科学网—COHP-初探:为了忘却的纪念vs wxDragon数据处理 - 叶小球...

来自 : blog.sciencenet.cn/blog-567091 发布时间：2021-03-24

关注：

1） COHP原理、参数设置、运行过程中警告warning及其对结果影响分析

2） extended Hückel method 与http://yaehmop.sourceforge.net/

3) mulitwfn http://multiwfn.codeplex.com/

COHP/COOP原理、解薛定谔方程时，有正的重叠积分表示成键态，反的表示反键态。

两种元素的PDOS有重叠，表明这两种元素之间有成键作用。共价、离子及金属键作用如何看出？

Finally, the COOP indicator results from multiplying the DOS by the overlap population (hence its name), and it adds an additional dimension—the precious bonding information:

COOP adopts positive values (bonding, because of the positive overlap population) in the lower region of the band, and negative values (which identify antibonding interactions) at higher energy levels. By comparing the band structure and its orbital icons with the COOP diagram, it is obvious why the nearest-neighbor COOP is bonding at low energies and antibonding at high energies.

Welcome to the YAeHMOP home page. This page has been set up to provide online support for the freely available extended Huckel calculation and visualization package YAeHMOP.

Yet Another extended Huckel Molecular Orbital Package (YAeHMOP) was developed by Greg Landrum whilest a graduate student in the research group of Professor Roald Hoffmann at Cornell University. YAeHMOP is intended to be an easy to use, transparent, extended Huckel calculation and visualization package which can perform calculations on both molecular and extended materials in 1,2, or 3 dimensions.

Multiwfn全称为Multifunctional wavefunction analyzer，是由北京科技大学化学与生物工程学院卢天编写的一个十分强大的波函数分析程序，能够实现量子化学领域几乎全部最重要的波函数分析方法[1]。此程序的用户遍及世界各地，目前已被超过两百篇学术论文或书籍所使用

COHP手册解读

运行总结：

1.产生full k-mesh的INCAR应该与静态计算用的INCAR相同，只是静态计算时需注释掉下面的项：

#LSORBIT = .TRUE.; ISYM=0

2.-pCOHP 0 反键区域，-pCOHP 0，成键区域，费米能级向上(反键区域）移动，材料失稳；反之，材料稳定性增加。

The electronic situation is perfectly optimized and any electronic density hypothetically added would push the Fermi level up into the antibonding area ( ), thereby destabilizing the crystal. It is also convenient that the pCOOP gives qualitatively the same result.

3. 如何对待运行out文件中的splitting参数，越大说明什么问题？

4. _sv、_pv势为什么不能用

5.用Origin重绘图时，需减去费米能级处能量值

6.-pCOHP、COHP、COOP单位问题

INCAR文件如下所示：

PREC = Accurate
#LREAL = Auto
LREAL = .FALSE.
ISMEAR = -5

#LSORBIT = .TRUE.; ISYM=0

NSW = 0 ; ISIF = 0
#NSW = 100 ; ISIF = 3 ; IBRION = 2
EDIFF = 1.0d-7
EDIFFG = -1.0d-4

NBANDS = 48
NPAR = 1

NEDOS = 801
LORBIT = 12

必须使两次计算的INCAR一致(尤其是这些参数保持一致)，才能产生可归一化的满足计算要求的full k-mesh，如不一致，则会出现如下错误：

1 Getting Started

1.1 Installation

1.2 Preparing your VASP calculation----a static run (no movements of atoms, NSW = 0).

At this time, you should be ready to run your first calculation. Keep in mind that we process plane-wave/PAW output; at the moment, that of VASP. In other words, you need to prepare a VASP wavefunction, and it is absolutely necessary that this is done in a static run (no movements of atoms, NSW = 0). Take care to have the WAVECAR file written to disk (LWAVE = .TRUE.). Remove any previously created WAVECAR file.

1.2.1 INCAR

Ti的INCAR

PREC = Accurate
#LREAL = Auto
LREAL = .FALSE.I

SMEAR = -5 #important!!!!!!!!!!!!!!!!!!!!!!!

