diff --git a/arbdmodel/__init__.py b/arbdmodel/__init__.py index 92abb73aa8c921bbbd365097888c801317f81d36..ce41736bbdcdeb9c7831e56142f64c25907ca6c7 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):