Profil de MartinMartin's FactoryPhotosBlogListes Outils Aide

Martin

La liste est vide.

Martin's Factory

do till you fly
28 janvier

Work Out and Drink Up

Work Out and Drink Up

Thursday, Jan. 24, 2008 By SANJAY GUPTA, M.D.
A new study of cardiac health has yielded a happy formula: start with moderate exercise, at least 30 min. to 1 hr. a day and add moderate alcohol consumption
Erik Isakson / Getty; Maren Caruso / Getty

If you want to live a long and healthy life, you're probably trying to eat right, exercise regularly and get enough sleep. Good steps. Now how about adding a little alcohol to your regimen?

Related Articles

Hormone Therapy Redeemed

Aging is never easy, particularly during menopause. But for 30 years women could at least depend on ...

Mild Exercise May Counter Dementia

Moderate physical activity even an unhurried 30-minute stroll a day may diminish the risk for vascul...

Pollution: Dangerous to Joggers

Living in a bustling, vibrant city can certainly expose you to a lot of things, not the least of whi...

College Drinking and Heart Problems

In many ways, I was a pretty typical pre-med student. I studied hard with hopes of becoming a doctor...

That's right. It is well documented that tossing a few drinks back in a week (and that means a few: up to one a day for women, up to two for men) has potential heart benefits. But researchers in Denmark decided to look further. Could drinking alcohol have a benefit similar to that of exercise?

"If you don't want to exercise too much," asks Dr. Morten Gronbaek, epidemiologist with Denmark's National Institute of Public Health, "can you trade it for one to two drinks per day and be fine?" A study Gronbaek and colleagues just published in the European Heart Journal suggests the answer just may be yes. That finding, not surprisingly, has proved to be a crowd-pleaser.

There are a number of reasons a drink can be such a tonic. First, alcohol and exercise affect your heart health in similar ways. "They help increase good cholesterol, or HDL [high-density lipoproteins], and clean the circulatory system's pipes," says Dr. Arthur Klatsky, a cardiologist and researcher at Kaiser Permanente Northern California. "HDL helps remove fatty deposits, created by bad cholesterol, or LDL [low-density lipoproteins], from blood-vessel walls. The higher the HDL, the less likely vascular disease becomes. The lower the HDL, the more likely."

Gronbaek and his team surveyed 12,000 people over a 20-year period. They found that exercise and drinking alcohol each had an independent beneficial effect on the heart and a compounded effect when practiced together. The investigators got even greater insight when they separated the study participants into four categories.

People who don't drink at all and don't exercise had the highest risk of heart disease. People who drink moderately and exercise had a 50% lower risk. Teetotaling exercisers had a 30% decreased risk, as did moderately drinking couch potatoes. "There's an additional protective effect to doing both," says Gronbaek. "That's the new finding."

This study is part of a growing body of work that makes a medical virtue out of what was once seen as a vice. There is evidence that alcohol in combination with caffeine can limit the damage to your brain after a stroke, even though it may not lower your risk of having a stroke in the first place. Other possible benefits include lowering your risk of diabetes, improving insulin sensitivity in postmenopausal women and decreasing dementia rates in older adults who had been consuming one to six drinks per week.

Before you rush off to hit the bar after your workout, keep in mind that your age matters. Alcohol may do you no coronary good until you reach the age at which heart disease becomes an appreciable risk. "You wouldn't advise everyone to drink," says Gronbaek. "You shouldn't even think about doing it until age 45 or 50. There's absolutely no proof of a preventative and protective effect before age 45." Also, younger women who have a higher risk of breast cancer and anyone who has a family history of alcoholism should pass on the pint and order a soda.

And remember, moderation is everything. Gronbaek's study, like most, stuck to the one-drink-a-day standard for women and up to two a day for men. It did not distinguish between type (wine vs. beer) or size (pint vs. shot). But here common sense must rule. A 10-oz. martini is a lot more than a 6-oz. serving of wine, even if they each fit in one glass. And it goes without saying that you should never drink your weekly allotment all at once.

