prepare chapter 5

chapter-5-transport/README.md

@@ -1,29 +1,12 @@
-# phonon-dos-matlab
-A 20-line MATLAB function for calculating phonon density of states from velocity data
 
-* This code can be used to obtain the phonon density of states (PDOS) from velocity data obtained from molecular dynamics simulation:
- * First, the normalized velocity autocorrelation function (VACF) is calculated from the velocity data.
- * Then, the PDOS is calculated from the normalized VACF by discrete cosine tranform.
+# 《分子动力学模拟入门》第五章：输运性质的分子动力学模拟
 
-* The orignianl reference for this method is
- * [1] J. M. Dickey and A. Paskin, Computer Simulation of the Lattice Dynamics of Solids, Phys. Rev. 188, 1407 (1969).
-* For more backgrounds, see section 3.8 of the manual of the GPUMD code (https://github.com/brucefan1983/GPUMD).
 
-## File organizations
+# Table of contents
+- [时间关联函数](#时间关联函数)
+- [线性响应理论](#线性响应理论)
+ - [扩散系数](#扩散系数)
+ - [粘滞系数](#粘滞系数)
+ - [热导率](#热导率)
 
-* There is a single Matlab function in the `find_pdos.m` file:
- * `[vacf_output,pdos]=find_pdos(v_all,Nc,dt,omega)`
 
-* Inputs of the function 
- * `v_all`: all the velocity data, which is an `N*3*Nf` matlab array. Here, `N` is the number of atoms, `3` refers to the space dimension, and `Nf` is the number of velocity frames. The units of the velocity data are not important.
- * `Nc`: number of correlation steps.
- * `dt`: time interval between two velocity frames, in units of ps. The maximum correlation time is then `dt*Nc`.
- * `omega`: the `Nw` phonon angular frequency points you want to consider in units of THz, which can be a `1*Nw` or `Nw*1` array.
-
-* Outputs of the function 
- * `vacf_output`: the normalized (dimensionless) VACF, which is a `1*Nc` array
- * `pdos`: the PDOS in units of 1/THz, which is a `Nw*1` array.
-
-## Contact
-
-* Zheyong Fan: brucenju(at)gmail.com; zheyong.fan(at)aalto.fi; zheyongfan(at)163.com

chapter-5-transport/diffusion/README.md

@@ -0,0 +1,29 @@
+# phonon-dos-matlab
+A 20-line MATLAB function for calculating phonon density of states from velocity data
+
+* This code can be used to obtain the phonon density of states (PDOS) from velocity data obtained from molecular dynamics simulation:
+ * First, the normalized velocity autocorrelation function (VACF) is calculated from the velocity data.
+ * Then, the PDOS is calculated from the normalized VACF by discrete cosine tranform.
+
+* The orignianl reference for this method is
+ * [1] J. M. Dickey and A. Paskin, Computer Simulation of the Lattice Dynamics of Solids, Phys. Rev. 188, 1407 (1969).
+* For more backgrounds, see section 3.8 of the manual of the GPUMD code (https://github.com/brucefan1983/GPUMD).
+
+## File organizations
+
+* There is a single Matlab function in the `find_pdos.m` file:
+ * `[vacf_output,pdos]=find_pdos(v_all,Nc,dt,omega)`
+
+* Inputs of the function 
+ * `v_all`: all the velocity data, which is an `N*3*Nf` matlab array. Here, `N` is the number of atoms, `3` refers to the space dimension, and `Nf` is the number of velocity frames. The units of the velocity data are not important.
+ * `Nc`: number of correlation steps.
+ * `dt`: time interval between two velocity frames, in units of ps. The maximum correlation time is then `dt*Nc`.
+ * `omega`: the `Nw` phonon angular frequency points you want to consider in units of THz, which can be a `1*Nw` or `Nw*1` array.
+
+* Outputs of the function 
+ * `vacf_output`: the normalized (dimensionless) VACF, which is a `1*Nc` array
+ * `pdos`: the PDOS in units of 1/THz, which is a `Nw*1` array.
+
+## Contact
+
+* Zheyong Fan: brucenju(at)gmail.com; zheyong.fan(at)aalto.fi; zheyongfan(at)163.com