标准及扩展cfg文件格式简介

cfg是晶体学中非常常用的一种文件格式,很多可视化软件都支持,而且包含的信息量要比xyz文件格式要大,比如晶胞信息。

对于进行分子动力学,尤其是使用lammps进行分子动力学的筒子,我强烈推荐使用这种格式。

cfg格式主要包括两种:标准cfg格式和扩展cfg格式。两者略有不同。

1. 标准CFG格式

下面以一例简要介绍标准cfg格式。

Number of particles = 1727
# (required) this must be the first line
 A = 1.0 Angstrom (basic length-scale)
# (optional) basic length-scale: default A = 1.0 [Angstrom]
H0(1,1) = 32.5856986704313 A
H0(1,2) = 0 A
H0(1,3) = 0 A
# (required) this is the supercell's 1st edge, in A

H0(2,1) = 8.64689152483509e-16 A
H0(2,2) = 32.5856986704313 A
H0(2,3) = 0 A
# (required) this is the supercell's 2nd edge, in A

H0(3,1) = 8.64689152483509e-16 A
H0(3,2) = 8.64689152483509e-16 A
H0(3,3) = 32.5856986704313 A
# (required) this is the supercell's 3rd edge, in A
Transform(1,1) = 1
Transform(1,2) = 0
Transform(1,3) = 0
Transform(2,1) = 0
Transform(2,2) = 1
Transform(2,3) = 0
Transform(3,1) = 0
Transform(3,2) = 0
Transform(3,3) = 1
# (optional) apply additional transformation on H0:  H = H0 * Transform;
# default = Identity matrix.

eta(1,1) = 0
eta(1,2) = 0
eta(1,3) = 0
eta(2,2) = 0
eta(2,3) = 0
eta(3,3) = 0
# (optional) apply additional Lagrangian strain on H0:
# H = H0 * sqrt(Identity_matrix + 2 * eta);
# default = zero matrix.
# ENSUING ARE THE ATOMS, EACH ATOM DESCRIBED BY A ROW
# 1st entry is atomic mass in a.m.u.
# 2nd entry is the chemical symbol (max 2 chars)

# 3rd entry is reduced coordinate s1 (dimensionless)
# 4th entry is reduced coordinate s2 (dimensionless)
# 5th entry is reduced coordinate s3 (dimensionless)
# real coordinates x = s * H,  x, s are 1x3 row vectors

# 6th entry is d(s1)/dt in basic rate-scale R
# 7th entry is d(s2)/dt in basic rate-scale R
# 8th entry is d(s3)/dt in basic rate-scale R
R = 1.0 [ns^-1]
# (optional) basic rate-scale: default R = 1.0 [ns^-1]
28.0855 Si .0208333333333333 .0208333333333333 .0208333333333333 0 0 0
28.0855 Si .0625 .0625 .0625 0 0 0
28.0855 Si .0208333333333333 .104166666666667 .104166666666667 0 0 0
28.0855 Si .0625 .145833333333333 .145833333333333 0 0 0
28.0855 Si .104166666666667 .0208333333333333 .104166666666667 0 0 0
28.0855 Si .145833333333333 .0625 .145833333333333 0 0 0
....

其中的注释已经比较清楚,不做过多介绍。

需要强调的是,标准CFG格式中的数据列部分,必须包括原子坐标和速度,而不能包括其他属性,比如势能。

标准CFG格式例子下载:SiVacancy.cfg | Si_screw_dipole.cfg | Cu_NanoXtal.cfg.bz2

2. 扩展CFG格式

Number of particles = 16200
A = 4.37576470588235 Angstrom (basic length-scale)
H0(1,1) = 127.5 A
H0(1,2) = 0 A
H0(1,3) = 0 A
H0(2,1) = 0 A
H0(2,2) = 119.501132067411 A
H0(2,3) = 0 A
H0(3,1) = 0 A
H0(3,2) = 0 A
H0(3,3) = 3 A
.NO_VELOCITY.
entry_count = 11
auxiliary[0] = kine [reduced unit]
auxiliary[1] = pote [reduced unit]
auxiliary[2] = s11 [reduced unit]
auxiliary[3] = s22 [reduced unit]
auxiliary[4] = s12 [reduced unit]
auxiliary[5] = hydro [reduced unit]
auxiliary[6] = mises [reduced unit]
auxiliary[7] = Lmin [reduced unit]
1.000000
Ar
0.005 0.01232 0.5 0 -2.9819 0.79705 2.3326 0.022255 1.5648 0.76808 102.82
....

扩展CFG格式中,原子的速度已经不是必须的了,而且可以任意定义其他的原子属性,只要指定就可以。

扩展CFG格式例子下载:BubbleRaftBefore.cfg | BubbleRaftAfter1.cfg

3. CFG可视化软件

推荐的可视化软件为 atomeye,主要是在linux操作系统下。

可以参考博文:可视化软件atomeye简介、使用方法及常用快捷键

备注:本编大部分信息来自 李巨 的网站,表示感谢!

标签: 文件格式, lammps

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