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标题: Shermo 2.6发布，已支持读取xtb输出的文件计算热力学量 [打印本页]

作者
Author: sobereva 时间: 2024-2-11 20:20
标题: Shermo 2.6发布，已支持读取xtb输出的文件计算热力学量
下文介绍的现在很流行的计算热力学量的程序Shermo今日发布了2.6版，主要改进是支持了基于xtb程序输出的文件计算热力学量。对目前最新的xtb 6.6.1版测试可用，对很老的版本不一定支持。
使用Shermo结合量子化学程序方便地计算分子的各种热力学数据
http://sobereva.com/552（http://bbs.keinsci.com/thread-17494-1-1.html）

具体来说，用xtb做--hess或--ohess任务后会得到g98.out文件，是伪Gaussian输出文件，这个文件可以作为Shermo的输入文件算热力学量。有一点特别的是，g98.out里不包含电子能量信息，如果你也没通过settings.ini的参数E（或命令行方式运行Shermo时用-E参数）来提供能量信息，那么Shermo载入这个文件后，还会让你输入xtb输出文件的路径（输出文件指诸如xtb kastoria.xyz --ohess > kastoria.out产生的kastoria.out文件），Shermo会从里面读取最后一次输出的电子能量；而如果你不输入路径而直接按回车，则电子能量视为0。

作者
Author: LiHuaYu 时间: 2024-3-23 21:01
Entropy is no more consistent with entropy calculated by Gaussian. Not sure why?

作者
Author: sobereva 时间: 2024-3-23 21:32

LiHuaYu 发表于 2024-3-23 21:01
Entropy is no more consistent with entropy calculated by Gaussian. Not sure why?

Shermo by default uses QRRHO model, which is much better than RRHO used in Gaussian when there are very low frequency modes.

作者
Author: LiHuaYu 时间: 2024-3-23 22:44

sobereva 发表于 2024-3-23 21:32
Shermo by default uses QRRHO model, which is much better than RRHO used in Gaussian when there are ...

Version 2.3.6 gives exact entropy values as in Gaussian outputs. I wonder if there is an option to make Shermo 2.6 entropy compatible with Gaussian entropy?

作者
Author: sobereva 时间: 2024-3-24 11:05

LiHuaYu 发表于 2024-3-23 22:44
Version 2.3.6 gives exact entropy values as in Gaussian outputs. I wonder if there is an option to ...

使用Shermo结合量子化学程序方便地计算分子的各种热力学数据
http://sobereva.com/552（http://bbs.keinsci.com/thread-17494-1-1.html）

carefully check this description:

经常有Shermo的用户问为什么Shermo算的热力学校正量和Gaussian输出的不一致，在此专门说一下。要想Shermo输出的热力学校正量和Gaussian直接输出的严格一致，Shermo的settings.ini里的设定必须满足：
• T=和P=分别与Gaussian计算时设的温度和压力一致（Gaussian默认的情况相当于T= 298.15、P= 1.0）
• 频率校正因子和Gaussian设的一致（如果Gaussian计算时没用scale关键词指定，则sclZPE、sclheat、sclS都应当为1.0）
• 热力学量计算模型和Gaussian一致。Gaussian用的是RRHO模型，对应于ilowfreq= 0
如果以上都满足，结果还不一致，且体系结构有对称性，大概率是Gaussian的振动分析部分的代码对体系的点群判断有误，导致转动对称数判断不对，进而导致算出的转动对热力学校正量的贡献错误。而Shermo判断点群的功能明显更稳健，不一致的情况一律以Shermo为准（有多次用户问我此问题的时候我最后都发现俩程序对点群判断不一致，每次都是Shermo是正确的而Gaussian是错误的。可能是Gaussian判断点群的阈值过于严格）。

作者
Author: LiHuaYu 时间: 2024-3-24 12:33

sobereva 发表于 2024-3-24 11:05
使用Shermo结合量子化学程序方便地计算分子的各种热力学数据
http://sobereva.com/552（http://bbs.kein ...

Here, most of the parameters are the same and were used for two version 2.3.6 and 2.6. Total entropy values are totally different.

