I am new to DFT calculation and I want to compute DFT total energy and atomic forces of an atomic configuration, given the atomic positions and lattice vectors.
I have an extended xyz with DFT energy and forces from a paper. XYZ file is pasted at the end of the question.
My goal is to do my own DFT calculation using the atomic position information and reproduce the energy and forces data. However, I haven't been able to do so.
In the paper, the authors used VASP with PBE exchange-correlation function, 500 eV energy cutoff, and 4x4x4 grid points. I don't have access to VASP, and I was trying to do the calculation using quantum espresso. With my initial attempt, the atomic forces that I got differed by about 1e-2 eV/angstrom, but the energy that I got was about -16,000 eV vs -500 in the paper/xyz file.
I don't know why my energy is off by a lot, while the forces are pretty close. Is this an expected behavior from comparing calculations using 2 different DFT software? Is there another way to compute DFT total energy and forces given xyz file?
Note: I used quantum espresso calculator in ASE to do the calculation.
Code
from ase.io import read
from ase.calculators.espresso import Espresso
# Read the xyz file
atoms = read("inst_cubic_diamond_temp300_strain0.0_step1001.xyz", format="extxyz")
# Calcualtor
calc = Espresso(
pseudopotentials={"C": "C.pbe-n-kjpaw_psl.1.0.0.UPF"},
tstress=True,
tprnfor=True,
outdir=<outdir>,
pseudo_dir=<pseudo_dir>,
kpts=(4, 4, 4),
koffset=True,
)
atoms.calc = calc
# Compute energy and forces
energy = atoms.get_potential_energy()
print("Energy:", energy)
forces = atoms.get_forces()
XYZ file
64
Lattice="7.10842262195238 0 0 0 7.10842262195238 0 0 0 7.10842262195238 " PBC="1 1 1" Properties=species:S:1:pos:R:3:force:R:3 Energy="-512.86187833"
C 2.515720524176340e-02 3.867550579089600e-03 7.089434672581682e+00 -5.37951000e-01 -9.43653100e-01 8.96908860e-01
C 1.776933986593727e+00 1.732049273644261e+00 2.572083207130320e-02 4.26181090e-01 1.51736004e+00 3.81343080e-01
C 7.082577532701300e+00 1.802144789342045e+00 1.769809143517475e+00 1.13683654e+00 -6.10598840e-01 7.06415680e-01
C 1.730755114222064e+00 7.103866760858615e+00 1.834766904598202e+00 5.28662040e-01 3.17688010e-01 -1.12025143e+00
C 8.721281061942280e-01 8.735364979679285e-01 8.966439895472150e-01 1.05603720e-01 2.62228850e-01 5.75211080e-01
C 2.696528798085684e+00 2.679314544279508e+00 9.295221501861438e-01 -7.81283670e-01 -5.78397410e-01 -1.85532276e+00
C 9.346490289165925e-01 2.672186644581529e+00 2.654060735574339e+00 -2.03034942e+00 1.70433750e-01 -3.59527500e-02
C 2.678101420875179e+00 9.199713446381380e-01 2.689016972481999e+00 -6.26726520e-01 -1.33007226e+00 1.56036970e-01
C 3.511187368839771e+00 7.101188022878494e+00 7.107915220793385e+00 9.31579400e-02 -4.02755650e-01 8.05187710e-01
C 5.312681026669824e+00 1.769173081861437e+00 7.067010726921535e+00 6.70675890e-01 -1.36012410e-01 1.35187542e+00
C 3.546168769563506e+00 1.802083870160192e+00 1.830411431890475e+00 8.04017590e-01 -7.92153530e-01 -1.76726650e+00
