平时在计算时会用到python和julia,利用anaconda中的jupyter可以在浏览器中很方便的同时使用多种语言,在这里整理一下Anaconda的安装以及jupyter的使用.同时把一些平时计算用的最基本的东西也都整理到一起,算是对新手的一个指引,里面的内容不是很详细,我只是想介绍一下自己平时用到的软件还有编程语言的最基本的一些操作.
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软件下载

1.官网下载
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安装过程

1)在“Select Installation Type”界面的“Install for”中选择“All Users(requires admin privileges)”单选按钮

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2)在“Choose Install Location”界面中查看“Destination Folder”，可能为C:\ProgramData\Anaconda3，注意检查该路径不能包含非英文字符

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3)在“Advanced Installation Options”界面中选中“Register Anaconda as my default Python 3.6”复选框。

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建议这里不要选则将Anaconda增加到系统的环境变量中,增加太多会导致系统上的环境变量较为混乱.如果单独出来,后面对于Anaconda的包管理来说,也是较为简洁的,可以通过它自带的命令行来进行包管理.

4)安装完成后，开始==>所有程序中，出现文件夹anaconda3（64-bit）

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Anaconda包管理

  • 1.包更新升级

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    conda upgrade --all

  • 2.包安装

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    conda install numpy scipy pandas

    conda install numpy=1.10  安装指定版本的包

  • 3.包移除

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    conda remove package_name

    Jupyter使用

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VsCode使用

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Plotly

Installation

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pip install plotly==4.10.0

conda install -c plotly plotly=4.10.0

Jupyter Notebook Support

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conda install "notebook>=5.3" "ipywidgets>=7.2"

plot

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import plotly.graph_objects as go

# Valid color strings are CSS colors, rgb or hex strings
colorscale = [[0, 'gold'], [0.5, 'mediumturquoise'], [1, 'lightsalmon']]

fig = go.Figure(data =
    go.Contour(
        z=[[10, 10.625, 12.5, 15.625, 20],
           [5.625, 6.25, 8.125, 11.25, 15.625],
           [2.5, 3.125, 5., 8.125, 12.5],
           [0.625, 1.25, 3.125, 6.25, 10.625],
           [0, 0.625, 2.5, 5.625, 10]],
        colorscale=colorscale)
)
fig.show()

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体积图

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import plotly.graph_objects as go
import numpy as np
X, Y, Z = np.mgrid[-1:1:30j, -1:1:30j, -1:1:30j]
values =    np.sin(np.pi*X) * np.cos(np.pi*Z) * np.sin(np.pi*Y)

fig = go.Figure(data=go.Volume(
    x=X.flatten(),
    y=Y.flatten(),
    z=Z.flatten(),
    value=values.flatten(),
    isomin=-0.1,
    isomax=0.8,
    opacity=0.1, # needs to be small to see through all surfaces
    surface_count=21, # needs to be a large number for good volume rendering
    ))
fig.show()

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import plotly.graph_objects as go
import numpy as np
X, Y, Z = np.mgrid[-1:1:30j, -1:1:30j, -1:1:30j]
values =    np.sin(np.pi*X) * np.cos(np.pi*Z) * np.sin(np.pi*Y)

fig = go.Figure(data=go.Volume(
    x=X.flatten(),
    y=Y.flatten(),
    z=Z.flatten(),
    value=values.flatten(),
    isomin=-0.5,
    isomax=0.5,
    opacity=0.1, # max opacity
    opacityscale=[[-0.5, 1], [-0.2, 0], [0.2, 0], [0.5, 1]],
    surface_count=21,
    colorscale='RdBu'
    ))
fig.show()

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服务器程序编译执行

Linux基本命令

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ls or ls -al 显示当前文件夹中的所有文件
pwd  打印当前路径
mkdir f1 创建一个名为f1的文件夹
clear  清除中断显示的所有内容
cd /home 切换到根目录下的home文件夹,这个命令可以配合pwd使用,可以自己决定切换到哪一个目录,只要路径名称是正确的,其你是拥有文件的访问权限
vim te.f90  在终端打开te.f90文件
gedit te.f90  以图形界面的方式打开te.f90文件
diff  f1  f2  比较两个文件之间的差异
cat f1.f90  将文件名为f1.f90的内容全部打印到终端
tail -n f1.f90  将文件名为f1.f90倒数n行打印到终端
head -n f1.f90  将文件名为f1.f90前n行打印到终端

新手可以先在本地将程序写好之后传到服务器端进行编译运行,或者使用Xshell之后可以直接使用gedit在服务器端利用图形界面对代码进行直接修改,vim使用需要一定的学习.