#LSORBIT = .TRUE.; ISYM=0

NSW = 0 ; ISIF = 0
#NSW = 100 ; ISIF = 3 ; IBRION = 2
EDIFF = 1.0d-7
EDIFFG = -1.0d-4

NBANDS = 18 # 2ions+8electrons=10,10/2=5 important!!!!!!!!!!!!!!!!!!!!!!!
NPAR = 1 # important!!!!!!!!!!!!!!!!!!!!!!!

NEDOS = 801
LORBIT = 12 #important!!!!!!!!!!!!!!!!!!!!!!!

GaAs的INCAR

PREC = Accurate
LREAL = .FALSE.
ISMEAR = -5
NBANDS = 8 #2ions+(3+5)electrons=10,10/2=5
NPAR = 1

NSW = 0 ; ISIF = 0
EDIFF = 1.0d-7

NEDOS = 801
LORBIT = 12

NBANDS and NPAR=1设置说明

This is an important point, so we have given it a separate section. You need to use as many bands as there are orbitals in your local basis, for simple mathematical reasons. The default setting of VASP is usually lower (and this is fine for all that VASP does!); for a LOBSTER analysis, however, you need to manually set NBANDS in the INCAR file of the final run.

If you run VASP in parallel (NPAR 1), keep in mind that NBANDS may be automatically adjusted (VASP notifies you about this in its output). To definitely get the number of bands you requested, put the following into the INCAR:
NPAR = 1

1.2.2 KPOINTS说明

LOBSTER does not yet deal with k-point symmetry—in other words, your VASP WAVECAR must contain results for the entire mesh, not only the irreducible one usually given in the IBZKPT file.

To get out of trouble, switch off symmetry in the INCAR (ISYM = 0), add LSORBIT = .TRUE. in the INCAR and have the non-collinear version of VASP run for a short time. (This is a cheap trick, admittedly, but it creates a full k-point mesh very conveniently.) The IBZKPT file should now contain all points with equal weight (the last column should contain only 1’s). After a moment, interrupt VASP, remove the LSORBIT line again and do the following：

cp IBZKPT KPOINTS

1.2.3 POTCAR说明

In the current version, do not use ultrasoft pseudopotentials (“US-PP”) in your POTCAR; please use PAW potentials instead. Also, the gamma-only version of VASP is not supported; please run the single-point calculation with the “default” (complex) version, no matter which k points you are looking at. Finally, we currently recommend avoiding _sv potentials in the single-point calculation.

1.4 Running LOBSTER

~ lobster

2 The lobsterin File
2.1 How the input works

LOBSTER is controlled by a single file called lobsterin. This file is designed such that it needs only minimal user input. Usually, the default parameters are fine:

you should only need to set the energetic window, the local basis (e.g., “4s 4p” for gallium, or also “4s 4p 3d”, depending on your plans).

The lobsterin file also contains those atom pairs for which you intend to do pCOOP/pCOHP analysis.
The lobsterin file is not cAsE sEnSiTiVe, and comments may be added using an exclamation mark. (Everything in a line before an exclamation mark, however, will be read and processed!)

! This is an example for the lobster control file lobsterin.
! Comments are marked with a !! basisSet koga ! works up to Lr (Z 104)

2.2 An example input file

! This is an example for the lobster control file lobsterin.
! (See, here we are using the comment function!)
!
! First, enter the energetic window in eV (relative to the Fermi level):
COHPstartEnergy -10
COHPendEnergy 5
!
! Then, specify which types of valence orbitals to use:
includeorbitals s p d
!
! Now define the pairs for which COHP analysis etc. should be done.
! The atoms are numbered as per order in the POSCAR file.
! When in doubt, check it with wxDragon (press CTRL+6)
cohpbetween atom 1 atom 10

