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watermall

金虫 (小有名气)

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注册: 2005-11-27
专业: 固体无机化学

[交流] 【讨论】pwscf中建立晶体模型

因为pwscf没有像ms中的visualizer一样的可视化的建立晶体的模块，很多时候很不方便。
这里就来学习如何利用MS的visualizer进行晶体结构的输入。
下面是Input_PW中关于pwscf中的晶体系统的信息。
-------------------------------------------------------------------------------

  ibrav is the structure index:

ibrav       structure                celldm(2)-celldm(6)

   0       "free", see above                not used
   1       cubic P (sc)                   not used
   2       cubic F (fcc)                   not used
   3       cubic I (bcc)                   not used
   4       Hexagonal and Trigonal P       celldm(3)=c/a
   5       Trigonal R                   celldm(4)=cos(alpha)
   6       Tetragonal P (st)             celldm(3)=c/a
   7       Tetragonal I (bct)             celldm(3)=c/a
   8       Orthorhombic P                celldm(2)=b/a,celldm(3)=c/a
   9       Orthorhombic base-centered(bco) celldm(2)=b/a,celldm(3)=c/a
   10       Orthorhombic face-centered    celldm(2)=b/a,celldm(3)=c/a
   11       Orthorhombic body-centered    celldm(2)=b/a,celldm(3)=c/a
   12       Monoclinic P                   celldm(2)=b/a,celldm(3)=c/a,
                                             celldm(4)=cos(ab)
   13       Monoclinic base-centered       celldm(2)=b/a,celldm(3)=c/a,
                                             celldm(4)=cos(ab)
   14       Triclinic                      celldm(2)= b/a,
                                             celldm(3)= c/a,
                                             celldm(4)= cos(bc),
                                             celldm(5)= cos(ac),
                                             celldm(6)= cos(ab)

  For P lattices: the special axis (c) is the z-axis, one basal-plane
  vector (a) is along x, the other basal-plane vector (b) is at angle
  gamma for monoclinic, at 120 degrees for trigonal and hexagonal
  lattices, at 90 degrees for cubic, tetragonal, orthorhombic lattices

  sc simple cubic
  ====================
  a1 = a(1,0,0),  a2 = a(0,1,0),  a3 = a(0,0,1)

  fcc face centered cubic
  ====================
  a1 = (a/2)(-1,0,1),  a2 = (a/2)(0,1,1), a3 = (a/2)(-1,1,0).

  bcc body entered cubic
  ====================
  a1 = (a/2)(1,1,1),  a2 = (a/2)(-1,1,1),  a3 = (a/2)(-1,-1,1).

  simple hexagonal and trigonal(p)
  ====================
  a1 = a(1,0,0),  a2 = a(-1/2,sqrt(3)/2,0),  a3 = a(0,0,c/a).

  trigonal(r)
  ===================
  for these groups, the z-axis is chosen as the 3-fold axis, but the
  crystallographic vectors form a three-fold star around the z-axis,
  and the primitive cell is a simple rhombohedron. The crystallographic
  vectors are:
      a1 = a(tx,-ty,tz), a2 = a(0,2ty,tz), a3 = a(-tx,-ty,tz).
  where c=cos(alpha) is the cosine of the angle alpha between any pair
  of crystallographic vectors, tc, ty, tz are defined as
   tx=sqrt((1-c)/2), ty=sqrt((1-c)/6), tz=sqrt((1+2c)/3)

  simple tetragonal (p)
  ====================
   a1 = a(1,0,0),  a2 = a(0,1,0),  a3 = a(0,0,c/a)

  body centered tetragonal (i)
  ================================
   a1 = (a/2)(1,-1,c/a),  a2 = (a/2)(1,1,c/a),  a3 = (a/2)(-1,-1,c/a).

  simple orthorhombic (p)
  =============================
   a1 = (a,0,0),  a2 = (0,b,0), a3 = (0,0,c)

  bco base centered orthorhombic
  =============================
   a1 = (a/2,b/2,0),  a2 = (-a/2,b/2,0),  a3 = (0,0,c)

  face centered orthorhombic
  =============================
   a1 = (a/2,0,c/2),  a2 = (a/2,b/2,0),  a3 = (0,b/2,c/2)

  body centered orthorhombic
  =============================
   a1 = (a/2,b/2,c/2),  a2 = (-a/2,b/2,c/2),  a3 = (-a/2,-b/2,c/2)

  monoclinic (p)
  =============================
   a1 = (a,0,0), a2= (b*sin(gamma), b*cos(gamma), 0),  a3 = (0, 0, c)
  where gamma is the angle between axis a and b

  base centered monoclinic
  =============================
   a1 = (  a/2,       0,             -c/2),
   a2 = (b*cos(gamma), b*sin(gamma), 0),
   a3 = (  a/2,       0,                c/2),
  where gamma is the angle between axis a and b

  triclinic
  =============================
   a1 = (a, 0, 0),
   a2 = (b*cos(gamma), b*sin(gamma), 0)
   a3 = (c*cos(beta),  c*(cos(alpha)-cos(beta)cos(gamma))/sin(gamma),
         c*sqrt( 1 + 2*cos(alpha)cos(beta)cos(gamma)
                  - cos(alpha)^2-cos(beta)^2-cos(gamma)^2 )/sin(gamma) )
  where alpha is the angle between axis b and c
      beta is the angle between axis a and c
      gamm  is the angle between axis a and b
----------------------------------------------------------------------
下面以Si为例子
在MS中建立Si的元胞，show symmetry, 我们得到这样一些信息：primitive of face centered-cubic，转换到单胞
a=b=c=5.4307A,转换为原子单位，为：10.25a.u.。三个角为60度,元胞中有2个si原子
坐标分别为：
0 0 0
0.25 0.25 0.25
那么在pwscf中，输入&system部分
ibrav=  2, celldm(1) =10.25, nat=  2, ntyp= 1,
输入&electrons
ATOMIC_POSITIONS
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
========================================================================
下面以Al为例子，
在MS中建立Al的元胞，show symmetry，得到：primitive of face centered-cubic，转换到单胞，a=b=c=4.0495A，为7.64a.u.,三个角为60度.元胞中只有1个Al原子
坐标为：
0 0 0
&system
ibrav=  2, celldm(1) =7.64, nat=  1, ntyp= 1,
&electrons
ATOMIC_POSITIONS
Al 0.00 0.00 0.00
=========================================================================
下面以FeSi2为例子，
在MS中建立FeSi2元胞，show symmetry，得到：Tetragonal ，其中元胞内有Si原子，所以为Tetragonal I，ibrav=7，
a=b=2.684A，c=5.128A。celldm(1)=5.06,celldm(3)=1.9.
Fe 0 0 0
Si 0.5 0.5 0.27

=========================================================================
下面讨论如何建立Al的单原子线
Al晶体中，Al-Al的键长大约为2.385A，即为1.264a.u.，为了避免线与线直接的相互作用，把celldm(1)=12a.u.,那么celldm(3)=0.375
Al 0 0 0
=========================================================================

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