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单位

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能量     1 a.u. = 1 Hartree
质量 1 a.u. = 1 m_e (电子质量)
长度 1 a.u. = 1 Bohr (Bohr半径,a_0)
电量 1 a.u. = 1 e = 1.6022^{-19} C (e= Elementary charge,电子电量的绝对值。原子电荷使用此单位)
电子密度 1 a.u. = 1 Bohr^{-3}
偶极矩 1 a.u. = 1 e*Bohr = 0.97174^22 V/m² = 2.5417462 Debye
静电势 1 a.u. = 1 Hartree/e
电场 1 a.u. = 1 Hartree/(Bohr*e) = 51.421 V/Ångström

轨道波函数无单位,死活非要写则 1 a.u. = 1 Bohr^{-3/2}
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1 Hartree (Ha或E_h) = 2625.500 kJ/mol = 627.51 kcal/mol
= 27.2113838 eV = 4.3597482E-18 J = 219474.6363 cm-1
= 等于两个电子相距 1 Bohr 的互斥能 = 两倍氢原子电离势
= 2 Rydberg (Ry)

1 eV = 96.485354 kJ/mol = 23.058731765 kcal/mol
= 1.602176462E-19 J = 8065.5447 cm-1

1 kcal =4.184 kJ
(1239.842/k) : nm 与 eV 转换
(45.5633/k) : nm 与 Hartree 转换
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1 Bohr = 0.529177210903 Ångström
1 Ångström(埃,Å) = 1*10^{-10} m = 0.1 nm
1 nm= 10 Ångström = 1*10^{-9} m

注:碳的共价半径为 0.76 Å,范德华半径为 1.7 Å

vasp

geo opt

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bader 电荷

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mkdir chg
cp KPOINTS POTCAR chg/
cp CONTCAR chg/
cp ../INCAR_CHG chg/INCAR
cp ../sub.vasp chg/
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chgsum.pl AECCAR0 AECCAR2
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bader CHGCAR -ref CHGCAR_sum

dos

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mkdir dos
cp CONTCAR dos/POSCAR
cp KPOINTS POTCAR WAVECAR CHGCAR dos/
cp ../INCAR_DOS dos/INCAR
cp ../sub.vasp dos/
  • 用 python 绘图
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# iil:
# conda install -n chem_py39 pymatgen
#
def get_element_d_pdos(e_num:int, f_name:str, x_lim:tuple, y_lim:tuple,
lb_loc:str = "upper right", lb_fontsize:str = "xx-large",
lb_borderpad:int = 0.3, lb_labelspacing:int = 0.3,
lb_handlelength:int = 1.8, lb_handletextpad:int = 0.6) -> None:
"""
Args:
e_num:int :in CONTCAR
lb_loc:str :xx-small, x-small, small, medium, large, x-large, xx-large
"""
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.electronic_structure.plotter import DosPlotter
from pymatgen.electronic_structure.core import Orbital

dos_vasprun = Vasprun("./vasprun.xml")
complete_dos = dos_vasprun.complete_dos

periodic_site = complete_dos.structure.sites[e_num]
pdos_dxy = complete_dos.get_site_orbital_dos(periodic_site, Orbital.dxy)
pdos_dyz = complete_dos.get_site_orbital_dos(periodic_site, Orbital.dyz)
pdos_dxz = complete_dos.get_site_orbital_dos(periodic_site, Orbital.dxz)
pdos_dz2 = complete_dos.get_site_orbital_dos(periodic_site, Orbital.dz2)
pdos_dx2_y2 = complete_dos.get_site_orbital_dos(periodic_site, Orbital.dx2)

plt_d = DosPlotter(stack=False)
plt_d.add_dos("dxy", pdos_dxy)
plt_d.add_dos("dyz", pdos_dyz)
plt_d.add_dos("dxz", pdos_dxz)
plt_d.add_dos("dz2", pdos_dz2)
plt_d.add_dos("dx2-y2", pdos_dx2_y2)

axes = plt_d.get_plot(xlim=x_lim, ylim=y_lim)

handles, labels = axes.get_legend_handles_labels()
unique_dict = {label: handle for handle, label in zip(handles, labels)}
unique_handles = list(unique_dict.values())
unique_labels = list(unique_dict.keys())

axes.legend(
unique_handles, unique_labels, loc = lb_loc, fontsize = lb_fontsize,
borderpad = lb_borderpad, labelspacing = lb_labelspacing,
handlelength = lb_handlelength, handletextpad = lb_handletextpad
)

fig = axes.get_figure()
fig.savefig(f_name, dpi = 300)

return



if __name__ == "__main__":
get_element_d_pdos(121, "Ru_d_pdos.png", (-2, 5), (-8.5, 8))
get_element_d_pdos(122, "La_d_pdos.png", (-10, 10), (-2.5, 3.5))

DIMER

  • 行数保持一致
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modemake.pl r1_CONTCAR POSCAR
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less DIMCAR
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dimmode.pl CENTCAR NEWMODECAR 32 0.5
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grep converged OUTCAR

CINEB

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dist.pl r1_CONTCAR r2_CONTCAR
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nebmake.pl r1_CONTCAR r2_CONTCAR 1
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python iddp.py r1_CONTCAR r2_CONTCAR 1
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cp r1_OUTCAR 00/OUTCAR
cp r2_OUTCAR 02/OUTCAR
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nebmovie.pl 0
cat 00/POSCAR.xyz 01/POSCAR.xyz 02/POSCAR.xyz 03/POSCAR.xyz 04/POSCAR.xyz > movie.xyz
  • 预收敛
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nebresults.pl
gunzip 0*/OUTCAR.gz
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neb2dim.pl

freq

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mkdir freq
cp KPOINTS POTCAR freq/
cp CONTCAR freq/POSCAR
cp 01/CONTCAR freq/POSCAR
cp ../INCAR_FREQ freq/INCAR
cp ../sub.vasp freq/
sh
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vaspkit
402

vmd

  • cpk, position Z

1753163596808

  • 正交视角

1753163910018

  • rep Hbonds

1753164730559

  • -X image

1753164964198

  • 不同区域显示

1753173092209

  • 第一帧和最后一帧叠加

1753173263163

VESTA

  • 旋转晶格

1753171471942

  • 自定义等值面数值

1753866364832

MS

  • 左边小窗口