simulate

(1) spipy.simulate.sim

+ work_dir:str

+ config_default:dict

+ :void = generate_config_files (pbd_file:str, #workdir:str/None, #params:dict/{})

+ :void = run_simulation()

• parameters : refer to Example
  • "parameters|detd" : distance between sample and detector [unit : mm]
  • "parameters|lambda" : wave length of laser [unit : angstrom]
  • "parameters|detsize" : detector size in width/height [unit : pixel]
  • "parameters|pixsize" : pixel size of detector [unit : mm]
  • "parameters|stoprad" : radius of a circle region at the center of pattern that to be masked out [unit : pixel]
  • "parameters|polarization" : correction due to incident beam polarization, value from 'x', 'y' or 'none'
  • "make_data|num_data" : how many patterns do you want to generate
  • "make_data|fluence" : laser fluence [unit : photons/pulse], usually 1e10 ~ 1e14 is reasonable for most situations

--

• work_dir : directory you project locates

--

• config_default : default configuration parameters, a dict:

         {'parameters|detd' : 200, 'parameters|lambda' : 2.5,
         'parameters|detsize' : 128, 'parameters|pixsize' : 0.3,
         'parameters|stoprad' : 0, 'parameters|polarization' : 'x',
         'make_data|num_data' : 100, 'make_data|fluence' : 1e14}

--

• generate_config_files : configure simulation parameters, make project dir and copy neccessary files to your work_dir, NO return
  • pdb_file : path of your pdb file used in simulation [/..../xx.pdb]
  • #workpath : choose a path to set up your project, ABSOLUTE PATH ! default is current dir
  • #name : give your project a name, default is None, program will choose a name for you
  • #params : parameters dict, { "section_1|param_1": value_1, ... }, for default program will use 'config_default'

--

• run_simulation : start simulation after configuing, NO return
  • NO input