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xcid

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[求助] 请问有没有人用Vasp算过声子，我们组里还没有人会跑，各位大神，拜托，拜托

我们老师叫我和师姐到vasp主页上去看phonony，并要求知道怎么算，因为我们老师以前都没有算过。向各位用过vasp算过声子的大神求教，谢谢了!

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1楼2012-10-29 18:48:53

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10楼: Originally posted by iamikaruk at 2012-10-31 09:22:50
基本上不需要修改什么吧？ubuntu的确是比较好装一点，不过suse只要有那几个库，应该也是没有问题的。...

安装numpy所提示错误：
Traceback (most recent call last):
  File "setup.py", line 3, in
import numpy
  File "/root/Desktop/phonopy-1.2.1/numpy/__init__.py", line 127, in
ImportError: Error importing numpy: you should not try to import numpy from
      its source directory; please exit the numpy source tree, and relaunch
      your python intepreter from there.
安装numpy提示：
Running from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg'
/bin/sh: svnversion: command not found
F2PY Version 2
blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib64
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib64
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib64
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib
  NOT AVAILABLE

atlas_blas_info:
  libraries f77blas,cblas,atlas not found in /usr/local/lib64
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries f77blas,cblas,atlas not found in /usr/lib64
  libraries f77blas,cblas,atlas not found in /usr/lib
  NOT AVAILABLE

/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/system_info.py:1414: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
blas_info:
  libraries blas not found in /usr/local/lib64
  libraries blas not found in /usr/local/lib
  libraries blas not found in /usr/lib64
  libraries blas not found in /usr/lib
  NOT AVAILABLE

/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/system_info.py:1423: UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
  warnings.warn(BlasNotFoundError.__doc__)
blas_src_info:
  NOT AVAILABLE

/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/system_info.py:1426: UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
  warnings.warn(BlasSrcNotFoundError.__doc__)
  NOT AVAILABLE

/bin/sh: svnversion: command not found
lapack_opt_info:
lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib64
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib64
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64
  libraries lapack_atlas not found in /usr/local/lib64
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib64
  libraries lapack_atlas not found in /usr/lib64
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_threads_info
  NOT AVAILABLE

atlas_info:
  libraries f77blas,cblas,atlas not found in /usr/local/lib64
  libraries lapack_atlas not found in /usr/local/lib64
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries f77blas,cblas,atlas not found in /usr/lib64
  libraries lapack_atlas not found in /usr/lib64
  libraries f77blas,cblas,atlas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_info
  NOT AVAILABLE

/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/system_info.py:1330: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
lapack_info:
  libraries lapack not found in /usr/local/lib64
  libraries lapack not found in /usr/local/lib
  libraries lapack not found in /usr/lib64
  libraries lapack not found in /usr/lib
  NOT AVAILABLE

/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/system_info.py:1341: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
  warnings.warn(LapackNotFoundError.__doc__)
lapack_src_info:
  NOT AVAILABLE

/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/system_info.py:1344: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
  warnings.warn(LapackSrcNotFoundError.__doc__)
  NOT AVAILABLE