【原子的指定，可借助VESTA来从POSCAR中选择可能发生键合的原子考察】
!
! If you are interested in single orbital COHPs, you can get all the pairs ! like s-s, s-p_x, ..., p_z-p_z. Uncomment this line to switch it on:
! cohpbetween atom 1 atom 2 orbitalwise
!
! If you want to generate the COHPPairs automatically, use this to include ! all pairs in a given distance range (in Angstrom, not in atomic units):
! cohpGenerator from 1.4 to 1.5
!
! Lobster chooses the type of basis set automatically for you.
! If you wish to override this selection for some reason, you can do
! so by uncommenting one of the following lines:
! basisSet bunge ! works up to Xe (Z 55)
! basisSet koga ! works up to Lr (Z 104)

3 Output and Visualization

3.1 Output files
If everything went smoothly, LOBSTER provides you with the following files:
lobsterout: This is the general output file, and it duplicates all the information which has also been written to your terminal. It is a good idea to keep this file as a receipt, for looking up spilling values, and so on.

DOSCAR.lobster: This file contains the orbital-projected electronic DOS and their sum. The format is similar to VASP’s DOSCAR file but the energy has been shifted such that the Fermi level lies at zero eV.

COHPCAR.lobster:

File that contains the pCOHPs as requested in the lobsterin file. It resembles the format of TB-LMTO-ASA’s COPL file, which is organized as follows:

o Starting in line 3, the labels for the interactions are presented, followed by the actual data.
o Column 1: energy axis, shifted such that the Fermi level lies at zero eV.
o Column 2: pCOHP averaged over all atom pairs specified 画图用Column1、Column2?
o Column 3: integrated pCOHP (IpCOHP) averaged over all atom pairs
o Column 4: pCOHP of the 1st interaction 【什么是第一作用？] 画图用Column1、Column4?
o Column 5: integrated pCOHP of the 1st interaction
o and so on...

COOPCAR.lobster: same as above, just for pCOOP and its integral (IpCOOP).

ICOHPLIST.lobster: gives you a list of the particular IpCOHP values, integrated up to the Fermi level, for each atom–atom interaction you specified.

ICOOPLIST.lobster: same as above, just for IpCOOP.

3.2 Visualizing your results

Now it is time to look at your results. As the output formats are designed to resemble those of VASP, TB-LMTO-ASA etc., you could just employ the same visualization software you already prefer for looking at those DOSCAR or COPL files.

It is possible to use gnuplot; this route, however, is currently a little cumbersome unless you are comfortable with tools like head, tail, cut, and paste.

Hence, we strongly suggest you try the visualization program

wxDragon, of which a free trial version is available at
www.wxdragon.de. Simply open the files by typing
wxdragon DOSCAR.lobster
wxdragon COHPCAR.lobster

怎样选择NBANDS的数目：

How to choose NBANDS?

As said above, you need to set NBANDS equal to the number of basis functions used by LOBSTER【如果不等怎么办？】.

If you do not specify anything else in the lobsterin, LOBSTER will build the local atom-centered basis as follows:
check which orbitals are occupied in the free atom
for each l quantum number, select only those with highest n

We strongly recommend that you always define the local, auxiliary basis explicitly. This is because there can be no “universal”, automatic selection rule for many systems.

It simply depends on your chemistry.
Let us look at some examples:
A POSCAR containing two titanium atoms (as in the tutorial files):
2×[1×(4s) + 3×(3p) + 5×(3d)] = 2×9 = 18
Note that we chose the respective lowest -lying occupied orbitals (that is, the 3p, not 4p levels of titanium).

Ti--[Ar] 3d24s2

COHPstartEnergy -6
COHPendEnergy 6
includeOrbitals spd

Sc4H4

Sc--[Ar]3d14s2 H 1s1

4×[1×(4s) + 3×(3p) + 5×(3d)] +4x[1x(1s)]= 4×9+4 = 40

A cell containing two iron atoms and one nitrogen:
2×[1×(4s)+3×(3p)+5×(3d)] + 1×[1×(2s)+3×(2p)] = 2×9 + 4 = 22

