pwtools.crys.call_vmd_measure_gofr¶
- pwtools.crys.call_vmd_measure_gofr(trajfn, dr=None, rmax=None, sel=['all', 'all'], fntype='xsf', first=0, last=-1, step=1, usepbc=1, datafn=None, scriptfn=None, logfn=None, tmpdir=None, verbose=False)[source]¶
Call VMD’s “measure gofr” command. This is a simple interface which does in fact the same thing as the gofr GUI, only scriptable. Accepts a file with trajectory data.
Only orthogonal boxes are allowed (like in VMD).
- Parameters:
trajfn (filename of trajectory which is fed to VMD (e.g. foo.axsf))
dr (float) – dr in Angstrom
rmax (float) – Max. radius up to which minimum image nearest neighbors are counted. For cubic boxes of side length L, this is L/2 [AT,MD].
sel (list of two strings, optional) – string to select atoms, [“name Ca”, “name O”], [“all”, “all”], …, where sel[0] is selection 1, sel[1] is selection 2 in VMD
fntype (str, optional) – file type of fn for the VMD “mol” command
first (int, optional) – Select which MD steps are averaged. Like Python, VMD starts counting at 0. Last is -1, like in Python.
last (int, optional) – Select which MD steps are averaged. Like Python, VMD starts counting at 0. Last is -1, like in Python.
step (int, optional) – Select which MD steps are averaged. Like Python, VMD starts counting at 0. Last is -1, like in Python.
usepbc (int {1,0}, optional) – Whether to use the minimum image convention.
datafn (str, optional) – temp file where VMD results are written to and loaded
scriptfn (str, optional) – temp file where VMD tcl input script is written to
logfn (str, optional) – file where VMD output is logged
tmpdir (str, optional) – dir where auto-generated tmp files are written
verbose (bool, optional) – display VMD output
- Returns:
array (len(rad), 3), colums 0,1,2
rad (1d array) – radius (x-axis) with spacing dr, each value r[i] is the middle of a histogram bin
hist (1d array, (len(rad),)) – the function values g(r)
num_int (1d array, (len(rad),)) – the (averaged) number integral
number_density*hist*4*pi*r**2.0*dr