科学网

 找回密码
  注册

tag 标签: 参数设置

相关帖子

版块 作者 回复/查看 最后发表

没有相关内容

相关日志

[转载]Origin科学制图的方法
jylmechanics 2019-1-16 22:54
文章转载于 “人人网-http://blog.renren.com/share/225440475/12720285666/0”。 科技绘图还是用Matlab好,但操作较为繁琐困难。另外,它还有个缺点:坐标轴的位置太死板。虽然网上有些代码可以设置其位置。不过据我所知,好像都不如默认的坐标轴效果好,例如坐标轴线宽和刻度字体设置不变,缩放效果没有保证等等。这些问题是可以通过相应的命令解决的,但没有通用性。期待Matlab下一个版本完善这个Bug吧。 相比于Excel图形的粗糙、Matlab的专业,Origin兼得了图形美观和易于操作的优点。关于Origin本身的设置帖子很多了,但是如何精确控制Origin输出到Word中图片的大小图例的方法很难找到,而科技论文投稿中对图片尺寸的要求较高。绘图完成后通过Word自带的剪切功能或者PS修改都多多少少的造成一些失真,即使没有,我依然觉得原版的好。 第一部分:精确控制Origin输出到Word中图片的大小——包括线宽、文字、图例 1. Tool——Option里设置如下几个量: (1) Page——在Copy Page Setting下的Ratio选择100,其他可继续设置,如Advance:Set Resolutior 600 (设置复制比例100%,可以将此设为默认)。这一步设置保证复制比例为100%,建议将此设为默认。 图1 Origin中选项操作示意图 (2) Text Fonts——勾选WYSIWYG in Page View Model。Origin默认是视图方式是Page View,而WYSIWYG是指所见即所得,这样可以保证打印效果与屏幕显示的一致。这里也可以设置字体格式及其大小。 3. 将图片所有信息粗略调整到Page空间中(步骤2启用后,Page可能很小,需要后续细致设置)。然后,View——Whole Page (快捷键Ctrl + W)。此时屏幕上图片的尺寸可能大于设置尺寸,但不影响输出效果(如果你对自己的眼神很有信心,也可以跳过这一步)。 4. 详细设置图片格式,建议线宽0.5、图标3磅、字体9~10磅、坐标轴Title Format——Thickness:0.5,Major Tick:3。 5. Edit——Copy Page (快捷键Ctrl + J),可以在Word直接Ctrl + V,也可以“复制”——“选择性粘贴”——“图元文件”。前者可在Word中打开修改,后者仅仅是图片。看看图片大小效果吧,ps. 1 inch = 2.54 centimeter。 第二部分:保持Origin作图格式一致 如果做好了一幅图,它的格式如下: 图片:7.5 cm×7.5 cm 字体:Times New Roman,10号 线宽:0.5磅; 图例:3磅; 坐标轴:Thickness:0.5,Major Tick:3 如果要画同一格式的很多图,一一设置显然低效。另外,按上述要求设置图片可以满足大多数期刊投稿要求,因此,这也希望能快速设置,减少工作量。Origin的自定义模板可以实现此目的。 1. 在已经完成各项设置的图片上点击右键选择:Save Format as Theme,弹出如下对话框: 2. 在Name of the new里自定义一个名字,建议把Form ats to Save里All前面的勾去掉,选择Fonts,Colors,Symbol,Dimension,Background和Text。注意,All Styles和Scale不建议选(注意:如果选择Set as System Theme,以后画的图都是这个图的格式了。在确定满意之前,最好检验下,所以这里先不选这一项)。点击OK,保持模板。 3. 另画一幅图,然后在菜单Tools里选择Theme Organizer,找到你自定义的模板,例如ACS S,点击右侧Apply Now; 4. 检查应用模板后的图片是否满足要求。如果满足要求,希望以后的图片都是这种格式,则选中该模板,右击选择Set as System Theme。如果不满足要求,举一反三,自己搞定吧。 感谢该博主对Origin科学制图的讲解,再次将文章内容记录在科学网中,后需希望随着自己对Origin软件的操作,将此用于自己后续的数据分析中,同时将自己的使用心得不断添加进来。 2019年1月16日 于哈尔滨-科学院A栋
个人分类: 科技绘图|5638 次阅读|0 个评论
[转载]怎么设置贝叶斯Mrbayes中各种碱基替换模型参数
Bearjazz 2018-1-21 17:42
# 编者信息 熊荣川 明湖实验室 xiongrongchuan@126.com http://blog.sciencenet.cn/u/Bearjazz ##GTR lset applyto=() nst=6 # GTR lset applyto=() nst=6 rates=propinv # GTR + I lset applyto=() nst=6 rates=gamma # GTR + gamma lset applyto=() nst=6 rates=invgamma # GTR + I + gamma ##SYM lset applyto=() nst=6 # SYM prset applyto=() statefreqpr=fixed(equal) lset applyto=() nst=6 rates=propinv # SYM + I prset applyto=() statefreqpr=fixed(equal) lset applyto=() nst=6 rates=gamma # SYM + gamma prset applyto=() statefreqpr=fixed(equal) lset applyto=() nst=6 rates=invgamma # SYM + I + gamma prset applyto=() statefreqpr=fixed(equal) ##HKY lset applyto=() nst=2 # HKY lset applyto=() nst=2 rates=propinv # HKY + I lset applyto=() nst=2 rates=gamma # HKY + gamma lset applyto=() nst=2 rates=invgamma # HKY + I + gamma ##K2P lset applyto=() nst=2 # K2P prset applyto=() statefreqpr=fixed(equal) lset applyto=() nst=2 rates=propinv # K2P + I prset applyto=() statefreqpr=fixed(equal) lset applyto=() nst=2 rates=gamma # K2P + gamma prset applyto=() statefreqpr=fixed(equal) lset applyto=() nst=2 rates=invgamma # K2P + I + gamma prset applyto=() statefreqpr=fixed(equal) ##F81 lset applyto=() nst=1 # F81 lset applyto=() nst=1 rates=propinv # F81 + I lset applyto=() nst=1 rates=gamma # F81 + gamma lset applyto=() nst=1 rates=invgamma # F81 + I + gamma Jukes Cantor lset applyto=() nst=1 # JC prset applyto=() statefreqpr=fixed(equal) lset applyto=() nst=1 rates=propinv # JC + I prset applyto=() statefreqpr=fixed(equal) lset applyto=() nst=1 rates=gamma # JC + gamma prset applyto=() statefreqpr=fixed(equal) lset applyto=() nst=1 rates=incgamma # JC + I + gamma prset applyto=() statefreqpr=fixed(equal) 转载自以下网址 https://gist.github.com/brantfaircloth/895282 注:K80模型设置同 HKY
个人分类: 我的研究|4688 次阅读|0 个评论
