python ovito模块计算某一类原子的MSD均方位移

 此文章为用python ovito模块计算某一类原子的MSD

ovito.modifiers.CalculateDisplacementsModifier 基于ovito.pipline.ReferenceConfigurationModifier

ovito GUI界面 Affine mapping of simulation cell 三个选项 Off，To reference, To current分别对应
Off          --> ReferenceConfigurationModifier.AffineMapping.Off
To reference --> ReferenceConfigurationModifier.AffineMapping.TOReference
To current   --> ReferenceConfigurationModifier.AffineMapping.ToCurrent

Default: ReferenceConfigurationModifier.AffineMapping.Off

即下图红框中所示：

ovito GUI 界面 Use minimum image convention对应：minimum_image_convention
若GUI界面勾选，则为：minimum_image_convention=True，
若不勾选则为：minimum_image_convention=False。
Default： True

ovito GUI界面 Reference animation frame 选项下： 1.Constant reference configuration
                                                2.relative to current frame
use_frame_offset=False 则对应 Constant reference configuration，
使用reference_frame 设定所需要的值(Defalut值为0)
use_frame_offset=True，则对应relative to current frame，
使用frame_offset设定值(Default值为-1)

若使用relative to current frame时，使用python脚本输出文件第一帧（因为frame=0）会报错，需要从第二帧开始

ovito GUI界面Reference configuration source下External file

来自ovito 手册关于python部分:

ovito.pipline.ReferenceConfigurationModifier

# The modifier that requires a reference config:
mod = CalculateDisplacementsModifier()
 
# Load the reference config from a separate input file.
mod.reference = FileSource() # Note: You may have to import FileSource from the ovito.pipeline module. 
mod.reference.load('input/simulation.0.dump')

from ovito.io import import_file, export_file
from ovito.modifiers import CalculateDisplacementsModifier, SelectTypeModifier, DeleteSelectedModifier
from ovito.pipeline import ReferenceConfigurationModifier

import numpy

pipeline = import_file("dump.shear1")

# CalculateDisplacementsModifier 是基于 ovito.pipline.ReferenceConfigurationModifier

# 在ovito GUI界面 Affine mapping of simulation cell 三个选项 Off，To reference, To current分别对应
# ReferenceConfigurationModifier.AffineMapping.Off
# ReferenceConfigurationModifier.AffineMapping.TOReference
# ReferenceConfigurationModifier.AffineMapping.ToCurrent
# Default: ReferenceConfigurationModifier.AffineMapping.Off

# Use minimum image convention对应：minimum_image_convention
# 若GUI界面勾选，则为True，若不勾选则为False
# Default：True

# 关于Reference animation frame 选项下 1.Constant reference configuration
#                                    2.relative to current frame
# use_frame_offset 若为False(Default值)则为Constant reference configuration，
# 使用reference_frame 设定所需要的值(Defalut值为0)
# 若为True，则为relative to current frame，使用frame_offset设定值(Default值为-1)
# 若使用relative to current frame时，输出文件第一帧（因为frame=0）会报错，需要从第二帧开始

# 若使用Reference configuration source下External file
'''
# The modifier that requires a reference config:
mod = CalculateDisplacementsModifier()
 
# Load the reference config from a separate input file.
mod.reference = FileSource() # Note: You may have to import FileSource from the ovito.pipeline module. 
mod.reference.load('input/simulation.0.dump')
'''

mod = CalculateDisplacementsModifier(
    affine_mapping=ReferenceConfigurationModifier.AffineMapping.Off,
    minimum_image_convention=True,
    use_frame_offset=True
)

# 下列为选择所需要的原子种类
sat = SelectTypeModifier(property="Particle Type",
                         types={'Type 1', 'Type 2', 'Type 3', 'Type 4', 'Type 5', 'Type 6', 'Type 7', 'Type 8'})
pipeline.modifiers.append(sat)

# 删除所勾选的原子种类，剩下所需要计算的原子种类
pipeline.modifiers.append(DeleteSelectedModifier())

pipeline.modifiers.append(mod)


# ovito python手册 Code examples-->Example M1
def calculate_msd(frame, data):
    displacement_magnitudes = data.particles["Displacement Magnitude"]
    print(displacement_magnitudes[0])
    msd = numpy.sum(displacement_magnitudes ** 2) / len(displacement_magnitudes)
    data.attributes["MSD"] = msd


pipeline.modifiers.append(calculate_msd)

# 对输出文件更为精细的控制可通过 关键词： start_frame, end_frame, every_nth_frame实现
# ovito python手册中ovito.io下export_file()
export_file(pipeline, "output.txt", format="txt/attr", columns=["Timestep", "MSD"],
            multiple_frames=True, start_frame=1)