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

naonao5205 · 发表于 Post on 2020-7-11 14:53:30

sob老师发现了疑似一个BUG 无法正确得到自由能校正量以下是输出文件

[naonao5205@localhost done]$ Shermo CH4.log -sclZPE 0.9699
Shermo: A general code for calculating molecular thermochemistry properties
Version 2.0.1 Release date: 2020-May-20
Developer: Tian Lu (sobereva@sina.com)
Beijing Kein Research Center for Natural Sciences (http://www.keinsci.com)
Official website: http://sobereva.com/soft/shermo
If this code is utilized in your work, PLEASE CITE:
Tian Lu, Qinxue Chen, Shermo: A general code for calculating molecular thermodynamic properties, ChemRxiv (2020) DOI: 10.26434/chemrxiv.12278801
Loading running parameters from settings.ini...
Command of invoking Shermo:
Shermo CH4.log -sclZPE 0.9699
Note: One or more running parameters are overridden by arguments
Running parameters:
Printing individual contribution of vibration modes: No
Temperature: 298.150 K
Pressure: 1.000 atm
Scale factor of vibrational frequencies for ZPE: 0.9699
Scale factor of vibrational frequencies for U(T)-U(0): 1.0000
Scale factor of vibrational frequencies for S(T): 1.0000
Scale factor of vibrational frequencies for CV: 1.0000
Low frequencies treatment: Harmonic approximation
Default atomic masses: Same as the output file
Loading Gaussian output file...
Note: The electronic energy loaded from input file will be used
Detecting point group...
Point group has been successfully detected
Warning: Rotational symmetry number cannot be identified for this point group
======= Molecular information =======
Electronic energy: -40.45014800 a.u.
Spin multiplicity: 1
Atom 1 (C ) Mass: 12.000000 amu
Atom 2 (H ) Mass: 1.007830 amu
Atom 3 (H ) Mass: 1.007830 amu
Atom 4 (H ) Mass: 1.007830 amu
Atom 5 (H ) Mass: 1.007830 amu
Total mass: 16.031320 amu
Point group: Td
Rotational symmetry number: 0
Principal moments of inertia (amu*Bohr^2):
11.547243 11.547249 11.547256
Rotational constants relative to principal axes (GHz):
156.291956 156.291877 156.291784
Rotational temperatures (K): 7.500822 7.500819 7.500814
This is not a linear molecule
There are 9 frequencies (cm^-1):
1318.9 1318.9 1318.9 1538.8 1538.8 3052.9 3196.7 3196.7 3196.7
Note: Only for translation, U is different to H, and CV is different to CP
======= Translation =======
Translational q: 1.519356E+030 q/NA: 2.522950E+006
Translational U: 3.718 kJ/mol 0.889 kcal/mol
Translational H: 6.197 kJ/mol 1.481 kcal/mol
Translational S: 143.349 J/mol/K 34.261 cal/mol/K -TS: 10.21 kcal/mol
Translational CV: 12.472 J/mol/K 2.981 cal/mol/K
Translational CP: 20.786 J/mol/K 4.968 cal/mol/K
========= Rotation ========
Rotational q: Infinity
Rotational U: 3.718 kJ/mol 0.889 kcal/mol =H
Rotational S: Infinity J/mol/K Infinity cal/mol/K -TS:Infinity kcal/mol
Rotational CV: 12.472 J/mol/K 2.981 cal/mol/K =CP
======== Vibration ========
Vibrational q(V=0): 1.006382E+000
Vibrational q(bot): 2.416432E-021
Vibrational U(T)-U(0): 0.104 kJ/mol 0.025 kcal/mol =H(T)-H(0)
Vibrational U: 114.258 kJ/mol 27.308 kcal/mol =H
Vibrational S: 0.400 J/mol/K 0.096 cal/mol/K -TS: 0.029 kcal/mol
Vibrational CV: 2.294 J/mol/K 0.548 cal/mol/K =CP
Zero-point energy (ZPE): 114.15 kJ/mol, 27.28 kcal/mol 0.043479 a.u.
======== Electron excitation ========
Electronic q: 1.000000E+000
Electronic U: 0.000 kJ/mol 0.000 kcal/mol =H
Electronic S: 0.000 J/mol/K 0.000 cal/mol/K -TS: 0.000 kcal/mol
Electronic CV: 0.000 J/mol/K 0.000 cal/mol/K =CP
===========================
========== Total ==========
===========================
Total q(V=0): Infinity
Total q(bot): Infinity
Total q(V=0)/NA: Infinity
Total q(bot)/NA: Infinity
Total CV: 27.238 J/mol/K 6.510 cal/mol/K
Total CP: 35.552 J/mol/K 8.497 cal/mol/K
Total S: Infinity J/mol/K Infinity cal/mol/K -TS: Infinity kcal/mol
Thermal correction to U: 121.695 kJ/mol 29.086 kcal/mol 0.046351 a.u.
Thermal correction to H: 124.174 kJ/mol 29.678 kcal/mol 0.047295 a.u.
Thermal correction to G: -Infinity kJ/mol -Infinity kcal/mol -Infinity a.u.
Electronic energy: -40.4501480 a.u.
Sum of electronic energy and ZPE, namely U/H/G at 0 K: -40.4066689 a.u.
Sum of electronic energy and thermal correction to U: -40.4037969 a.u.
Sum of electronic energy and thermal correction to H: -40.4028527 a.u.
Sum of electronic energy and thermal correction to G: -Infinity a.u.