With reporting by A. Chris Gajilan/New York

26 septembre

赝势方法;模型势方法;pseudo-potential method

 分子式:
CAS号:

性质:又称模型势方法。即价电子从头计算法。其基本思想是,所研究体系的哈密顿算符仅显含价电子部分,而将原子内层的全部电子连同原子核构成的核实对外层价电子的作用用适当的模型势函数(即赝势pseudo potential)表示,同时引入表示投影算符的势以便将价电子波函数与内层电子波函数分离开来,然后对价电子进行变分并用自洽迭代处理,计算出价电子轨道波函数和能级值等。所引入的两个势均通过全电子的原子从头计算确定,随后用于分子计算。常见的赝势有两类,一类是基于固体物理理论的菲利普斯-克兰曼(Phillips-Kleinman)赝势原理发展起来的,一类是从早期的价电子概念出发,由赫律纳加(Huzinaga)等提出的模型。赝势方法主要用于含有重元素的化合物或原子簇的研究。

VASP赝势文件POTCAR详解

 
POTCAR 赝势文件

  可以理解为分子力学模拟中的力场文件 但包括的信息更多
  VASP4.6将各元素优化的INCAR里的参数也包括在这里了,作为支持PREC的缺省选择
  通常各元素的POTCAR已经包括在软件包里了
  我们只需要按照POSCAR里的顺序,将各元素的POTCAR按顺序连接起来就可以了
  如以下命令:
  cat file1 file2 file3 > POTCAR

  软件包自带的绝大多数赝势是超软赝势(US-PP)了,但不少元素有两个版本,如何
  选取呢?
  一个简单的办法是看后缀
  标准的没有后缀 _h 硬一点 _s 软一点
  _pv,_sv,_d 就是说semi-core的p,s或者d也当做价态处理了
  如果是数字的话,表示的可能是不同的半径截距

  也可以参考各版本同目录下的V_RHFIN file ,PSCTR file
  这两个文件告知该版本的赝势是如何生成的。比如:
  V_RHFIN file
  Sc: 6p d2 s1
   8 21. .002000 44.95590 125. .25E-05 .300 200FCA 12.00000
   .7 1.0 0
   1.0 .0 .5 -320.8847 2.0000
   2.0 .0 .5 -34.4217 2.0000
   2.0 1.0 1.5 -28.2366 6.0000
   3.0 .0 .5 -3.7944 2.0000
   3.0 1.0 1.5 -2.2591 6.0000
   3.0 2.0 2.5 -.1113 2.0000
   4.0 .0 .5 -.2699 1.0000
   4.0 3.0 2.5 -.1000 .0000
  第一行是注释行 给出基本的信息
  第二行是最重要的控制行
   8 21. .00 2000 44.95590 125. .25E-05 .300 200 F CA 12.00000
   J Z XION N AM H DELRVR PHI NC1 | CH QCOR
   |
   GREEN

  J - 轨道数 Z - 原子序数 XION - 离子化程度 一般设为0 N - 格点数
  AM - 原子质量 H - 决定格点间距 DELRVR - 自洽收敛标准
  PHI - 线性拟合参数 NC1 - 最大自洽循环次数 GREEN - 是否存在初始的势
  CH - 交换相关能(XC)类型
   Slater-XC
   HL Hedin Lundquist (1971)
   CA Ceperly and Alder parameterized by J.Perdew and Zunger
   WI Wigner interpolation
   PB Perdew -Becke
   PW Perdew -Wang 86
   LM Langreth-Mehl-Hu
   91 Perdew -Wang 91
  QCOR - 非价键电子数(core electrons)
  第三行开始是每个轨道的具体参数,依次为
  n l j(=l±1/2) 原子轨道能 占有率

  PSCTR file of LDA/H1.25
   TITEL = US H
   LULTRA = T use ultrasoft PP ?
   RWIGS = 0.57 nn distance ! Wigner-Seitz radius

   RCLOC = .65
   NE = 100
   LCOR = .TRUE.
   QCUT = -1
   RMAX = 3.0 ! core radius for proj-oper

   Description
   l E TYP RCUT TYP RCUT(cutoff radius)
   0 0 15 0.80 23 1.25
   0 0.5 15 0.80 23 1.25
   1 -0.2 15 0.80 23 1.25
  最重要的地方上面已经用颜色标出来啦:)
  说明一下,TYP是指赝势的类型,RCUT是半径截距,TYP可取的值如下:
  正则
  1 BHS
  2 TM
  3 VAN
  6 XNC
  7 RRKJ wave function possibly with node
  15 RRKJ wave function strictly no node
  非正则 +8

  最后一个问题是LDA or GGA。貌似没有定论目前。
  这个最好是两个一起做做看啦。或者看文献别人验证过哪个数据好。
  其实据说目前最好的是PAW(P.E.Blochl,Phys.Rev.B 50,17953(1994).,Phys.Rev.B 59,1758(1999).)。

VASP新手入门十个简单问题

1.TEBEG,TEEND的单位是K吗?
  答:是K为单位的。

  2.在运算中,直接COPY POSCAR文件到工作目录就可以吗,用不用再POSCAR或INCAR文件中设定参数来控制POSCAR的赝势的选取方法?
  答:不大明白你的问题。在一个工作目录准备好INCAR,POSCAR,POTCAR,KPOINTS这四个文件。先看POTCAR中LEXCH后面的值是什么,如果是CA,那么INCAR中就不用设置GGA了;如果是91,那么就在 INCAR 中输入GGA=91;如果是PE,那么就设置GGA=PE。