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Fortran

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ifort -mkl t1.f90 -o output.x  编译t1.f90文件，生成可执行文件output.x

./output.x &  执行output.x 并放到后台执行

如果矩阵维数较大,需要加入额外的编译选项

ifort -mkl -mcmodel=large t1.f90 -o output.x  !-mcmodel=large 是为了让编译器可以接受维数更大的矩阵

ifort -mkl -O3 t1.f90 -o output.x  加入-O3选项可以让编译器对一些内容进行默认操作,文档说这是一种相对激进的编译选项,可以有一定速度提升

Cheevd

Module

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module pub
implicit none
integer xn,yn,ne
parameter(xn = 30,yn = 30,ne = 1000)
integer,parameter::N = xn*yn*8
integer::lda = N
integer,parameter::lwmax=2*N+N**2
real,allocatable::w(:)
complex*8,allocatable::work(:)
real,allocatable::rwork(:)
integer,allocatable::iwork(:)
integer lwork   ! at least 2*N+N**2
integer lrwork    ! at least 1 + 5*N +2*N**2
integer liwork   ! at least 3 +5*N
integer info
end module pub

对角化函数调用
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subroutine eigsol()
use pub
integer m
lwork = -1
liwork = -1
lrwork = -1
call cheevd('V','Upper',N,Ham,lda,w,work,lwork,rwork,lrwork,iwork,liwork,info)
lwork = min(2*N+N**2, int( work( 1 ) ) )
lrwork = min(1+5*N+2*N**2, int( rwork( 1 ) ) )
liwork = min(3+5*N, iwork( 1 ) )
call cheevd('V','Upper',N,Ham,lda,w,work,lwork,rwork,lrwork,iwork,liwork,info)
if( info .GT. 0 ) then
    open(11,file="mes.txt",status="unknown")
    write(11,*)'The algorithm failed to compute eigenvalues.'
    close(11)
end if
open(12,file="eigval.dat",status="unknown")
do m = 1,N
    write(12,*)m,w(m)
end do
close(12)
return
end subroutine eigsol

程序示例

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! Author:YuXuanLi
! E-Mail:yxli406@gmail.com
! Article:Majorana Corner Modes in a High-Temperature Platform
! Doi:10.1103/PhysRevLett.121.096803
!==========================================
    module param
    implicit none
    integer xn,yn,nkx,nky,ne,nkxy
    parameter(nkx=50,nky=50,ne=1000)
    integer,parameter::N = 4
    complex,parameter::im = (0.,1.) !Imagine unit
    real,parameter::pi = 3.14159265358979
    complex Ham(N,N) ! Hamiltonian Matrix
    real mu ! Chemical Potential
    real tx,ty  ! hopping term energy
    real ax,ay  ! copule energy
    real m0  !Driac mass
    real kx,ky
    ! LAPACK PACKAGE PARAM
    integer::lda = N
    integer,parameter::lwmax = 2*N+N**2
    real,allocatable::w(:)
    complex,allocatable::work(:)
    real,allocatable::rwork(:)
    integer,allocatable::iwork(:)
    integer lwork   ! at least 2*N+N**2
    integer lrwork    ! at least 1 + 5*N +2*N**2
    integer liwork   ! at least 3 +5*N
    integer info
    end module param
!========== PROGRAM START ==========================
    program sol
    use param
    integer m,l ! loop variales
    !================ Physics memory allocate =================
    allocate(w(N))
    allocate(work(lwmax))
    allocate(rwork(1+5*N+2*N**2))
    allocate(iwork(3+5*N))
    ! paramater set value
    m0 = 1.5   ! effective mass
    tx = 1.0   ! hopping energy in x direction
    ty = 1.0   ! hopping energy in y direction
    mu = 0.2   ! chemical potential
    ax = 1.0  ! couple energy in x direction
	  ay = 1.0  ! couple energy in y direction
    call band()
    stop
    end program
!===========================================================
    subroutine matrix_set()
    use param
    Ham = 0
    !----------------------------------------------
    Ham(1,1) = m0 - tx*cos(kx) - ty*cos(ky) + mu
    Ham(2,2) = -(m0 - tx*cos(kx) - ty*cos(ky)) + mu
    Ham(3,3) = m0 - tx*cos(kx) - ty*cos(ky) + mu
    Ham(4,4) = -(m0 - tx*cos(kx) - ty*cos(ky)) + mu
    !-----------------------------------------------
    Ham(1,2) = ax*sin(kx) - im*ay*sin(ky) 
    Ham(2,1) = ax*sin(kx) + im*ay*sin(ky) 
    Ham(3,4) = -ax*sin(kx) - im*ay*sin(ky) 
    Ham(4,3) = -ax*sin(kx) + im*ay*sin(ky) 
    !--------------------------------------------------
    call ishermitian()
    end subroutine matrix_set
!============================================================
    subroutine band()
    ! Evaluate the density of state in (x,y) position
    use param
    integer m,l,k,i! circle variable
    open(12,file="tiband.dat")
    !   (0,0)------>(pi,0)
    do k = 0,nky
        kx = pi*k/nkx  ! discrete wavevector in x direction
        !kx = 0
        ky = 0  ! discrete wavevector in y direction
        ! 不同的kx和ky重新进行哈密顿量矩阵的构造和求解
        call matrix_set() ! 新的kx和ky下重新填充矩阵，并求解对应本征值
        call eigSol()
        write(12,"(6f9.5)")kx,ky,(w(i),i=1,N)
    end do
    !   (pi,0)---->(pi,pi)
    do k = 0,nkx   
        kx = pi
        ky = pi*k/nkx  ! discrete wavevector in y direction
        ! 不同的kx和ky重新进行哈密顿量矩阵的构造和求解
        call matrix_set() ! 新的kx和ky下重新填充矩阵，并求解对应本征值
        call eigSol()
        write(12,"(6f9.5)")kx,ky,(w(i),i=1,N)
    end do
    !   (pi,pi)---->(0,0)
    do k = 0,nkx-1   
        kx = pi-pi*k/nkx  ! discrete wavevector in x direction
        ky = pi-pi*k/nky  ! discrete wavevector in y direction
        call matrix_set() ! 新的kx和ky下重新填充矩阵，并求解对应本征值
        call eigSol()
        write(12,"(6f9.5)")kx,ky,(w(i),i=1,N)
    end do
    close(12)
    end subroutine band
!============================================================
      subroutine ishermitian()
      use param
      integer i,j
      integer ccc
      ccc = 0
      open(16,file = 'verify.dat')
      do i = 1,N
        do j = 1,N
            if (Ham(i,j) .ne. conjg(Ham(j,i)))then
                ccc = ccc +1
                write(16,*)i,j
                write(16,*)Ham(i,j)
                write(16,*)Ham(j,i)
            end if
        end do
      end do
      write(16,*)ccc
      close(16)
      return
      end subroutine ishermitian
!================= Hermitain Matrices solve ==============
      subroutine eigSol()
      use param
      integer m
      lwork = -1
      liwork = -1
      lrwork = -1
      call cheevd('V','Upper',N,Ham,lda,w,work,lwork,rwork,lrwork,iwork,liwork,info)
      lwork = min(2*N+N**2, int( work( 1 ) ) )
      lrwork = min(1+5*N+2*N**2, int( rwork( 1 ) ) )
      liwork = min(3+5*N, iwork( 1 ) )
      call cheevd('V','Upper',N,Ham,lda,w,work,lwork,rwork,lrwork,iwork,liwork,info)
      if( info .GT. 0 ) then
            open(101,file="mes.txt",status="unknown")
            write(101,*)'The algorithm failed to compute eigenvalues.'
            close(101)
      end if
      open(100,file="eigval.dat",status="unknown")
      do m = 1,N
            write(100,*)m,w(m)
      end do
            close(100)
      return
      end subroutine eigSol