Fe [Ar]3d64s2 N 1s22s22p3

GaAs

PREC = Accurate
LREAL = .FALSE.
ISMEAR = -5
NBANDS = 8
NPAR = 1

NSW = 0 ; ISIF = 0
EDIFF = 1.0d-7

NEDOS = 801
LORBIT = 12

(1) Ga [Ar]3d104s24p1 As [Ar]3d104s24p3

1×[1×(4s)+3×(3p)+5×(3d)+3x(4p)] + 1×[1×(4s)+3×(3p)+5×(3d)+3x(4p)] =24？

(2)见lobsterin:

COHPstartEnergy -14
COHPendEnergy 6

includeOrbitals sp #---NBANDS=8?

cohpbetween atom 1 and atom 2

Why do I need so many bands? They are unoccupied anyway!
We know this can be annoying, but the matrix equation that reconstructs the Hamiltonian matrix cannot be solved exactly if the number of bands deviates from the number of basis functions. L

OBSTER detects this deviation and gives a warning. It will continue running, but we strongly advise you to take this warning seriously.

VASP手册关于NBANDS的选取原则

NBANDS-tag NBANDS = [integer]

Default:

NBANDS=NELECT/2 + NIONS/2 (non-spinpolarized)
=0.6*NELECT + NMAG (spin-polarized)

NBANDS determines the actual number of bands in the calculation.

One should choose NBANDS such that a considerable number of empty bands is included in the calculation. As a minimum we require one empty band. VASP will give a warning, if this is not the case.

NBANDS is also important from a technical point of view: In iterative matrix-diagonalization schemes eigenvectors close to the top of the calculated number of vectors converge much slower than the lowest eigenvectors. This might result in a significant performance loss if not enough empty bands are included in the calculation. Therefore we recommend to set NBANDS to NELECT/2 + NIONS/2, this is also the default setting of the makeparam utility and of VASP.4.X. This setting is safe in most cases. In some cases, it is also possible to decrease the number of additional bands to NIONS/4 for large systems without performance loss, but on the other hand transition metals do require a much larger number of empty bands (up to 2*NIONS).

To check this parameter perform several calculations for a fixed potential (ICHARG=12) with an increasing number of bands (e.g. starting from NELECT/2 + NIONS/2). An accuracy of should be obtained in 10-15 iterations. Mind that the RMM-DIIS scheme (IALGO=48) is more sensitive to the number of bands than the default CG algorithm (IALGO=38).

tetrahedron method with Bl chl corrections (use a -centered k-mesh, see sec.5.5 ) For the calculation of the total energy in bulk materials we recommend the tetrahedron method with Bl chl corrections (ISMEAR=-5). This method also gives a good account for the electronic density of states (DOS). The only drawback is that the methods is not variational with respect to the partial occupancies. Therefore the calculated forces and the stress tensor can be wrong by up to 5 to 10 % for metals. For the calculation of phonon frequencies based on forces we recommend the method of Methfessel-Paxton (ISMEAR0). For semiconductors and insulators the forces are correct, because partial occupancies do not vary and are zero or one.

LORBITLORBIT = .TRUE. | .FALSE. (VASP.3.2)
LORBIT = 0 | 1 | 2 | 5 | 10 | 11 | 12 (VASP.4.X and later)

Default

LORBIT=0 (.FALSE.)

logicalintegerRWIGS line in INCARfiles written
.FALSE.0line requiredDOSCAR and PROCAR file

1line requiredDOSCAR and extended PROCAR file
.TRUE.2line requiredDOSCAR and PROOUT file

10not readDOSCAR and PROCAR file

11not readDOSCAR and PROCAR file with phase factors

12
not supported

VASP.4.6 behaviour:

integerRWIGS line in INCARfiles written
0line requiredDOSCAR and PROCAR file
1line requiredDOSCAR and lm decomposed PROCAR file
2line requiredDOSCAR and lm decomposed PROCAR file + phase factors
5line requiredPROOUT file
10not readDOSCAR and PROCAR file
11not readDOSCAR and lm decomposed PROCAR file
12not readDOSCAR and lm decomposed PROCAR file + phase factors

This flag determines, together with an appropriate RWIGS (see section 6.33), whether the PROCAR or PROOUT files (see section 5.21) are written.