[转载]vdW-DF functional of Langreth and Lundqvist et al.
yxx554243496 2017-3-28 17:52
vdW-DF functional of Langreth and Lundqvist et al. http://cms.mpi.univie.ac.at/vasp/vasp/vdW_DF_functional_Langreth_Lundqvist_et_al.html The vdW-DF proposed by Dion et al. is a non-local correlation functional that approximately accounts for dispersion interactions. In VASP the method is implemented using the algorithm of Roman-Perez and Soler which transforms the double real space integral to reciprocal space and reduces the computational effort. Several propsed versions of the method can be used: the original vdW-DF , the ``opt functionals (optPBE-vdW, optB88-vdW, and optB86b-vdW) where the exchange functionals were optimised for the correlation part , and the vdW-DF2 of Langreth and Lundqvist groups . This method is available since the 5.2.12.26May2011 version of VASP for the calculation of total energies and forces. The stress calculation for the cell optimisation (ISIF=3) is available since the VASP 5.2.12.11Nov2011 version for spin unpolarised systems and VASP 5.3.1 for spin polarised systems. N.B. : This feature has been implemented by J. Klimeš. If you make use of the vdW-DF functionals presented in this section, we ask that you cite the following paper: J. Klimeš, D. R. Bowler, and A. Michaelides, Phys. Rev. B 83 , 195131 (2011). Correlation functionals The method is invoked by setting LUSE_VDW = .TRUE. Moreover, the PBE correlation correction needs to be removed since only LDA correlation is used in the functionals. This is done by setting AGGAC = 0.0000 The two tags above need to be used for all of the following functionals. Exchange functionals The GGA tag is further used to choose the appropriate exchange functional. The original vdW-DF of Dion et al uses revPBE, therefore the vdW-DF can be chosen by setting GGA = RE LUSE_VDW = .TRUE. AGGAC = 0.0000 More accurate exchange functionals for the vdW correlation functional have been proposed in and . To use these functionals set: GGA = OR LUSE_VDW = .TRUE. AGGAC = 0.0000 【1】 for optPBE-vdW , GGA = BO PARAM1 = 0.1833333333 PARAM2 = 0.2200000000 LUSE_VDW = .TRUE. AGGAC = 0.0000 【2】 for the optB88-vdW functional or for the optB86b-vdW functional: GGA = MK PARAM1 = 0.1234 PARAM2 = 1.0000 LUSE_VDW = .TRUE. AGGAC = 0.0000 【3】 In the vdW-DF2 functional the rPW86 exchange functional is used: GGA = ML LUSE_VDW = .TRUE. Zab_vdW = -1.8867 AGGAC = 0.0000 An overview of the performance of the different approaches can be found for example in for gas phase clusters and in for solids. Important remarks : The method needs a precalculated kernel which is distributed via the VASP download portal (VASP - src - vdw_kernel.bindat) and on the ftp server (vasp5/src/vdw_kernel.bindat). If VASP does not find this file, the kernel will be calculated. This, however, is rather demanding