From 99b3e224d98e0b6983c615b1a2ef90f849b13f14 Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Wed, 3 Apr 2019 15:11:40 -0500
Subject: [PATCH] Added support for restart_file
---
arbdmodel/__init__.py | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/arbdmodel/__init__.py b/arbdmodel/__init__.py
index 92abb73..ce41736 100644
--- a/arbdmodel/__init__.py
+++ b/arbdmodel/__init__.py
@@ -727,7 +727,7 @@ class ArbdModel(PdbModel):
if typeA != typeB:
self.nbSchemes.append( (nbScheme, typeB, typeA) )
- def simulate(self, output_name, output_directory='output', num_steps=100000000, timestep=None, gpu=0, output_period=1e4, arbd=None, directory='.', replicas=1):
+ def simulate(self, output_name, output_directory='output', num_steps=100000000, timestep=None, gpu=0, output_period=1e4, arbd=None, directory='.', restart_file=None, replicas=1):
assert(type(gpu) is int)
num_steps = int(num_steps)
@@ -771,7 +771,7 @@ class ArbdModel(PdbModel):
self.writePdb( output_name + ".pdb" )
self.writePsf( output_name + ".psf" )
- self.writeArbdFiles( output_name, numSteps=num_steps, outputPeriod=output_period )
+ self.writeArbdFiles( output_name, numSteps=num_steps, outputPeriod=output_period, restart_file=restart_file )
os.sync()
## http://stackoverflow.com/questions/18421757/live-output-from-subprocess-command
@@ -798,7 +798,7 @@ class ArbdModel(PdbModel):
# Methods for printing model #
# -------------------------- #
- def writeArbdFiles(self, prefix, numSteps=100000000, outputPeriod=10000):
+ def writeArbdFiles(self, prefix, numSteps=100000000, outputPeriod=10000, restart_file=None):
## TODO: save and reference directories and prefixes using member data
d = self.potential_directory = "potentials"
if not os.path.exists(d):
@@ -817,7 +817,7 @@ class ArbdModel(PdbModel):
self._writeArbdDihedralFile()
self._writeArbdExclusionFile()
self._writeArbdPotentialFiles( prefix, directory = d )
- self._writeArbdConf( prefix, numSteps=numSteps, outputPeriod=outputPeriod )
+ self._writeArbdConf( prefix, numSteps=numSteps, outputPeriod=outputPeriod, restart_file=restart_file )
# def _writeArbdCoordFile(self, filename):
# with open(filename,'w') as fh:
@@ -844,7 +844,7 @@ class ArbdModel(PdbModel):
- def _writeArbdConf(self, prefix, randomSeed=None, numSteps=100000000, outputPeriod=10000, restartCoordinateFile=None):
+ def _writeArbdConf(self, prefix, randomSeed=None, numSteps=100000000, outputPeriod=10000, restart_file=None):
## TODO: raise exception if _writeArbdPotentialFiles has not been called
filename = "%s.bd" % prefix
@@ -859,10 +859,10 @@ class ArbdModel(PdbModel):
# params['coordinateFile'] = "%s.coord.txt" % prefix
params['particleFile'] = "%s.particles.txt" % prefix
- if restartCoordinateFile is None:
+ if restart_file is None:
params['restartCoordinates'] = ""
else:
- params['restartCoordinates'] = "restartCoordinates %s" % restartCoordinateFile
+ params['restartCoordinates'] = "restartCoordinates %s" % restart_file
params['outputPeriod'] = outputPeriod
for k,v in zip('XYZ', self.dimensions):
--
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