  3.模拟表面,一般SLAB选多厚?
  答:自己多测试不同的厚度后,来确定slab 的厚度

  4.在KPOINT文件中,如果选取MONKHORST-pack的K点产生办法,K点相对自动网格移动时怎么回事?
  答:你可以看看monkhorst,pack1976年在phys. rev. b上的文献,他们在文献中给出了对于sc,bcc和fcc三种格子的一种效率很高的k点选取标准。但是这种k-mesh的选取方法并不是将第一个点取在倒空间的原点处,而是有一个shift,比如对于fcc而言,这个shift时(1/8,1/8, 1/8)。但是这种mp方法对于正交格子适用,而对于三方或者六方的格子则并不好。因此这时建议采用\gamma点为中心的k-mesh(vasp用户手册)

  
  5.想做表面重构,VASP 能做吗,能用分子动力学模拟吗,怎么设置参数?
  答:做重构的计算,一般用分子动力学的方式来模拟。你可以参考文献上模拟表面体系重构的作法。大多是采用比较几个表面模式的能量以及相关的热力学量。
  
  6.不指定电子的总SPIN,会有影响吗,一般 什么体系才考虑自旋?
  答:你做的体系是否包含3d-过渡金属离子(V至Ni)或其他含f电子的原子,如果没有的话,可以不考虑自旋极化的计算。
  
  7.表面的原子或分子的运动,扩散还有重构,IBRION怎么设定?
  答:是扩散的化,一般用NEB的方法计算其扩散路径或扩散势垒。

  8.如果知道一个化合物的组成,想计算它的总能一般应怎么办?同时如果一直组成如何在常温下计算它的稳定结构,比如FeMgCl2?
  答:计算总能,自己准备好vasp的输入文件,运算后就直接得到。可能考虑它的结合能比较好。

  9.在计算一个系统的稳定结构时,SMASS参数如何设置?
  答:看你是计算这个稳定结构的什么性质:计算总能和DOS,用ISMEAR=-5,不用管SMASS。

  10.具体给介绍一下STM图像的模拟办法,如何计算特定的能带,还有计算完成后一般去那个文件查找对自己有用的数据?
  答:一般来说用parchg做个图就可以了,当然以上方法仅限于T-H近似。 

如何用VASP计算晶格常数

 

我们用Pd金属作为例子。
  Pd金属的实验上的晶格常数为3.89A。在这里,我们用VASP计算它的晶格常数。
  首先将Pd所对应的POTCAR文件拷贝到目录下。然后准备好INCAR和KPOINTS文件。POSCAR文件我们将通过一个tcsh的script来产生。

  KPOINTS文件可以如下:
  Monkhorst Pack
  0
  Monkhorst Pack
   11 11 11
   0 0 0

  INCAR文件可以如下:
   SYSTEM = Pd bulk calculation
   Startparameter for this run:
   PREC = Accurate
   ISTART = 0 job : 0-new 1-cont 2-samecut
   ICHARG = 2 charge: 1-file 2-atom 10-const
   ISPIN = 1 spin polarized calculation?

   Electronic Relaxation 1
   EDIFF = 0.1E-03 stopping-criterion for ELM
   LREAL = .FALSE. real-space projection
   Ionic relaxation
   EDIFFG = 0.1E-02 stopping-criterion for IOM
   NSW = 0 number of steps for IOM
   IBRION = 2 ionic relax: 0-MD 1-quasi-New 2-CG
   ISIF = 2 stress and relaxation

   POTIM = 0.10 time-step for ionic-motion
   TEIN = 0.0 initial temperature
   TEBEG = 0.0; TEEND = 0.0 temperature during run

   DOS related values:
   ISMEAR = 0 ; SIGMA = 0.05 gaussian smear

   Electronic relaxation 2 (details)

   Write flags
   LWAVE = F write WAVECAR
   LCHARG = F write CHGCAR

  
  产生POSCAR和计算晶格常数的工作可以用以下的PBS script来完成。
  #!/bin/tcsh
  #PBS -S /bin/sh
  #PBS -l nodes=4:athlon:ppn=2
  #PBS -l cput=384:00:00
  #PBS -m ae
  #PBS -o output
  #PBS -e error.log

