Sky Blue's Blog

tar -xvf WIEN2k_11.tar (skip this if you downloaded files separately)
gunzip *.gz
chmod +x ./expand_lapw
./expand_lapw

This will expand all files and copies various shell-scripts. In $WIENROOT/SRC you find the postscript version of the usersguide (160 pages). Proceed with reading chapter "Installation". You can then configure and compile WIEN using:

./siteconfig_lapw

After successfull installation, every user should run:

./userconfig_lapw

catalyst study by using DFT calculations

2011-09-18T13:44:00.000-07:00

The first-principles calculations can be used to study the catalyst. The quantities needed are the total energy and vibrational frequencies of the reaction species on the catalyst surfaces.

Inequivalence between PBE and PW91

2011-05-23T18:54:00.000-07:00

Nonequivalence of the generalized gradient approximations PBE and PW91

HSE calculation using VASP

2011-05-23T18:34:00.000-07:00

Self-consistent calculation
ISTART = 1
ICHARG = 1

#PREC = High
LREAL = .FALSE. #Auto
#ISIF=3

EDIFF = 1E-04 stopping-criterion for ELM

IBRION = 1
EDIFFG = -0.01 #eV/A
NSW = 1024

#IALGO = 38

#LWAVE=.FALSE.

ISMEAR = 0 #-5
SIGMA = 0.01 #0.05

LHFCALC = .TRUE.
HFSCREEN = 0.20
ALGO = N
TIME = 0.4

flashplayer for 64 bit linux, firefox

2011-05-21T02:07:00.000-07:00

On page http://labs.adobe.com/downloads/flashplayer10_square.html
download http://download.macromedia.com/pub/labs/flashplayer10/flashplayer10_2_p3_64bit_linux_111710.tar.gz and unzip it.

cp libflashplayer.so /usr/lib/mozilla/plugins/.
restart firefox

sftp, sshfs fail while ssh works well

2011-05-20T21:13:00.000-07:00

sftp and sshfs may fail when trying to connect the remote server if there are shell initialization (.profile, .bashrc, .cshrc, etc) which produces output for non-interactive sessions. This can be verified by entering

ssh host /usr/bin/true

On my machine, I got the following output:

LD_LIBRARY_PATH: Undefined variable.
/usr/bin/true: Command not found.

After commenting out the defination of LD_LIBRARY_PATH in the ~/.cshrc on host, everything is working well.

slow password prompt when doing ssh

2011-05-20T19:16:00.000-07:00

change in /etc/nsswitch.conf
hosts: files mdns4_minimal [NOTFOUND=return] dns mdns4
to
hosts: files dns
client operating system: ubuntu 10.04

pymol 安装

2011-03-10T19:12:00.000-08:00

编译的时候遇到找不到ce_types.h的错误：
cp modules\cealign\src\ce_types.h to layer4\ce_types.h

./configure
make
python setup.py install
python setup2.py install
sudo cp pymol /usr/bin/.

Screen flicker after updating to ubuntu 10.04

2011-03-06T08:55:00.000-08:00

The way to fix this problem.

dynamical compilation of lapack

2011-01-03T17:10:00.001-08:00

add -fPIC to compile option

cp INSTALL/slamch.o and INSTALL/dlamch.o into SRC directory

In the folder of SRC, type

cc -shared -Wl,-soname,liblapack.so -o liblapack.so *.o

In the folder of BLAS/SRC, type

cc -shared -Wl,-soname,libblas.so -o libblas.so *.o

installation of xmgrace on Slackware 13.1

2011-01-03T08:30:00.000-08:00

I am installing grace-5.1.9 with t1lib-5.1.2 installed.

Problems:

t1fonts.c:(.text+0x336b): undefined reference to `T1_Get_no_fonts'
fontwin.c:(.text+0x141): undefined reference to `CheckForFontID'

Solutions:

change T1_Get_no_fonts in src/t1fonts.c to T1_GetNoFonts
change CheckForFontID in src/fontwin.c to T1_CheckForFontID

shortcuts of openoffice are not working on slackware 13.1

2010-12-17T13:03:00.000-08:00

chown root /opt/openoffice.org3/share/xdg/*

scim on slackware 13.1

2010-12-15T20:08:00.000-08:00

1. add "export LANG=en_US.UTF-8" in ~/.profile

2. chmod +x /etc/profile.d/scim.*

3. create a script file scim.sh containing the followings lines:
#!/bin/bash
scim -f socket -c socket -d

4. chmod +x scim.sh

5. restart kde

Fedora 12 & Nvidia Video Card

2010-11-26T15:05:00.000-08:00

Each time after updating the kernel, the Nvidia driver should be re-configured.
Press Ctrl-Alt-F2 to enter the command-line mode and login as root.
Reinstall the driver by running

./NVIDIA-Linux-x86_64-190.53-pkg2.run

and after that run

init 5

to enter the normal x11 mode.

Linux commands

2010-07-20T05:23:00.000-07:00

How to change a file's owner and group in Linux