calculation. The kernel needs to be either copied to the VASP run directory for each calculation or can be stored in a central location and read from there. The location needs to be set in routine PHI_GENERATE. This does not work on some clusters and the kernel needs to be copied into the run directory in such cases. The distributed file uses little endian convention and won't be read on big endian machines. The big endian version of the file is available from the VASP team. There are no special POTCARs for the vdW DF functionals and the PBE or LDA POTCARs can be used. Currently the evaluation of the vdW energy term is not done fully within the PAW method but the sum of the pseudo-valence density and partial core density is used. This approximation works rather well, as is discussed in , and the accuracy generally increases when the number of valence electrons is increased or when harder PAW datasets are used. For example, for adsorption it is recommended to compare the adsorption energy obtained with standard PAW datasets and more electron POTCARs for both PBE calculation and vdW DF calculation to assess the quality of the results. The spin polarised calculations are possible, but strictly speaking the nonlocal vdW correlation is not defined for spinpolarised systems. For spinpolarised calculation the nonlocal vdW correlation energy is evaluated on the sum of the spin-up and spin-down densities. The evaluation of the vdW energy requires some additional time. Most of it is spent on performing FFTs to evaluate the energy and potential. Thus the additional time is determined by the number of FFT grid points in the calculation, basically size of the simulation cell. It is almost independent on the number of the atoms in the cell. Thus the relative cost of the vdW DF method depends on the“filling of the cell and increases with the amount of vacuum in the cell. The relative increase is high for isolated molecules in large cells, but small for solids in smaller cells with many k-points. This feature has been implemented by J. Klimeš. If you make use of the vdW-DF functionals presented in this section, we ask that you cite the following paper: J. Klimeš, D. R. Bowler, and A. Michaelides, Phys. Rev. B 83 , 195131 (2011).
个人分类: VASP计算|1810 次阅读|0 个评论
写了篇Citespace基础教程的文章
mpcer 2014-8-29 20:53
结合前段时间使用citespace的经历,写了篇题为《CiteSpace可视化流程与分析范式研究》的文章,专门讲解Citespace引文分析的基本过程和范式,有需要的可到知网下载参考(http://www.cnki.net),希望对您有点意义。等您点评拍砖。
个人分类: CiteSpace|4126 次阅读|0 个评论
citespace时间分区(TimeSlicing)杂谈
mpcer 2014-4-20 11:46
时间分割( TimeSlicing )包括 时间跨度 和 时间分区长度 2项参数。时间跨度指定引文发表的年份( PY 字段值)范围,取值由引文年份分布和分析者所关注的时间段决定。时间分区长度是对整个时间跨度的划分,以年为单位,最短为一年,最长到整个时间跨度,建议采用等长时间分区(年数除以时间分区长度为整数),在时间分区内引文按阈值独立筛选,各时间分区阈值可不同 ,这取决于阈值的设置方式。
11869 次阅读|0 个评论
mysql使用笔记
liujd 2011-12-5 10:59
1,查询设置mysql参数 查询: show VARIABLES like '%max_allowed_packet%'; 设置:mysql --max_allowed_packet=32M 2,启动mysql service mysqld restart/stop/start 3,关于TINYTEXT、TEXT、MEDIUMTEXT和LONGTEXT数据长度 对应的长度为:256, 2 16 -1,2 24 -1,2 32 -1 太长时需要设置max_allowed_packet值,否则数据会丢失 4,blod和text区别 blod不检查字符,都当作二进制处理;text要进行合法字符检查,如果不是合法字符,那么会丢失。 5,查看创建表格或者视图的命令 show create table tablename 如:show create table booktb; 6,清除mysql的屏幕 ctrl+L或者
个人分类: mysql|930 次阅读|0 个评论

Archiver|手机版|科学网 ( 京ICP备07017567号-12 )

GMT+8, 2024-5-23 11:47

Powered by ScienceNet.cn

Copyright © 2007- 中国科学报社

返回顶部