running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building py_modules sources
building library "npymath" sources
customize GnuFCompiler
Could not locate executable g77
Could not locate executable f77
customize IntelFCompiler
Found executable /bin/ifort
customize LaheyFCompiler
Could not locate executable lf95
customize PGroupFCompiler
Could not locate executable pgf90
Could not locate executable pgf77
customize AbsoftFCompiler
Could not locate executable f90
customize NAGFCompiler
Could not locate executable f95
customize VastFCompiler
customize CompaqFCompiler
Could not locate executable fort
customize IntelItaniumFCompiler
customize IntelEM64TFCompiler
customize IntelEM64TFCompiler
customize IntelEM64TFCompiler using config
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fwrapv -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.6 -c'
gcc: _configtest.c
gcc -pthread _configtest.o -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fwrapv -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.6 -c'
gcc: _configtest.c
_configtest.c:1: 警告：与内建函数‘exp’类型冲突
gcc -pthread _configtest.o -o _configtest
_configtest.o: In function `main':
/root/Desktop/phonopy/numpy-1.6.1/_configtest.c:6: undefined reference to `exp'
collect2: ld 返回 1
_configtest.o: In function `main':
/root/Desktop/phonopy/numpy-1.6.1/_configtest.c:6: undefined reference to `exp'
collect2: ld 返回 1
failure.
removing: _configtest.c _configtest.o
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fwrapv -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.6 -c'
gcc: _configtest.c
_configtest.c:1: 警告：与内建函数‘exp’类型冲突
gcc -pthread _configtest.o -lm -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
conv_template:> build/src.linux-x86_64-2.6/numpy/core/src/npymath/npy_math.c
conv_template:> build/src.linux-x86_64-2.6/numpy/core/src/npymath/ieee754.c
conv_template:> build/src.linux-x86_64-2.6/numpy/core/src/npymath/npy_math_complex.c
building extension "numpy.core._sort" sources
Generating build/src.linux-x86_64-2.6/numpy/core/include/numpy/config.h
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fwrapv -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.6 -c'
gcc: _configtest.c
_configtest.c:1:20: 错误：Python.h：没有那个文件或目录
_configtest.c:1:20: 错误：Python.h：没有那个文件或目录
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
  File "setup.py", line 196, in
setup_package()
  File "setup.py", line 189, in setup_package
configuration=configuration )
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/core.py", line 186, in setup
return old_setup(**new_attr)
  File "/usr/lib64/python2.6/distutils/core.py", line 152, in setup
dist.run_commands()
  File "/usr/lib64/python2.6/distutils/dist.py", line 975, in run_commands
self.run_command(cmd)
  File "/usr/lib64/python2.6/distutils/dist.py", line 995, in run_command
cmd_obj.run()
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/command/install.py", line 55, in run
r = old_install.run(self)
  File "/usr/lib64/python2.6/distutils/command/install.py", line 582, in run
self.run_command('build')
  File "/usr/lib64/python2.6/distutils/cmd.py", line 333, in run_command
self.distribution.run_command(command)
  File "/usr/lib64/python2.6/distutils/dist.py", line 995, in run_command
cmd_obj.run()
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/command/build.py", line 37, in run
old_build.run(self)
  File "/usr/lib64/python2.6/distutils/command/build.py", line 134, in run
self.run_command(cmd_name)
  File "/usr/lib64/python2.6/distutils/cmd.py", line 333, in run_command
self.distribution.run_command(command)
  File "/usr/lib64/python2.6/distutils/dist.py", line 995, in run_command
cmd_obj.run()
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/command/build_src.py", line 152, in run
self.build_sources()
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/command/build_src.py", line 169, in build_sources
self.build_extension_sources(ext)
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/command/build_src.py", line 328, in build_extension_sources
sources = self.generate_sources(sources, ext)
  File "/root/Desktop/phonopy/numpy-1.6.1/numpy/distutils/command/build_src.py", line 385, in generate_sources
source = func(extension, build_dir)
  File "numpy/core/setup.py", line 410, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
  File "numpy/core/setup.py", line 41, in check_types
out = check_types(*a, **kw)
  File "numpy/core/setup.py", line 271, in check_types
"Cannot compile 'Python.h'. Perhaps you need to "\
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.

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坚持就是胜利，哈哈

11楼2012-10-31 09:31:52

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iamikaruk

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★ ★
franch: 金币+2, 谢谢回帖交流， 2012-10-29 22:26:36

(1)用phonopy生成单胞加倍的POSCAR-XXX
(2)用VASP做静态自洽计算，得到对应于不同POSCAR-XXX的vasprun.xml
(3)用phonopy将所有的vasprun.xml结果汇总得到力常数矩阵以及声子色散关系

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[img]http://osu.ppy.sh/stat2/iamikaruk-0.png[/img]

2楼2012-10-29 21:00:42

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xcid

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引用回帖:

2楼: Originally posted by iamikaruk at 2012-10-29 21:00:42
(1)用phonopy生成单胞加倍的POSCAR-XXX
(2)用VASP做静态自洽计算，得到对应于不同POSCAR-XXX的vasprun.xml
(3)用phonopy将所有的vasprun.xml结果汇总得到力常数矩阵以及声子色散关系

我在vasp主页上下载了phonoy软件压缩包，只有几M，在linux系统下解压缩了，是不是就可以用了？

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小菜一碟

3楼2012-10-30 16:51:24

已阅回复此楼关注TA 给TA发消息送TA红花 TA的回帖

iamikaruk

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引用回帖:

3楼: Originally posted by xcid at 2012-10-30 16:51:24
我在vasp主页上下载了phonoy软件压缩包，只有几M，在linux系统下解压缩了，是不是就可以用了？...

vasp主页上有phonopy么？
需要用python编译

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[img]http://osu.ppy.sh/stat2/iamikaruk-0.png[/img]

4楼2012-10-30 17:04:28

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