ovito在linux下安装教程,linux下超详细教程安装phonopy

参考资料：

phonopy安装：

第一步：准备文件

1、python-3.6  (https://www.python.org/downloads/source/)

2、numpy-1.11.2  (http://www.scipy.org/scipylib/download.html)

3、lxml-3.6.4  (http://lxml.de/)

4、matplotlib-1.5.0  (https://sourceforge.net/projects/matplotlib/files/)

6、phonopy-1.11.0 (https://sourceforge.net/projects/phonopy/)

第二步：安装Python-3.6.0b3.tar.xz

Øtar xvf Python-3.6.0b3.tar.xz

Øcd Python-3.6

Ø./configure --prefix= /home/…/phonopy/Python-3.6/build

(在python解压目录事先新建build目录，省略部分根据每个人电脑而定)

Ømake

Ømake install

设置环境变量

Øvi  ~/.bashrc

在.bashrc文件末尾加入：

Øexport LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/…/phonopy/Python-3.6/build/lib

export PATH=$PATH:/home/…/phonopy/Python-3.6/build/bin

export PATH=/home/…/phonopy/Python-3.6:$PATH

Øsource  ~/.bashrc

测试

Ø命令行输入python3.6，若成功会出现(避免和系统自带/usr/bin混淆)

Python 3.6.0b3 (default, Nov  6 2016, 02:12:05)

[GCC 4.9.3] on linux

Type "help", "copyright", "credits" or "license" for more information.

>>>

第三步：安装numpy-1.11.2.tar.gz

Øtar xzvf numpy-1.11.2.tar.gz

Øcd numpy-1.11.2

Øcp site.cfg.example site.cfg

Øvi site.cfg：

Ø修改文件中如下所示部分：

# [mkl]

# library_dirs = /opt/intel/mkl/10.0.1.014/lib/32/

# lapack_libs = mkl_lapack

# mkl_libs = mkl, guide

注意：mkl前面的注释一定要去掉，此外，左端不能留空格。

Ø修改后的如下(根据实际情况修改)：

[mkl]

library_dirs = /opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64

include_dirs = /opt/intel/composer_xe_2013_sp1.2.144/mkl/include

lapack_libs = mkl_lapack95_lp64

mkl_libs = mkl_def,mkl_intel_lp64,mkl_intel_thread,mkl_core,guide,iomp5

(最后一行逗号为英文输入法下面的)

Øpython3.6 setup.py build --help-fcompiler查看下可用的编译器，结果发现--fcompiler=intelem可用

Øpython3.6 setup.py build --fcompiler=intelem

Øpython3.6 setup.py install --home=Python3.6解压目录/pymodule

(pymodule是自己在python解压目录下新建的numpy安装目录)

Øvi  ~/.bashrc添加下面内容：

PYTHONPATH="${PYTHONPATH}:/home/…/phonopy/Python3.6/pymodule/lib

/python"

export PYTHONPATH

export PATH=/home/…/phonopy/Python-3.6/pymodule/bin:$PATH

export PYTHONPATH=/home/…/phonopy/Python-3.6/pymodule/lib/python

Øsource  ~/.bashrc

让python知道到哪里去找模块

Ø测试python是否能够调用numpy：

Øcd .. (退出numpy的目录)

这一步一定要做，不然会出错，ImportError: Error importing numpy.

Ø输入：python3.6进入python界面

Øimport numpy

执行numpy看是否出错

第四步：安装lxml-3.6.4.tgz

Øtar xzvf lxml-3.6.4.tgz

Øcd lxml-3.6.4

Øvi  ~/.bashrc添加下面内容：

PYTHONPATH="${PYTHONPATH}:/home/…/phonopy/Python3.6/lxml/lib

/python"

(lxml是自己在python解压目录下新建的lxml安装目录)

Øsource  ~/.bashrc

Øpython3.6 setup.py install --home=Python3.6解压目录/lxml

第五步：安装matplotlib-1.5.0.tar.gz

Øtar xzvf matplotlib-1.5.0.tar.gz

Øcd matplotlib-1.5.0

Øvi  ~/.bashrc添加下面内容：

PYTHONPATH="${PYTHONPATH}:/home/…/phonopy/Python3.6/matplotlib /lib/python"

(matplotlib是自己在python解压目录下新建的matplotlib安装目录)

Øsource  ~/.bashrc

Øpython3.6 setup.py install --home=Python3.6解压目录/ matplotlib

第六步：安装PyYAML-3.12.tar.gz

Øtar xzvf PyYAML-3.12.tar.gz

Øcd PyYAML-3.12

Øvi  ~/.bashrc添加下面内容：

PYTHONPATH="${PYTHONPATH}:/home/…/phonopy/Python3.6/pyyaml/lib

/python"

(pyyaml是自己在python解压目录下新建的pyyaml安装目录)

Øsource  ~/.bashrc

Øpython3.6 setup.py test

Øpython3.6 setup.py install --home=Python3.6解压目录/pyyaml

第七步：安装phonopy-1.11.0.tar.gz

Øtar xzvf phonopy-1.11.0.tar.gz

Øcd phonopy-1.11.0

Øpython3.6 setup.py install

Ø把/home/…/phonopy/phonopy-1.11.0/build/scripts-3.6的phonopy拷贝到usr/bin

测试

Ø在phonopy目录下命令行输入phonopy：

结果显示：

_ __ | |__   ___  _ __   ___   _ __  _   _

| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |

| |_) | | | | (_) | | | | (_) || |_) | |_| |

| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |

|_|                            |_|    |___/

1.11.0

Crystal structure file of POSCAR (default file name) could not be found.

___ _ __ _ __ ___  _ __

/ _ \ '__| '__/ _ \| '__|

|  __/ |  | | | (_) | |

\___|_|  |_|  \___/|_|