原子分子物理中用高斯画态密度图的方法.doc

用GaussSum用高斯画态密度图的方法 1、用实验室现成的GaussSum做DOS图时，发现log文件过大分析不了，下载到最新版本的问题就解决了。2、经常出现cclib has problems parsing *.log问题，检查自己的log文件是否完整。3、关于做PDOS（重点哈），做单点能计算时必须要有pop=full iop(3/33=1,3/36=-1),关键字，这在GaussSum帮助文件和例子里面写得很详细。至于做PDOS的时候，需要有group.txt文件，选择做atoms时，具体的两个要求是每个原子要列出以及所列原子不能重复，这里我还得补充一点group.txt格式，atomspart1（你所想要分析的某个分子部分）1-5,8-20,30（该部分原子序号）part26-7,21-29,31-33（注意了，直接保存就可以，下面不能有空行，我被这个给整惨了）在选择用orbitals时，大致一样，唯一不同就是不必列出所有的轨道。4、就以上例子分析，我要的结果是part1和part2的PDOS,但GaussSum做出来的part1和part2的图的结果是part1和total（图上显示的是part2，经过数据对比很明显就是total）或者part2和total（同理），估计是我下载的软件bug，但可以从它产生的DOS Spectrum.txt文件（里面有你想要的part1，part2，total）提取数据在origin里面作图，结果就很好了。5、在做COOP时，和做PDOS一个样。关于做其他图，遇到的问题就没什么了，只要你的log文件没错，基本就okay！Worked ExampleDescriptionA study of the electronic structure and vibrational spectrum of 1,4-divinyl-benzene (at the B3LYP/STO-3G level of theory) using Gaussian03W.Configuring GaussSumI opened the Settings dialog box, by clicking on File/Settings, and verified that the location of the Gnuplot executable was correct by clicking on the Test button.Geometry optimisation Input file:PhCCCC_gopt.gjf Partial output file:PhCCCC_gopt_partial.out Complete output file:PhCCCC_gopt.outDuring the initial SCF calculation, I ran GaussSum (Monitor SCF; defaults; PhCCCC_gopt_partial.out) to see whether the calculation was converging. The result is shown below. The line is heading towards zero, which indicates that the SCF is converging.The progress of the geometry optimisation was also monitored during the calculation. The geometry optimisation proceeded smoothly to an energy minimum as shown by the graph below (Monitor GeoOpt; defaults; PhCCCC_gopt.out).Molecular orbital information Input file:PhCCCC_gopt.gjf Output file:PhCCCC_gopt.out GaussSum outputs:gausssum2.1/orbital_data.txtgausssum2.1/DOS_spectrum.txtI extracted the molecular orbital information from the output file of the geometry optimisation (Orbitals; defaults; PhCCCC_gopt.out). Molecular orbital information was written to the orbital_data.txt file in a subdirectory called gausssum2.1. Information on the frontier orbitals is shown below.MOeVSymmetry40L+47.42BG39L+34.96AU38L+23.01BG37L+12.46AU36LUMO1.02AU35HOMO-4.17BG34H-1-5.31BG33H-2-5.78AU32H-3-7.17BG31H-4-7.82AGA density of states diagram was convoluted from the molecular orbital data (Orbitals; DOS, start=-15, end=8, FWHM=0.3; PhCCCC_gopt.out). It is shown below. The data used to draw this graph is contained in gausssum2.1/DOS_spectrum.txt. Input:PhCCCC_pop.gjf Output:PhCCCC_pop.out GaussSum input:gausssum2.1/groups.txt GaussSum outputs:gausssum2.1/orbital_data.txtgausssum2.1/DOS_spectrum.txtgausssum2.1/origin_orbs.txtI wanted to describe each molecular orbital in terms of a percent contribution from the benzene portion, and a percent contribution from the divinyl portion. GaussSum can use Mulliken population analysis to do this (please be aware that Mulliken population analysis has some severe shortcomings). First of all, I needed to make Gaussian output orbital overlap information and information on the molecular orbital coefficients. This required a single point energy calculation with the keywords POP=FULL IOP(9/33=1,9/36=-1).Next, I created a file called groups.txt in the gausssum2.1 subdirectory, which contained the following lines:atomsC6H41-8,19-20C=C9-18Finally, I used GaussSum to calculate the molecular orbital contributions again (Orbitals; defaults; PhCCCC_pop.out, gausssum2.1/groups.txt). This time, orbital_data.txt contained more information (see below for information on the frontier orbitals). The HOMO is about 50/50 C6H4and divinyl. The so-called accurate values should be ignored, although they are required for the Electronic transitions option to calculate changes in electron density. (Note that these columns are tab-separated and so can be imported easily into spreadsheet software.)MOeVSymmetryC6H4C=CAccurate values (for the Electronic transitions module)38L+23.01BG17830.1684302093240.8315700245237L+12.46AU10000.9998186530490.00018185951061336LUMO1.02AU54460.5432821273180.45672539915335HOMO-4.17BG54460.5417785039970.45822859435434H-1-5.31BG10000.9998774411720.00014157036335933H-2-5.78AU15850.1548993041330.845103027118The initial DOS spectrum created by GaussSum did not include any of the virtual orbitals. As a result, I wanted to change the start and end point of the spectrum, but I did not want to recalculate all of the contributions of the groups. I set Use existing orbital_data.txt? to TRUE, and altered the values of start and end until I was happy (Orbitals; start=-15, end=8, FWHM=0.3, Use existing orbital_data.txt?