The file PROCAR contains the spd- and site projected wavefunction character of each band.

The wavefunction character is calculated, either by projecting the orbitals onto spherical harmonics that are non-zero within spheres of a radius RWIGS around each ion (LORBIT=1, 2), or using a quick projection scheme relying that works only for the PAW method (LORBIT=10,11,12, see below).

If the LORBIT flag is not equal zero, the site and l-projected density of states is also calculated.

The PROOUT file (LORBIT=2, written in VASP.4.4) contains the projection of the orbitals onto spherical harmonics centered at the position of the ions () and the corresponding augmentation part.

This information can be used to construct e.g. the partial DOS projected onto molecular orbitals or the so-called coop (crystal overlap population function).

If the projector augmented wave method is used, LORBIT can also be set to 10, 11 or 12. This alternative setting selects a quick method for the determination of the spd- and site projected wave function character and does not require the specification of a Wigner-Seitz radius in the INCAR file (the RWIGS line is neglected in this case). The method works only for PAW POTCAR files and not for ultrasoft or norm conserving pseudopotentials.

The parallel version has some restrictions: The site projected DOS is not evaluated in the parallel version in the following cases :

VASP.4.5, NPAR1no site projected DOSVASP.4.6, NPAR1, LORBIT=0-5no site projected DOS

LWAVE-tag, LCHARG-tag LWAVE = .TRUE. | .FALSE. LCHARG = .TRUE. | .FALSE.

Default

LWAVE=.TRUE.LCHARG=.TRUE.

Available up from VASP/VAMP version 2.0. These tags determine whether the orbitals (file WAVECAR), the charge densities (file CHGCAR and CHG) are written.

ISTART= 0 | 1 | 2

Default:


ISTART=1if WAVECAR exists
=0else

This flag determines whether to read the file WAVECAR or not. 0Start job: begin from scratch . Initialize the orbitals according to the flag INIWAV

摘录

（1）vasp中COOP计算设置方法，输出文件数据处理方法（LORBIT=2,嗯[/colo ...

hchfox(站内联系TA)如果真想得到COOP，3.0版的SIESTA已可得到COOP和COHP了，另外TB-LMTO-ASA可得到COHP（估计这个代码现在不容易搞到手的），其他的免费代码Rspt（一种FP-LMTO代码）也可得到类似的COOP ---- BCOOP，ASW代码也可得到类似COOP曲线，但是商业程序，不公开。。。哈哈，COOP大杂烩了。。。。。hakuna(站内联系TA)材料的和物理的可能对COOP没有太大兴趣，而化学的是有兴趣的，它能给出一个成键特性的直观表达，相比于物理人，化学人更喜欢直观......
KRESSE没有加它，我匿猜一下，因为他是物理出身的，如果他滑雪的话，没准就不用大家再讨论这个事情了......
你知道怎么得到COOP，不放给大家传授一下......
为什么从vasp结果得到的COOP不敢用，出了什么问题？

hchfox(站内联系TA)呵呵，看来学化学的果真对COOP感兴趣啊。。。但你的猜测我不敢苟同，其实用VASP得COOP曲线的文章早在2000年左右都出来了，而且有一篇是PRL，但也就是那两三篇，而且都出自VASP开发组，之后就一直这个“搁浅”状态了，manual是有那样一句可完全得到COOP信息之类的话，这话还让一些国人抓耳挠腮，兴奋不已，非得干出COOP不可。COOP就那么重要吗？除了得出成键、反键之类的信息外，还有什么啊，不太懂这个。类似地，在VASP不已可得到ELF了吗？金属键、离子键、共价键都可分析出来了，还不能得到满足啊。。。
我以前从VASP得到COOP与用其他方法得到的COHP图像差异太大了（不仅仅是相反的概念），只好放弃了。当然，这也可能是我弄错了什么地方。

hakuna(站内联系TA)