Python

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python3 te.py & 执行python程序，并放到后台执行(python不用编译)

julia的执行和python相同

Origin作图

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坐标轴样式调节

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建立自己的作图模板

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补充

  • 批量编译执行Fortran程序
    仅仅执行确定文件夹下的Fortran程序，再下一级目录中文件不会去执行

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    #!/bin/sh  
    #============ get the file name ===========  
    Folder="/home/yxli/te"  	#要批量编译哪个文件夹下面的Fortran
    for file_name in ${Folder}/*.f90
    do 
    	temp_file=`basename $file_name  .f90` 
    	ifort -mkl $file_name -o $temp_file.out 
    	./$temp_file.out &   # 编译成功之后自动运行
    done
    rm *out   # 删除编译后文件

  • 批量执行文件夹中所有的Fortran程序(文件夹中可以包含文件夹)
    递归搜寻文件夹下面所有的Fortran文件

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#!/bin/bash 
function getdir(){
    for element in `ls $1`
      do
        dir_or_file=$1"/"$element
    if [ -d $dir_or_file ]
      then
        getdir $dir_or_file
      else  # 下面的全是文件
	  	if [ "${dir_or_file##*.}"x = "f90"x ]||[ "${dir_or_file##*.}"x = "f"x ];then	# 筛选处特定后缀的文件
    		dir_name=`dirname $dir_or_file` # 读取目录
			file_name=`basename $dir_or_file .f90` # 读取以f90结尾的文件名
			out_file_name="$dir_name/$file_name"  # 定义编号成功的文件名称
			ifort -mkl $dir_or_file -o $out_file_name.out  # 编译后文件名以out结尾
			dir1=`dirname $out_file_name`  # 读取编译成功文件的路径,只提取目录
			cd $dir1  # 切换到具体的文件夹
			./$file_name.out 1>mes 2>bad &  # 执行该文件夹下面编译好的文件
			# ./$out_file_name.out 1>mes 2>bad &
			# rm $out_file_name.out
		fi
    fi
done
}
 
root_dir="/home/yxli/te"
getdir $root_dir

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Email

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