=TRUE; PhCCCC_pop.out):A nicer image can be created using spreadsheet software, or a program such as Microcal Origin, and the file gausssum2.1/DOS_spectrum.txt. The image below was created using Microcal Origin (for Linux, try Scigraphica or Grace).Instead of drawing a DOS curve, you may prefer to use a more straightforward depiction of the breakdown of molecular orbitals between various groups in a molecule. To do so, set Create originorbs.txt to TRUE, and rerun GaussSum (Orbitals; start=-15, end=8, FWHM=0.3, Use existing orbital_data.txt?=TRUE, Create originorbs.txt?=TRUE; PhCCCC_pop.out). Origin or Grace may then be used to create the image shown below using the data in gausssum2.1/origin_orbs.txt (it may take some practice - in Origin you need to set the columns XYXY, and plot the four columns using 2-point segments). Input:PhCCCC_pop.gjf Output:PhCCCC_pop.out GaussSum input:gausssum2.1/groups.txt GaussSum outputs:gausssum2.1/COOP_data.txtgausssum2.1/COOP_spectrum.txtThe interaction between the two groups can be visualised using a COOP (Crystal Orbital Overlap Population) diagram. This interaction is measured by the degree of positive/negative overlap for a particular molecular orbital. For more information on its use, see the paper of Herlem and Lakard listed in thebibliography. The diagram below was created from PhCCCC_pop.out using GaussSum (Orbitals; COOP, start=-15, end=8, FWHM=0.3; PhCCCC_pop.out, gausssum2.1/groups.txt).Vibrational spectrum Input:PhCCCC_IR.gjf Output:PhCCCC_IR.out GaussSum outputs:gausssum2.1/IRSpectrum.txtgausssum2.1/IRSpectrum.txt (after scaling)I calculated the vibrational frequencies of divinylbenzene and their associated IR intensities. GaussSum extracts this information from the log file into gausssum/IRSpectrum.txt (Frequencies; start=0, end=1000, num pts=500, FWHM=3, Scaling factors=(General,1.00); PhCCCC_IR.out):Normal ModesModeLabelFreq (cm-1)IR act1AU52.78810.03232BG83.93680.03AU148.15710.38264BU178.67270.2686I wanted to scale all normal modes greater than 1000 cm-1by 0.5 (this is not a real example! :-). I opened IRSpectrum.txt in Excel, and changed the values for the scaling factors from 1.00 to 0.5 for those normal modes greater than 1000 cm-1. I resaved IRSpectrum.txt in the same format (Tab-separated) and location. After choosing the Frequencies option I chose Individual scaling factors and ran GaussSum again (Frequencies; start=0, end=1000, num pts=500, FWHM=3, scaling factors=Individual; PhCCCC_IR.out, gausssum2.1/IRSpectrum.txt). The result is shown below.UV-Visible Spectrum Input:PhCCCC_TD.gjf Output:PhCCCC_TD.out GaussSum outputs:gausssum2.1/UVSpectrum.txtgausssum2.1/UVData.txtI wanted to calculate the UV-Vis absorption spectrum of divinylbenzene. I added the keyword IOP(9/40=2) to the TD-DFT command, to output information on smaller contributions to each electronic transition.I ran the Electronic transitions option with the default settings (Electronic transitions; start=300, end=800, num pts=500, fwhm=3000; PhCCCC_TD.out) but no graph was drawn, and there was a message There are no peaks in this wavelength range!. I looked at gausssum2.1/UVData.txt and saw that the lowest energy peak was at about 230nm. I ran the Electronic transitions option again, this time using more appropriate values for the start and end of the diagram (Electronic transitions; start=170, end=270, num pts=500, fwhm=3000; PhCCCC_TD.out) and the