Commit 945f40eb authored by eric pellegrini's avatar eric pellegrini

The time step is now part of the settings for DCD based converters

parent 13d3d99a
...@@ -229,7 +229,8 @@ class DCDFile(FortranBinaryFile, dict): ...@@ -229,7 +229,8 @@ class DCDFile(FortranBinaryFile, dict):
# This file was generated by CHARMM, or by NAMD > 2.5, with the angle # This file was generated by CHARMM, or by NAMD > 2.5, with the angle
# cosines of the periodic cell angles written to the DCD file. # cosines of the periodic cell angles written to the DCD file.
# This formulation improves rounding behavior for orthogonal cells # This formulation improves rounding behavior for orthogonal cells
# so that the angles end up at precisely 90 degrees, unlike acos(). # so that the angles end up at precisely 90 degrees, unlike acos().
# See https://github.com/MDAnalysis/mdanalysis/wiki/FileFormats for info
if numpy.all(abs(unitCell[3:]) <= 1): if numpy.all(abs(unitCell[3:]) <= 1):
unitCell[3:] = PI_2 - numpy.arcsin(unitCell[3:]) unitCell[3:] = PI_2 - numpy.arcsin(unitCell[3:])
else: else:
...@@ -280,8 +281,9 @@ class DCDConverter(Converter): ...@@ -280,8 +281,9 @@ class DCDConverter(Converter):
settings = collections.OrderedDict() settings = collections.OrderedDict()
settings['pdb_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','CHARMM','2vb1.pdb')}) settings['pdb_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','CHARMM','2vb1.pdb')})
settings['dcd_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','CHARMM','2vb1.dcd')}) settings['dcd_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','CHARMM','2vb1.dcd')})
settings['output_files'] = ('output_files', {'formats':["netcdf"]}) settings['time_step'] = ('float', {'default':1.0,'label':"Time step (ps)"})
settings['fold'] = ('boolean', {'default':False,'label':"Fold coordinates in to box"}) settings['fold'] = ('boolean', {'default':False,'label':"Fold coordinates in to box"})
settings['output_files'] = ('output_files', {'formats':["netcdf"]})
def initialize(self): def initialize(self):
""" """
...@@ -343,7 +345,7 @@ class DCDConverter(Converter): ...@@ -343,7 +345,7 @@ class DCDConverter(Converter):
self._universe.foldCoordinatesIntoBox() self._universe.foldCoordinatesIntoBox()
# The current time. # The current time.
t = (index+1)*self.configuration["dcd_file"]["instance"]['time_step'] t = (index+1)*self.configuration["time_step"]["value"]
# Store a snapshot of the current configuration in the output trajectory. # Store a snapshot of the current configuration in the output trajectory.
self._snapshot(data={'time': t}) self._snapshot(data={'time': t})
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment