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wanghan-iapcmwanghan-iapcm
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feat: support virial in qe/traj (#859)
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‎dpdata/qe/traj.py

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@@ -11,6 +11,8 @@
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if TYPE_CHECKING:
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from dpdata.utils import FileType
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import os
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from ..unit import (
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EnergyConversion,
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ForceConversion,
@@ -20,6 +22,7 @@
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ry2ev = EnergyConversion("rydberg", "eV").value()
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kbar2evperang3 = PressureConversion("kbar", "eV/angstrom^3").value()
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gpa2evperbohr = PressureConversion("GPa", "eV/bohr^3").value()
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length_convert = LengthConversion("bohr", "angstrom").value()
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energy_convert = EnergyConversion("hartree", "eV").value()
@@ -228,6 +231,29 @@ def to_system_data(input_name, prefix, begin=0, step=1):
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)
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except FileNotFoundError:
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data["cells"] = np.tile(cell, (data["coords"].shape[0], 1, 1))
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# handle virial
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stress_fname = prefix + ".str"
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if os.path.exists(stress_fname):
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# 1. Read stress tensor (in GPa) for each structure
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stress, vsteps = load_data(stress_fname, 3, begin=begin, step=step, convert=1.0)
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if csteps != vsteps:
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csteps.append(None)
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vsteps.append(None)
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for int_id in range(len(csteps)):
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if csteps[int_id] != vsteps[int_id]:
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break
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step_id = begin + int_id * step
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raise RuntimeError(
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f"the step key between files are not consistent. "
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f"The difference locates at step: {step_id}, "
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f".pos is {csteps[int_id]}, .str is {vsteps[int_id]}"
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)
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# 2. Calculate volume from cell. revert unit to bohr before taking det
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volumes = np.linalg.det(data["cells"] / length_convert).reshape(-1)
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# 3. Calculate virials for each structure, shape [nf x 3 x 3]
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data["virials"] = gpa2evperbohr * volumes[:, None, None] * stress
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return data, csteps
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‎tests/qe.traj/si.wrongstr/si.cel

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20 0.00241888
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10.64076206 0.00000000 0.00000000
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0.00000000 10.64076206 0.00000000
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0.00000000 0.00000000 10.64076206
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30 0.00362833
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10.64076206 0.00000000 0.00000000
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0.00000000 10.64076206 0.00000000
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0.00000000 0.00000000 10.64076206

‎tests/qe.traj/si.wrongstr/si.evp

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# nfi time(ps) ekinc T_cell(K) Tion(K) etot enthal econs econt Volume Pressure(GPa) EXX EVDW
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20 2.418884E-03 2.666551E-08 0.000000E+00 1.400063E-01 -45.33322432 -45.33322432 -45.33321900 -45.33321908 1.204809E+03 0.27729
3+
30 3.628326E-03 8.130638E-08 0.000000E+00 3.362418E-01 -45.33323102 -45.33323102 -45.33321824 -45.33321907 1.204809E+03 0.27691

‎tests/qe.traj/si.wrongstr/si.for

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20 0.00241888
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0.79213120739417E-03 0.17846941660539E-02 0.25659395900843E-02
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0.12296860773369E-02 -0.17575294070971E-02 -0.12077752684736E-02
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0.53449804771536E-03 0.15716728646909E-02 0.11885992380187E-02
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-0.20546369136946E-02 -0.31469738318253E-03 -0.13292260295548E-02
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0.92996278884107E-03 -0.19904509183874E-02 -0.94000783512887E-03
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0.25825132715153E-02 -0.17883694381162E-02 0.11238432666008E-02
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0.63315248883314E-03 0.14328752516010E-02 -0.24575206497776E-02
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-0.77380112683612E-03 -0.11964478769743E-02 0.14594402556008E-02
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30 0.00362833
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0.79771922134157E-03 0.17499394041424E-02 0.25186776447507E-02
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0.12196024429585E-02 -0.17540520532661E-02 -0.12026567384908E-02
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0.55342117414254E-03 0.15344688593791E-02 0.11794075108087E-02
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-0.20168463577813E-02 -0.33437869352471E-03 -0.13161886410156E-02
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0.92254287169080E-03 -0.19521664753444E-02 -0.92530766852405E-03
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0.25425245627026E-02 -0.17646733377723E-02 0.11236784179976E-02
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0.62964311964633E-03 0.14348901801160E-02 -0.24175435226922E-02
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-0.77656387976694E-03 -0.11736525993363E-02 0.14442073730829E-02

