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Format of input files (2)  

2011-08-19 20:32:00|  分类: Linux |  标签: |举报 |字号 订阅

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cell or vectors only defines the geometry of the cell, but not the location of atoms


It is recommanded that the cell parameters be used for input where possible as this ensures that symmetry can be used to accelerate optimisations.


3.  the internal coordinates of the atoms

The internal coordinates of the atoms can be given either in fractional or Cartesian form,  though the former is the more natural for a periodic system. Each line of input must contain at least the atom label followed by the coordinates, in which ever units. For example for the case of MgO:


fractional
Mg  core   0.0   0.0   0.0
O    core   0.5   0.5   0.5


Note that if the space group symmetry is to be given, then it is only necessary to specify the atoms of the asymmetric unit. Furthermore in any cases where a fractional coordinate is a recurring decimal,  such as 1/3,
then it is necessary to specify this value to six decimal places to be sure of it being recognised correctly as a special position.

如果下面要指定空间对称群, 这里只需指定非对称原子单元。进一步,如果给定的是循环小数,例如1/3,则必须指定6个空格来标识。

fractional
Mg   core   0.0   0.0   0.0
O     core   0.5   0.5   0.5
O     shel    0.5   0.5   0.5

不必特别指定原子数,或本小节的结束,这是由程序自动完成的,当程序发现紧接着的下面不是元素标识,或在在下一行开始处发现一个特别的字符。

坐标的选项:在z坐标指定后,可以增加相应的选项,他们是:(按顺序)
电荷
原子占位
离子半径(for  breathing shell model, default is 0.0)
3个表明几何位置变化的标识(1-变化,0-固定不变)

注意:几何变动标识只有在没有关键字规定几何变量时,才被读取。

因而,MgO的输入可以写为:

fractional
Mg   core   0.0   0.0   0.0   2.00000     1.0        0.0                    0  0  0
O     core   0.5   0.5   0.5   0.86902      1.0        0.0                    0  0  0
O     shel    0.5   0.5   0.5  -2.86902     1.0        0.0                    0  0  0

                                              电荷   占位   离子半径       变化标识

if we want to run a breathing shell calculation for MgO then the input might look like the following for a constant pressure run:

fractional
Mg   core   0.0   0.0   0.0           2.00000      1.0    0.0
O     core   0.5   0.5   0.5           0.86902      2.0    0.0
O     bshe   0.5   0.5   0.5          -2.86902     1.0    1.2

or for a mean field calculation of the energy of a 40/60  MgO/CaO material:

fractional
Mg    core    0.0   0.0   0.0        2.00000        0.4      0.0
Ca     core   0.0   0.0   0.0         2.00000         0.6     0.0
O       core   0.5   0.5   0.5         0.86902         1.0     0.0
O       shel   0.5    0.5   0.5       -2.86902         1.0     0.0




4. The space group symmetry can be specified either through:

space group number
or
standard Hermann-Mauguin symbol.

for MgO, either the following would be valid:

either the following would be valid:

space
225

or

space
FM3M

In general it is better to use the symbol rather than the number as the structure may be in a non-standard setting.


if the space option is absent, then GULP will assume that the structure is in P1 (i.e. no symmetry)


5. The origin option


origin option allows non-standard origins to be handled. The input for this option can take the form of a single integer (1 or 2) if you want to select one of the standard alternative origin settings.
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