soft:siman:md
cl = db[...] cl.res(show = 'xcarts.md_geo') #or cl.res(show = 'xcarts.md_geo.npt') # for npt cl.end.list_xcart - trajectory cl.list_etotal - energy per each MD step (kinetic + potential) cl.end.list_rprimd - list of vectors cl.list_stress - list of stress tensors
create new folder md and create in it md_analysis.py
write your functions in md_analysis.py
def mean_average(cl): cl.end.list_rprimd - list of vectors cl.end.list_xcart - trajectory cl.list_etotal - energy per each MD step
in class siman.core.calculation.Calculation add new method
def mean_average(self): from md.md_analysis import mean_average return mean_average(self)
Example of exerpt from OUTCAR
% ion-electron TOTEN = -833.476737 see above
kinetic energy EKIN = 1.781019 kin. lattice EKIN_LAT= 0.025267 (temperature 99.11 K) nose potential ES = 0.000000 nose kinetic EPS = 0.000000 --------------------------------------------------- total energy ETOTAL = -831.670451 eV
soft/siman/md.txt · Last modified: 2025/03/19 16:44 by admin