C 5.379223112984097e+00 3.912248340524160e-02 1.782229477108722e+00 -2.47505791e+00 -2.16700570e-01 -5.76459000e-03
C 4.425585354722698e+00 8.827204378245163e-01 8.970133431865501e-01 2.16665110e-01 8.11297010e-01 -2.73793900e-01
C 6.213865521165564e+00 2.672265050483028e+00 8.666035823024164e-01 2.11940450e-01 -9.71874700e-02 -3.56909090e-01
C 4.454692212824812e+00 2.667208331883838e+00 2.664322099047440e+00 1.78292390e-01 3.44728770e-01 2.32568650e-01
C 6.202805881832237e+00 9.258737522764287e-01 2.730940032231068e+00 4.33003680e-01 5.79964000e-02 -1.57874570e+00
C 3.423771754923000e-03 3.576000047014824e+00 7.096407537582318e+00 7.40474130e-01 -4.69554600e-01 5.82278100e-02
C 1.773121668458395e+00 5.291121536284495e+00 7.096664293807353e+00 5.47373550e-01 2.29641219e+00 -6.93962180e-01
C 7.061366710445481e+00 5.370766791266893e+00 1.766795669916178e+00 1.08575565e+00 -1.16270741e+00 -3.20823180e-01
C 1.783560955749675e+00 3.595632230775192e+00 1.744914310154615e+00 -1.61832200e-02 -1.34411611e+00 6.86037350e-01
C 9.147487865392240e-01 4.470236769241776e+00 8.314481673929444e-01 -1.97196630e+00 -7.49626810e-01 2.35244402e+00
C 2.602983378091007e+00 6.204381819127091e+00 9.149161188076987e-01 1.82101717e+00 -1.18240660e-01 -3.90261780e-01
C 7.917225343283958e-01 6.245417605564732e+00 2.701292578588703e+00 2.03609908e+00 -3.15842450e-01 -7.80305460e-01
C 2.658791177575270e+00 4.409512997926200e+00 2.662736565382049e+00 6.59346630e-01 2.03379123e+00 -1.16759940e+00
C 3.571911211239574e+00 3.541409467366737e+00 7.066099498225877e+00 1.32691510e-01 8.00661400e-02 1.22032686e+00
C 5.332296008047452e+00 5.301607810249293e+00 7.096567761428173e+00 -7.19261300e-01 1.61148671e+00 5.60174190e-01
C 3.599161989111380e+00 5.298915424097742e+00 1.755959945895381e+00 -1.45534256e+00 1.23807627e+00 5.26815840e-01
C 5.343400430443285e+00 3.555400122598969e+00 1.724019670536935e+00 -7.94688100e-02 -1.22034087e+00 1.68260656e+00
C 4.495938763993136e+00 4.410190288433433e+00 8.644839217613586e-01 -1.90959096e+00 6.98633670e-01 -3.14938090e-01
C 6.177803853456268e+00 6.250621184175251e+00 8.693900128852301e-01 1.68162569e+00 -6.84345710e-01 1.99048910e-01
C 4.467966552309626e+00 6.254770441542771e+00 2.656286880286244e+00 -7.57695100e-02 -1.03345062e+00 -3.54654490e-01
C 6.207880087151072e+00 4.401281444532239e+00 2.639561757040551e+00 7.66324170e-01 1.46387162e+00 -1.26064490e-01
C 7.092034222733816e+00 6.469645546521559e-02 3.611905542679158e+00 -3.69020620e-01 -1.32917779e+00 -7.38472440e-01
C 1.813401260897720e+00 1.798810015038325e+00 3.567437312210998e+00 -6.60443250e-01 1.25397500e-01 -5.29906640e-01
C 9.131195360747199e-03 1.777007203346713e+00 5.386779579481836e+00 1.49964985e+00 4.50847890e-01 -1.38667509e+00
C 1.762572342784958e+00 7.084367575685467e+00 5.258194825119071e+00 -1.44468190e-01 4.70378990e-01 2.27251762e+00
C 8.933156128238523e-01 9.138509927623180e-01 4.435922067475571e+00 2.19887730e-01 2.63211500e-01 6.47886620e-01
C 2.734726120286932e+00 2.672868982068823e+00 4.419541631642722e+00 -1.61252743e+00 -8.08281400e-02 1.02152425e+00
