stm-sim 0.5

An STM simulation python library.

stm_sim

An STM simulation python library from LDOS.

Installation

pip install -U stm-sim

Requirements

• ASE
• surface_construct
• Mayavi (optional)

Usage

from stm_sim.stm import STM
parchg_file = "PARCHG"
stm = STM(bias=(-0.1, 0.1))
stm.read_parchg(parchg_file)
x, y, z = stm.scan(scan_mode='constant_current', repeat=(2, 2), plot=True)

Parameters

• scan_mode: default is constant_current, support constant_height and constant_current
• repeat: repeat the simulated image along x,y axes
• plot: plot it with matplotlib or not, default is False
• startpoint: set the start point to find height can save time, used for scan_mode='constant_current'.
• height:
  • The height for scan_mode='constant_height'.
  • For scan_mode='constant_current', it is for the height of tip to obtain the average current: h_tip = height + 0.76, 0.76 is the radius of carbon.
    • For bottom=True, it use old get_avg_current_from_height.
• bottom: upper or bottom side of slab, default is False

TODO

• Export 2d data for external program plot.
• Generate INCAR for vasp task
• Support other program, like cp2k, fireball, fhi-aims, integrate multiwfn
• Use api design
• Autofocus method: height auto choose, current auto choose, bias auto choose
  • 使用傅立叶变换，目标是主频频率需要满足特定的规则，需要扩包；黑白要分明，最好对半分；高度差要在一个范围里面，用户可定义
  • 使用强化学习的方法，训练模型
  • 可能得到多个不同的图样，返回最大差异的图样
  • 默认频率的范围，用户可以手动确认
• 支持在台阶处的特殊处理