没错，COOP是早就出来，但后来少了是因为大家不知道怎么把它鼓捣出来了，以前那个orbidos配合德国人的ergrah可以得到coop，后来因为版权的原因，大家没办法在那么容易地得到COOP了，自然用得就少了。。。。
是啊，ELF可以表征一下共价键，离子键也可以通过电荷密度差和DOS去分析，但这些与COOP表征的意义还是有差别的......
VASP手册里那一句话，弄得多少人头疼不已....
其它基于第一原理的软件增加了计算coop的模块，但毕竟VASP占领的市场太大了，所以还是会有人关心vasp的coop。。
为什么滑雪人那么关注COOP呢？看看Hoffman早年发在angl... REv. Mod. Phy.的两篇长文就会明白了，这两篇长文是那本固体与表面的主要内容....

摘录：http://emuch.net/html/201204/4448615.html

各位，请问vasp计算时只用一个gamma点 和 使用Gamma point-only VASP编译版本 有什么区别？讨论一下，呵呵!

wzbhit(站内联系TA)

NGXhalf charge density reduced in X direction
wNGXhalf gamma point only reduced in X direction
不太明白编译这些版本有什么用处 还请区长讲讲 谢谢~

fzx2008(站内联系TA)Gamma-only 版本在1个k点（Gamma点）时，经测试速度要快得多！
在大体系（supercell、big box）优化时，效益明显！

lgxyz(站内联系TA)

我觉得 应该把gamma-only vasp也编译一下，需要用时也方便，如果要用gamma-only vasp算过渡态，还得把vtstcode也编译进去，呵呵

网络摘录：

http://vasp1860.blog.edu.cn/home.php?mod=space uid=1556291 do=blog id=480047

量化软件—输运软件名称 软件分类Siesta(Transiesta) Linux,免费软件, Unix, Windows, 密度泛函Atomistix ToolKit Linux Unix, 商业软件, Windows, 密度泛函, 集成计算平台, 可视化Green Linux, 免费软件, Unix, 紧束缚方法, 半经验方法Nextnano3 Linux 免费软件, Unix, Windows, MacOSOpenMX Linux, 免费软件, Unix, Windows, 密度泛函Smeagol Linux, 免费软件, Unix, 密度泛函WanT Linux, 免费软件, Unix, 密度泛函SIESTA星期二, 2009-06-16 02:13 — zork最新版本: 3.0 官方主页: http://www.icmab.es/siesta/评分: 3

简介
SIESTA用于分子和固体的电子结构计算和分子动力学模拟。SIESTA使用标准的Kohn-Sham自恰密度泛函方法，结合局域密度近似(LDA-LSD)或广义梯度近似(GGA)。计算使用完全非局域形式(Kleinman-Bylander)的模守恒赝势。基组是数值原子轨道的线性组合(LCAO)。它允许任意个角动量，多个zeta，极化和截断轨道。计算中把电子波函和密度投影到实空间网格中，以计算Hartree和XC势，及其矩阵元素。除了标准的Rayleigh-Ritz本征态方法以外，程序还允许使用占据轨道的局域化线性组合。使得计算时间和内存随原子数线性标度，因而可以在一般的工作站上模拟几百个原子的体系。程序用Fortran 90编写，可以动态分配内存，因此当要计算的问题尺寸发生改变时，无需重新编译。程序可以编译为串行和并行（需要MPI）模式。

功能
总能量和部分能量
原子力
应力张量
电偶极矩
原子，轨道和键分析 (Mulliken)
电子密度
几何松弛，固定或者改变晶胞
常温分子动力学
可变晶胞动力学 (Parrinello-Rahman)
自旋极化计算（共线或者非共线）
BZ区的k-取样
态的局域和轨道投影密度
能带结构

Siesta 2.0新增功能：
1. 通过过滤或移到原子格点的方法平滑“蛋箱效应”。
2. HF和杂化泛函。
3. QM/MM。
4. 用多格点方法对溶剂中的分子计算Poisson-Boltzman方程。
5. 其它的线性标度方法。
6. 增强的MD历史框架。