C 9.668444966470966e-01 2.659522421010190e+00 6.248003507545436e+00 -2.34920086e+00 -7.79319900e-02 -1.55410930e-01
C 2.621514609355990e+00 8.887661512628261e-01 6.206886542921475e+00 1.00247324e+00 -9.82742760e-01 2.23900990e-01
C 3.560229798179676e+00 1.192011389147800e-02 3.571414759003793e+00 -1.08340810e-01 -6.94958780e-01 -6.32829660e-01
C 5.303243173957251e+00 1.783785084314883e+00 3.608673698334975e+00 6.65906520e-01 1.93424360e-01 -2.00882610e-01
C 3.528356910667667e+00 1.767911834435971e+00 5.347927358304606e+00 7.39111180e-01 -2.47114860e-01 -1.04495492e+00
C 5.329030825201182e+00 7.096177437942109e+00 5.369101643268158e+00 -3.08175260e-01 -1.14381900e-02 1.84117730e-01
C 4.422761249499998e+00 8.668823746375728e-01 4.494489925294728e+00 3.83796370e-01 4.22127430e-01 -5.75045160e-01
C 6.241506267102304e+00 2.679197823980088e+00 4.509426711577681e+00 -9.90742090e-01 -1.47647882e+00 -1.25004513e+00
C 4.432864237317125e+00 2.645875244758956e+00 6.162178971863699e+00 2.14951310e-01 1.37021740e-01 2.03719183e+00
C 6.276550008692416e+00 8.743755050897671e-01 6.235059780796678e+00 -2.36728919e+00 4.92518030e-01 -1.75193300e-01
C 7.065680456712427e+00 3.515117189201012e+00 3.569630900347304e+00 2.01679955e+00 6.47574810e-01 -7.38426790e-01
C 1.744524484258135e+00 5.323755096101070e+00 3.489180474334740e+00 -2.31814270e-01 -5.78952010e-01 2.30748316e+00
C 7.087238738665912e+00 5.312598853304337e+00 5.367801939276317e+00 8.84590350e-01 6.63457880e-01 -2.04867967e+00
C 1.836661512479110e+00 3.526170004448624e+00 5.351513557516396e+00 -1.23618594e+00 5.61918680e-01 -1.49124744e+00
C 8.644019616485500e-01 4.381350493769153e+00 4.431205771235654e+00 6.54489790e-01 1.65426557e+00 5.88371370e-01
C 2.638706329462460e+00 6.199561100158887e+00 4.412298788750978e+00 5.65976410e-01 3.85331420e-01 -6.55854390e-01
C 8.855542105019791e-01 6.193752239362274e+00 6.199043180486793e+00 4.21980700e-01 3.69641240e-01 2.30177540e-01
C 2.676275196019875e+00 4.452567718556373e+00 6.202611111052449e+00 5.14470800e-01 -6.82406950e-01 -3.64222200e-02
C 3.579314420145626e+00 3.572309993748555e+00 3.522390171804665e+00 1.20915900e-02 -5.19302820e-01 8.08118950e-01
C 5.377902368061301e+00 5.343446208684958e+00 3.488438141760533e+00 -1.17684527e+00 1.56643050e-01 2.46875405e+00
C 3.545122765174973e+00 5.343271341488506e+00 5.291750347349461e+00 3.51595720e-01 -8.43737200e-01 5.14030800e-01
C 5.342069378307690e+00 3.526753748114178e+00 5.351913690625676e+00 -3.28223650e-01 2.01570343e+00 -1.31587457e+00
C 4.480059756291901e+00 4.450995690893960e+00 4.393124174154658e+00 -6.06505570e-01 2.54363480e-01 8.42964100e-01
C 6.221970331384210e+00 6.256644790419212e+00 4.501010623532506e+00 3.77290300e-02 -1.34160519e+00 -1.84268948e+00
C 4.403452996558423e+00 6.178451075335819e+00 6.250501549422556e+00 6.40125260e-01 1.35140560e+00 -1.06078985e+00
C 6.211810831607253e+00 4.482924592776214e+00 6.216467417097163e+00 8.36191500e-02 -2.43405957e+00 4.62511060e-01
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