Version 2.3.6
Total S:    747.803 J/mol/K    178.729 cal/mol/K -TS: -63.118 kcal/mol

Version 2.6
Total S:    712.211 J/mol/K    170.223 cal/mol/K -TS: -60.114 kcal/mol

Gaussian 16

                  E (Thermal)          CV             S
                  KCal/Mol       Cal/Mol-Kelvin Cal/Mol-Kelvin
Total                263.755          104.462          178.729

Parameters used for version 2.3.6

E= 0  //Electronic energy in a.u. If E= 0, then it will be loaded from input file
prtvib= 0  //1: Printing contribution of each vibrational mode.  -1: Printing to vibcontri.txt.  0: Do not print
T= 298.15  //in K. By specifying lower, upper limits and stepsize, e.g. 50,200,10, it can be scanned
P= 1.0  //in atm. By specifying lower, upper limits and stepsize, e.g. 0.5,20,0.1, it can be scanned
sclZPE= 1.0  //Frequency scale factor for ZPE
sclheat= 1.0  //Frequency scale factor for U(T)-U(0) (the same as that for H(T)-H(0))
sclS= 1.0  //Frequency scale factor for S(T)
sclCV= 1.0  //Frequency scale factor for heat capacity
ilowfreq= 2  //Treatment of low frequencies. 0: Harmonic. 1: Raising low frequencies. 2: Grimme's entropy interpolation
ravib= 100  //Raising lower frequencies to this value (cm^-1) when ilowfreq=1
imode= 0  //Mode of evaluating thermodynamic quantities. 0: Consider all terms. 1: Ignore translation and rotation
conc= 0  //If not 0, will calculate variation of Gibbs free energy due to concentration change from present state to the specific state. e.g. "conc= 1.5M" and "conc= 2.3atm"
outshm= 0  //1: Exporting .shm file after loading QC program output file. 0: Do not export
PGlabel= ?  //Point group, e.g. C1, C3v, Dih, Oh. If set to "?", then point group will be identified by Shermo according to geometry
defmass= 3  //Default atomic masses used during reading QC program output file. 1: Element mass. 2: Most abundant isotope. 3: Same as the output file
modmass  //Modification on default atomic masses can be specified below

Parameters used for version 2.6
E= 0  //Electronic energy in a.u. If E= 0, then it will be loaded from input file
prtvib= 0  //1: Printing contribution of each vibrational mode.  -1: Printing to vibcontri.txt.  0: Do not print
T= 298.15  //in K. By specifying lower, upper limits and stepsize, e.g. 50,200,10, it can be scanned
P= 1.0  //in atm. By specifying lower, upper limits and stepsize, e.g. 0.5,20,0.1, it can be scanned
sclZPE= 1.0  //Frequency scale factor for ZPE
sclheat= 1.0  //Frequency scale factor for U(T)-U(0) (the same as that for H(T)-H(0))
sclS= 1.0  //Frequency scale factor for S(T)
sclCV= 1.0  //Frequency scale factor for heat capacity
ilowfreq= 2  //Treatment of low frequencies. 0: Harmonic (RRHO). 1: Raising low frequencies (Truhlar). 2: Entropy interpolation (Grimme). 3: Entropy and internal energy interpolations (Minenkov)
ravib= 100  //Raising lower frequencies to this value (cm^-1) when ilowfreq=1
intpvib= 100 //Vibrational frequency threshold (cm^-1) used in interpolation when ilowfreq=2 and 3
imagreal= 0  //Treat imaginary frequencies with norm smaller than this value (in cm^-1) as real frequencies
imode= 0  //Mode of evaluating thermodynamic quantities. 0: Consider all terms. 1: Ignore translation and rotation
conc= 0  //If not 0, will calculate variation of Gibbs free energy due to concentration change from present state to the specific state. e.g. "conc= 1.5M" and "conc= 2.3atm"
outshm= 0  //1: Exporting .shm file after loading QC program output file. 0: Do not export
PGlabel= ?  //Point group, e.g. C1, C3v, Dih, Oh. If set to "?", then point group will be identified by Shermo according to geometry
defmass= 3  //Default atomic masses used during reading QC program output file. 1: Element mass. 2: Most abundant isotope. 3: Same as the output file
modmass  //Modification on default atomic masses can be specified below

作者
Author: sobereva 时间: 2024-3-25 11:14

LiHuaYu 发表于 2024-3-24 12:33
Here, most of the parameters are the same and were used for two version 2.3.6 and 2.6. Total entro ...