‎tests/qe.traj/si.wrongstr/si.in

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&control
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calculation = 'cp'
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restart_mode = 'reset_counters'
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prefix = 'si'
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outdir = './outdir'
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pseudo_dir='./'
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nstep=3000
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iprint=10
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isave=100
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dt=5.0
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ndr=51, ndw=52 !folder for reading and writing
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tstress=.true., tprnfor=.true.
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!etot_conv_thr=1.d-9
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!ekin_conv_thr=1.d-7
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/
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&system
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ibrav=8,
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celldm(1)=10.6407620646
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celldm(2) = 1
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celldm(3) = 1
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nat=8
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ntyp=1
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ecutwfc=50
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ecutrho=400,
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nr1b=20, nr2b=20, nr3b=20 !For US PP specify no. of points for FFT of aug. Charge
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/
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&electrons
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electron_dynamics = 'verlet'
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electron_velocities = 'zero'
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emass=300
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orthogonalization='ortho'
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ortho_eps=1d-11
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/
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&ions
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ion_dynamics = 'verlet'
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ion_velocities='zero'
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ion_temperature='nose'
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fnosep=25.0
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tempw=40.0
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/
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ATOMIC_SPECIES
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Si 28.0855 Si.pbe-n-rrkjus_psl.1.0.0.UPF
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ATOMIC_POSITIONS (crystal)
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Si 0.0000 0.0000 0.000 1 1 1
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Si 0.0000 0.5000 0.5000 1 1 1
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Si 0.5000 0.5000 0.0000 1 1 1
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Si 0.5000 0.0000 0.5000 1 1 1
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Si 0.25000 0.2500 0.2500 1 1 1
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Si 0.25000 0.7500 0.7500 1 1 1
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Si 0.75000 0.7500 0.2500 1 1 1
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Si 0.75000 0.2500 0.7500 1 1 1

‎tests/qe.traj/si.wrongstr/si.pos

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20 0.00241888
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-0.55955613343180E-03 -0.13280468681160E-01 -0.12170559744533E-01
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-0.13498425299770E-01 0.53348556364374E+01 0.53265822820792E+01
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0.53177169488520E+01 0.53125521646402E+01 -0.13687957707679E-02
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0.53300642326909E+01 0.90214941469176E-04 0.53336756691314E+01
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0.26530964223874E+01 0.26670146882442E+01 0.26685063320998E+01
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0.26474643772774E+01 0.79813721194718E+01 0.79737688869610E+01
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0.79764012327704E+01 0.79748937809524E+01 0.26729378003260E+01
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0.79873283657577E+01 0.26616463190589E+01 0.79793202591917E+01
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30 0.00362833
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-0.52107908654115E-03 -0.13021934024520E-01 -0.11855267397130E-01
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-0.13404740927597E-01 0.53346716430867E+01 0.53264251309777E+01
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0.53177219927670E+01 0.53127844169680E+01 -0.12267029514939E-02
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0.53297463825603E+01 0.86918798429361E-04 0.53335032260915E+01
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0.26531522876578E+01 0.26668005206457E+01 0.26683824157731E+01
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0.26477271882324E+01 0.79811839520919E+01 0.79739025595218E+01
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0.79764197425739E+01 0.79751074086469E+01 0.26726239769995E+01
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0.79871718245254E+01 0.26615315288521E+01 0.79794965352588E+01

‎tests/qe.traj/si.wrongstr/si.str

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20 0.00241888
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0.27927908 -0.02926875 -0.02277043
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-0.02926875 0.27823138 0.03779023
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-0.02277043 0.03779026 0.27434825
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30 0.00362833
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0.27885067 -0.02827892 -0.02066094
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-0.02827892 0.27775865 0.03660021
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-0.02066094 0.03660025 0.27411244
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40 0.00362833
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0.27885067 -0.02827892 -0.02066094
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-0.02827892 0.27775865 0.03660021
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-0.02066094 0.03660025 0.27411244

‎tests/qe.traj/si/si.cel

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20 0.00241888
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10.64076206 0.00000000 0.00000000
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0.00000000 10.64076206 0.00000000
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0.00000000 0.00000000 10.64076206
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30 0.00362833
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10.64076206 0.00000000 0.00000000
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0.00000000 10.64076206 0.00000000
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0.00000000 0.00000000 10.64076206

‎tests/qe.traj/si/si.evp

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# nfi time(ps) ekinc T_cell(K) Tion(K) etot enthal econs econt Volume Pressure(GPa) EXX EVDW
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20 2.418884E-03 2.666551E-08 0.000000E+00 1.400063E-01 -45.33322432 -45.33322432 -45.33321900 -45.33321908 1.204809E+03 0.27729
3+
30 3.628326E-03 8.130638E-08 0.000000E+00 3.362418E-01 -45.33323102 -45.33323102 -45.33321824 -45.33321907 1.204809E+03 0.27691

‎tests/qe.traj/si/si.for

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20 0.00241888
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0.53449804771536E-03 0.15716728646909E-02 0.11885992380187E-02
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-0.20546369136946E-02 -0.31469738318253E-03 -0.13292260295548E-02
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-0.77380112683612E-03 -0.11964478769743E-02 0.14594402556008E-02
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30 0.00362833
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0.79771922134157E-03 0.17499394041424E-02 0.25186776447507E-02
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0.12196024429585E-02 -0.17540520532661E-02 -0.12026567384908E-02
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0.55342117414254E-03 0.15344688593791E-02 0.11794075108087E-02
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-0.20168463577813E-02 -0.33437869352471E-03 -0.13161886410156E-02
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-0.77656387976694E-03 -0.11736525993363E-02 0.14442073730829E-02

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