Siesta 3.0新增功能：
1. 功能增強：TranSiesta功能；主程序模块化；计算COOP/COHP/PDOS曲线的新程序，用于化学分析；优化基组、赝势的工具程序；新的过滤流程，用于减少蛋箱结构的影响。
2. 新的工具：新版本denchar；新的检查蛋箱脚本；赝势文件解释器；加入新的STM-图像代码；Python、Matlab、Octave语言的脚本工具。
3. 新的功能：更灵活的产生基组选项；正确处理带电表面；Ordejon-Mauri线性标度泛函支持奇数电子；PBEsol和Wu-Cohen泛函；优化的增强；新的分子力学框架，包括Grimme型vdW；任意k点。

运行过程中警告warning及其对结果影响分析

LOBSTER v1.1.0 (g++ 4.8.1)
Code written and copyrighted (C) 2013-2014 by Stefan Maintz. All rights reserved.
starting on host mic on Sat May 24 01:30:09 2014

initialize PW-system...
initialize Augmentations...
initializing LCAO-system...
setting up local basis functions...
H (Bunge) 1s
Sc (Bunge) 4s 3p_y 3p_z 3p_x 3d_xy 3d_yz 3d_z2 3d_xz 3d_x2y2
INFO: There are more PAW bands than local basis functions available.
INFO: To prevent trouble in orthonormalization and Hamiltonian reconstruction
INFO: the PAW bands from 41 and upwards will be ignored.
setting up CO-interactions... found 1 interaction.
calculating overlaps...
projecting...
0% 10 20 30 40 50 60 70 80 90 100%
|----|----|----|----|----|----|----|----|----|----|
***************************************************

WARNING: 55 of 729 k-points could not be orthonormalized with an accuracy of 1.0E-5.
WARNING: Generally, this is not a critical error. But to help you analyze it,
WARNING: I dumped the band overlap matrices to the file bandOverlaps.
WARNING: Please check how much they deviate from the identity matrix and decide to
WARNING: use your results only, if you are sure that this is ok.
total spilling: 37.54%
charge spilling: 56.75%

calculating PDOS...
writing DOSCAR.lobster...
writing COOPCAR.lobster and ICOOPLIST.lobster...
calculating pCOHPs...
writing COHPCAR.lobster and ICOHPLIST.lobster...
done!

wxDragon程序不会修改数值，例如COHP绘图时显示的以Ef为零点，而采用origin重新绘图时，必须将数据减去Ef:

1）C:1-back-toZDSYSIMPORTANT-fromPro_Machangchu-techniquesLMTOelecwxDragon.exe

以管理员的身份执行wxDragon.exe，可得到直观的COHPCAR图，然后Expport as XY，命名为后缀.txt文件，即可用origin处理，绘图，但要注意减去EF

2） wxDragon程序值得探索，可更好理解DFT计算结果的物理意义。

为了忘却的纪念：

1） COHP到底是什么意思？

2) 如何计算？

拟考察原子的指定，可借助VESTA来从POSCAR中选择可能发生键合的原子考察，另外，从运行结果的distance可以进一步查看可能键合的原子是否选得恰当

如下面的H29、H25就表示POSCAR中的29号、25号原子

l(H29-H25) = 0.84797(0)

5 H29 H 0.50000 0.50914 0.75000 ( 0, 0, 0)+ x, y, z

4 H25 H 0.50000 0.61795 0.75000 ( 0, 0, 0)+ x, y, z

COHP# atomMU atomNU distance ICOHP(eF) for spin 1

1 4 9 0.99685 -1.44167

COHP# atomMU atomNU distance ICOHP(eF) for spin 1

1 6 11 0.99685 -1.43570

3) 计算结果如何绘图？

以管理员的身份执行wxDragon.exe，可得到直观的COHPCAR图，然后Expport as XY，命名为后缀.txt文件，即可用origin处理，绘图，但要注意减去EF

4）COHP的共价键、离子键各有什么特征

投影pCOHP方法描述离子键、共价键和金属晶体。

a bond index, IpCOHP？

手册摘录：

Thank you for downloading LOBSTER, our program for chemical-bonding analysis!