There results based on Grimme's QRRHO using Shermo 2.3.6 and 2.6 are completely the same, using examples\G16_remdesivir_optfreq.out as test file.

Without your file I cannot test

作者
Author: LiHuaYu 时间: 2024-3-25 15:34

sobereva 发表于 2024-3-25 11:14
There results based on Grimme's QRRHO using Shermo 2.3.6 and 2.6 are completely the same, using ex ...

I did more tests and found that in some cases total entropy is similar, but some are not. Attached is an example. The gaussian output log file could not be attached, so it was uploaded to swisstransfer.

(, 下载次数 Times of downloads: 1)

(, 下载次数 Times of downloads: 3)

https://www.swisstransfer.com/d/ ... 3-9b20-897b5195067d

作者
Author: sobereva 时间: 2024-3-26 00:54

LiHuaYu 发表于 2024-3-25 15:34
I did more tests and found that in some cases total entropy is similar, but some are not. Attached ...

The difference is clear from the output:

2.3.6
Low frequencies treatment: Harmonic approximation

2.6
Low frequencies treatment: Grimme's interpolation for entropy
Vibrational frequency threshold used in the interpolation is 100.00 cm^-1

You should always let Shermo find settings.ini. In your running, this file was not found by Shermo, as shown in the output:

Warning: settings.ini cannot be found in either current folder or the directory defined by Shermopath environment, thus default parameters are used!

2.3.6 and 2.6 have difference default settings.

作者
Author: LiHuaYu 时间: 2024-3-26 07:32

sobereva 发表于 2024-3-26 00:54
The difference is clear from the output:

2.3.6

Great thanks. My setting.ini was located in the same directory of Shermo, and I did not paid attention to the warning, my bad. After exporting the Shermopath environment, I can see that the newest version works like a charm. All data produced by the versions 2.3 and 2.6, and Gaussian 16 are now consistent. 多谢.

作者
Author: funyboy 时间: 2024-11-28 23:33
sob老师，我有个困惑，我用Gaussian计算时编写gjf文件用了--Link1--方式实现了多步计算，1、优化及振动分析；2、波函数稳定行分析；3、读取稳定波函数继续优化及振动分析。可是我发现这样得到的out文件会导致我在使用Shermo计算热力学数据时程序读取的是第一次振动分析的结果，而不是我想要的第三步波函数稳定性分析后再次优化振动分析的结果，由于好多个文件而且耗时长，重新单独计算得到单独任务的out文件显然不现实，请问可以设置让程序读取最后一次振动分析的结果吗？

作者
Author: sobereva 时间: 2024-11-28 23:40

funyboy 发表于 2024-11-28 23:33
sob老师，我有个困惑，我用Gaussian计算时编写gjf文件用了--Link1--方式实现了多步计算，1、优化及振动分析 ...

手动删掉前面的，只剩最后一个internal job的信息

作者
Author: funyboy 时间: 2024-11-29 00:07

sobereva 发表于 2024-11-28 23:40
手动删掉前面的，只剩最后一个internal job的信息

明白了，谢谢老师。

作者
Author: funyboy 时间: 2024-11-29 00:34

sobereva 发表于 2024-11-28 23:40
手动删掉前面的，只剩最后一个internal job的信息

老师，我再问一个问题，shermo读取的结果 (, 下载次数 Times of downloads: 4)
out文件结果：
(, 下载次数 Times of downloads: 4)

为何shermo读取的G的校正项和G与out中不一致？其他项倒是严格一致。

作者
Author: sobereva 时间: 2024-12-2 05:05

funyboy 发表于 2024-11-29 00:34
老师，我再问一个问题，shermo读取的结果
out文件结果：

使用Shermo结合量子化学程序方便地计算分子的各种热力学数据
http://sobereva.com/552（http://bbs.keinsci.com/thread-17494-1-1.html）
最后部分明确说了和Gaussian给出的差异

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