From 967b04d8ff959b18acb4c6d8fc569e6084c6ce77 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Mon, 10 Sep 2018 17:36:14 -0500
Subject: [PATCH] Added 'directory' option to arbdmodel.simulate
---
mrdna/model/arbdmodel.py | 96 ++++++++++++++++++++++------------------
1 file changed, 54 insertions(+), 42 deletions(-)
diff --git a/mrdna/model/arbdmodel.py b/mrdna/model/arbdmodel.py
index 3d565f0..048f3a6 100644
--- a/mrdna/model/arbdmodel.py
+++ b/mrdna/model/arbdmodel.py
@@ -676,56 +676,68 @@ class ArbdModel(PdbModel):
if typeA != typeB:
self.nbSchemes.append( (nbScheme, typeB, typeA) )
- def simulate(self, outputPrefix, outputDirectory='output', numSteps=100000000, timestep=None, gpu=0, outputPeriod=1e4, arbd=None):
+ def simulate(self, outputPrefix, outputDirectory='output', numSteps=100000000, timestep=None, gpu=0, outputPeriod=1e4, arbd=None, directory='.'):
assert(type(gpu) is int)
numSteps = int(numSteps)
- if timestep is not None:
- self.timestep = timestep
+ d_orig = os.getcwd()
+ try:
+ if not os.path.exists(directory):
+ os.makedirs(directory)
+ os.chdir(directory)
- if self.cacheUpToDate == False: # TODO: remove cache?
- self._countParticleTypes()
- self._updateParticleOrder()
+ if timestep is not None:
+ self.timestep = timestep
- if outputDirectory == '': outputDirectory='.'
-
- if arbd is None:
- for path in os.environ["PATH"].split(os.pathsep):
- path = path.strip('"')
- fname = os.path.join(path, "arbd")
- if os.path.isfile(fname) and os.access(fname, os.X_OK):
- arbd = fname
- break
-
- if arbd is None: raise Exception("ARBD was not found")
-
- if not os.path.exists(arbd):
- raise Exception("ARBD was not found")
- if not os.path.isfile(arbd):
- raise Exception("ARBD was not found")
- if not os.access(arbd, os.X_OK):
- raise Exception("ARBD is not executable")
-
- if not os.path.exists(outputDirectory):
- os.makedirs(outputDirectory)
- elif not os.path.isdir(outputDirectory):
- raise Exception("outputDirectory '%s' is not a directory!" % outputDirectory)
-
+ if self.cacheUpToDate == False: # TODO: remove cache?
+ self._countParticleTypes()
+ self._updateParticleOrder()
- self.writePdb( outputPrefix + ".pdb" )
- self.writePsf( outputPrefix + ".psf" )
- self.writeArbdFiles( outputPrefix, numSteps=numSteps, outputPeriod=outputPeriod )
- os.sync()
+ if outputDirectory == '': outputDirectory='.'
- ## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command
- cmd = (arbd, '-g', "%d" % gpu, "%s.bd" % outputPrefix, "%s/%s" % (outputDirectory, outputPrefix))
- cmd = tuple(str(x) for x in cmd)
+ if arbd is None:
+ for path in os.environ["PATH"].split(os.pathsep):
+ path = path.strip('"')
+ fname = os.path.join(path, "arbd")
+ if os.path.isfile(fname) and os.access(fname, os.X_OK):
+ arbd = fname
+ break
+
+ if arbd is None: raise Exception("ARBD was not found")
+
+ if not os.path.exists(arbd):
+ raise Exception("ARBD was not found")
+ if not os.path.isfile(arbd):
+ raise Exception("ARBD was not found")
+ if not os.access(arbd, os.X_OK):
+ raise Exception("ARBD is not executable")
+
+ if not os.path.exists(outputDirectory):
+ os.makedirs(outputDirectory)
+ elif not os.path.isdir(outputDirectory):
+ raise Exception("outputDirectory '%s' is not a directory!" % outputDirectory)
+
+
+ self.writePdb( outputPrefix + ".pdb" )
+ self.writePsf( outputPrefix + ".psf" )
+ self.writeArbdFiles( outputPrefix, numSteps=numSteps, outputPeriod=outputPeriod )
+ os.sync()
+
+ ## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command
+ cmd = (arbd, '-g', "%d" % gpu, "%s.bd" % outputPrefix, "%s/%s" % (outputDirectory, outputPrefix))
+ cmd = tuple(str(x) for x in cmd)
+
+ print("Running ARBD with: %s" % " ".join(cmd))
+ process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
+ for line in process.stdout:
+ sys.stdout.write(line)
+ sys.stdout.flush()
+
+ except:
+ raise
+ finally:
+ os.chdir(d_orig)
- print("Running ARBD with: %s" % " ".join(cmd))
- process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
- for line in process.stdout:
- sys.stdout.write(line)
- sys.stdout.flush()
# -------------------------- #
# Methods for printing model #
--
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