LOBSTER is built to read and process output data from plane-wave DFT packages, such as VASP.

By re-extracting atom-resolved information from the delocalized plane-wave basis sets (using the theories described below), LOBSTER gives you access to projected COOP and projected COHP curves, which you can use to visualize bonding and antibonding contributions in your everyday DFT calculations.

Allegedly, LOBSTER can also produce reasonable atom- and orbital-projected densities of states (DOS), and we plan to add more fancy features in the future.

COHPCAR.lobster的含义重新解读

File that contains the pCOHPs as requested in the lobsterin file. It resembles the format of TB-LMTO-ASA’s COPL file, which is organized as follows:

o Starting in line 3, the labels for the interactions are presented, followed by the actual data.
o Column 1: energy axis, shifted such that the Fermi level lies at zero eV.
o Column 2: pCOHP averaged over all atom pairs specified 画图用Column1、Column2?
o Column 3: integrated pCOHP (IpCOHP) averaged over all atom pairs
o Column 4: pCOHP of the 1st interaction 【什么是第一作用？] 画图用Column1、Column4?
o Column 5: integrated pCOHP of the 1st interaction
o and so on...

文献摘录：

Simple, yet predictive bonding models are essential achievements of

chemistry. In the solid state, in particular, they often appear in the form of visual

bonding indicators. Because the latter require the crystal orbitals to be constructed

from local basis sets, the application of the most popular density-functional theory

codes (namely, those based on plane waves and pseudopotentials) appears as being

ill-fitted to retrieve the chemical bonding information.

DFT代码很难提取化学键信息，从波函数电子结构计算重新提取Hamilton权重布居的方法--晶体轨道哈密顿布居方法。

In this paper, we describe a

way to re-extract Hamilton-weighted populations from plane-wave electronic structure

calculations to develop a tool analogous to the familiar crystal orbital Hamilton population (COHP) method.

投影pCOHP方法描述离子键、共价键和金属晶体。

We derive

the new technique, dubbed “projected COHP” (pCOHP), and demonstrate its viability using examples of covalent, ionic, and

metallic crystals (diamond, GaAs, CsCl, and Na).

For the first time, this chemical bonding information is directly extracted from the

results of plane-wave calculations.

（2）

“ the ionic and covalent type of interactions are stronger, the COHP
study gave maximum ICOHP for covalent compounds, e.g.,in the studied model
systems, C have a maximum ICOHP; ”

Next we examined the Sc-H COHP, shown for the two structures side by side in Figure S28.

A few more antibonding states are occupied for the rock-salt Fm-3m ScH;they disappear in the more stable (in calculations) P42/mmc structure. Table S8 shows the integral of pCOHPup to the Fermi level, a bond index, IpCOHP.

From the IpCOHP, we see that thenet bonding between Sc and H is larger than that inthe Fm-3mstructure, but the comparison is biased by unequal distances.

Figure S28 Calculated pCOHP curves for the Fm-3mand P42/mmc structures of ScH at 1 atm. Fermi levels (Efermi)are set at zero energy and marked by dash and dotted lines.

Table S8 The Nearest InteratomicDistances (in ) and Corresponding Integrated pCOHP (IpCOHP, eV per cell) at (Efermi)for the Fm-3mand P42/mmc structures of ScH at 1 atm.

Compounds

Sc-H distance

-IpCOHP

ScH (Fm-3m)

2.27

1.22

ScH (P42/mmc)

2.05

2.04

Actually, ScH is predicted to be unstable todisproportionation to Sc and ScH2 above ~27 GPa, as shown in Figure13 of the manuscript.Thus, it will be hard to form P42/mmcScH experimentally,though it is the most stable structure of ScH in the low pressure regime.

应该是根据Sc-H距离，通过VESTA确定的成键数量



CompoundsSc-H distance-IpCOHPNbondsnbonds value

ScH (P42/mmc)2.052.048240.255

ScH2 (Fm-3m)2.071.06321120.033125

ScH3 (P63)1.951.39660.231666667

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