder()
@@ -1327,3 +1335,45 @@ run {num_steps:d}
self.writePsf( output_name + ".psf" )
self.write_namd_configuration( output_name, output_directory = output_directory )
os.sync()
+
+ if not dry_run:
+ if namd2 is None:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ fname = os.path.join(path, "namd2")
+ if os.path.isfile(fname) and os.access(fname, os.X_OK):
+ namd2 = fname
+ break
+
+ if namd2 is None: raise Exception("NAMD2 was not found")
+
+ if not os.path.exists(namd2):
+ raise Exception("NAMD2 was not found")
+ if not os.path.isfile(namd2):
+ raise Exception("NAMD2 was not found")
+ if not os.access(namd2, os.X_OK):
+ raise Exception("NAMD2 is not executable")
+
+ if not os.path.exists(output_directory):
+ os.makedirs(output_directory)
+ elif not os.path.isdir(output_directory):
+ raise Exception("output_directory '%s' is not a directory!" % output_directory)
+
+ if num_procs is None:
+ import multiprocessing
+ num_procs = max(1,multiprocessing.cpu_count()-1)
+
+ cmd = [namd2, '+p{}'.format(num_procs), "%s.namd" % output_name]
+ cmd = tuple(str(x) for x in cmd)
+
+ print("Running NAMD2 with: %s" % " ".join(cmd))
+ if log_file is None or (hasattr(log_file,'write') and callable(log_file.write)):
+ fd = sys.stdout if log_file is None else log_file
+ process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
+ for line in process.stdout:
+ fd.write(line)
+ fd.flush()
+ else:
+ with open(log_file,'w') as fd:
+ process = subprocess.Popen(cmd, stdout=log_file, universal_newlines=True)
+ process.communicate()
--
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