  # set parameter
  set EXEC = 'vasp'
  set SRC = '/usr/common/executable'

  # change working directory
  cd $PBS_O_WORKDIR

  # copy fresh executable from depository
  cp -f $SRC/$EXEC .

  # execute mpi program
  foreach a (3.3 3.4 3.5 3.6 3.7)
  echo "a= $a"

  cat >POSCAR <
  cubic diamond
   $a
   0.5 0.5 0.0
   0.0 0.5 0.5
   0.5 0.0 0.5
   2
  direct
   0.0 0.0 0.0
   0.25 0.25 0.25
  !

  mpiexec -nostdin ./$EXEC

  set E=`tail -2 OSZICAR`
  echo $a $E >>SUMMARY

  end
  # remove executable
  rm -f $EXEC

  如果不用不需要用PBS script,则更加简单,如下即可。将其命名为lattice。
  #!/bin/tcsh
  foreach a (3.5 3.6 3.7 3.8 3.9 4.0 4.1 4.2)
  echo "a= $a"

  cat >POSCAR <
  fcc lattice
   $a
   0.5 0.5 0.0
   0.0 0.5 0.5
   0.5 0.0 0.5
   1
  cartesian
   0.0 0.0 0.0
  !

  ./vasp

  set E=`tail -1 OSZICAR`
  echo $a $E >>SUMMARY

  end

  用chmod +x lattice,将其改为可执行文件。然后在命令行里键入./lattice 即可。

  
  以下是用USPP-LDA运行完后的SUMMARY文件。每个计算用时13秒。 (在USPP中Pd的截断能量是198.955)
  3.5 1 F= -.52384500E+01 E0= -.52371846E+01 d E =-.253072E-02
  3.6 1 F= -.58695670E+01 E0= -.58683951E+01 d E =-.234381E-02
  3.7 1 F= -.62322232E+01 E0= -.62311104E+01 d E =-.222547E-02
  3.8 1 F= -.63932936E+01 E0= -.63921078E+01 d E =-.237151E-02
  3.9 1 F= -.64072233E+01 E0= -.64058584E+01 d E =-.272979E-02
  4.0 1 F= -.63162916E+01 E0= -.63147061E+01 d E =-.317085E-02
  4.1 1 F= -.61523489E+01 E0= -.61504748E+01 d E =-.374817E-02
  4.2 1 F= -.59418370E+01 E0= -.59396594E+01 d E =-.435530E-02
  用抛物线拟和得到的晶格常数为$3.888\AA$,固体中每个原子的能量是$E_{bulk}=-6.4257$。

  
  以下是采用PAW-LDA势运行完以后的SUMMARY文件。每个计算用时20秒。所以相对来说PAW势所需要的时间多一些,这是因为PAW势的energy cutoff相对比较高(在PAW中Pd的截断能量是250.832)。
  3.5 1 F= -.52393107E+01 E0= -.52377274E+01 d E =-.316665E-02
  3.6 1 F= -.58814938E+01 E0= -.58798653E+01 d E =-.325695E-02
  3.7 1 F= -.62451262E+01 E0= -.62437004E+01 d E =-.285149E-02
  3.8 1 F= -.64049388E+01 E0= -.64036223E+01 d E =-.263317E-02
  3.9 1 F= -.64158100E+01 E0= -.64143798E+01 d E =-.286044E-02
  4.0 1 F= -.63210060E+01 E0= -.63194198E+01 d E =-.317251E-02
  4.1 1 F= -.61536329E+01 E0= -.61518107E+01 d E =-.364433E-02
  4.2 1 F= -.59385695E+01 E0= -.59364165E+01 d E =-.430601E-02
  用抛物线拟和得到的晶格常数为$3.875\AA$,固体中每个原子的能量E_bulk=-6.4185eV

  
  可见,PAW-LDA和USPP-LDA给出的晶格常数都和实验吻合的非常好,两者之间的差别也很小。在以下所有的计算中,如果没有特殊声明,我们都默认采用PAW-LDA的势。
  结合能(cohesive energy)的定义如下:
  -E_coh = [E_bulk-N*E_atom]/N
 
所以我们要将固体中每个原子的能量减去单个Pd原子的能量,才能和实验的结合能相比较。对于过渡金属原子,计算单个原子的能量要特别注意。VASP的网页上给出了求结合能所需的单个原子能量的修正值(详见VASP手册Pseudopotentials supplied with the VASP package一章)。可以在上面查到,Pd每个原子LDA的修正值为1.46eV。所以我们得到LDA近似下Pd的结合能为4.998eV。此值和实验值比严重偏大,这是因为LDA
通常成键过强的关系。如果我们改用GGA的赝势,可以得到和实验比较吻合的结果。  

 
Photo 1 sur 5
La liste est vide.