If you are using GitLab outside of the ILL, then you will need to use HTTPS and not SSH for clone/push/pull operations. SSH will work normally if you are using the VPN.

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):
# 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.
# 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):
unitCell[3:] = PI_2 - numpy.arcsin(unitCell[3:])
......@@ -280,8 +281,9 @@ class DCDConverter(Converter):
settings = collections.OrderedDict()
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['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['output_files'] = ('output_files', {'formats':["netcdf"]})
def initialize(self):
......@@ -343,7 +345,7 @@ class DCDConverter(Converter):
# 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.
self._snapshot(data={'time': t})
Markdown is supported
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment