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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

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