复制代码

sobereva · 发表于 Post on 2020-7-12 09:00:18

naonao5205 发表于 2020-7-11 14:53
sob老师发现了疑似一个BUG 无法正确得到自由能校正量以下是输出文件

上传你的Gaussian输出文件我检查一下

naonao5205 · 发表于 Post on 2020-7-12 11:41:50

sobereva 发表于 2020-7-12 09:00
上传你的Gaussian输出文件我检查一下

这个文件，在linux和win10下输出均如上但可以用guassian自带的freqchk

sobereva · 发表于 Post on 2020-7-13 10:59:26

naonao5205 发表于 2020-7-12 11:41
这个文件，在linux和win10下输出均如上但可以用guassian自带的freqchk

是个bug，我已修正并更新了Shermo主页上的版本。这个问题只对Td点群有，是没有对转动对称数赋值所致。

naonao5205 · 发表于 Post on 2020-7-13 12:32:37

sobereva 发表于 2020-7-13 10:59
是个bug，我已修正并更新了Shermo主页上的版本。这个问题只对Td点群有，是没有对转动对称数赋值所致。

sob老师实测更新后win版本解决了但是linux执行文件依然有这个问题
我是centos8环境

sobereva · 发表于 Post on 2020-7-14 08:01:46

naonao5205 发表于 2020-7-13 12:32
sob老师实测更新后win版本解决了但是linux执行文件依然有这个问题
我是centos8环境

Linux版也解决了，之前弄错文件了

GoldenBaby · 发表于 Post on 2020-7-17 14:10:50

请问sob老师，Shermo支持MOPAC或者xtb的热力学数据计算吗？

sobereva · 发表于 Post on 2020-7-17 15:59:50

GoldenBaby 发表于 2020-7-17 14:10
请问sob老师，Shermo支持MOPAC或者xtb的热力学数据计算吗？

不支持

sobereva · 发表于 Post on 2020-7-23 21:39:14

Shermo今日发布了2.0.3版，解决了一个新发现的bug：对于某些体系在做热力学量扫描的时候，给出的转动熵错误，导致输出的熵和自由能错误。

请之前的Shermo用户尽快去http://sobereva.com/soft/shermo/下载新版本。

sobereva · 发表于 Post on 2020-9-17 20:31:11

给本文增加了第5节，专门给初学者介绍了怎么非常容易地调用Shermo批量计算

hzfish · 发表于 Post on 2020-9-29 10:22:42

sobereva 发表于 2020-7-14 08:01
Linux版也解决了，之前弄错文件了

2.0.4版对Th点群还是有同样的问题。

                        ===========================
                        ========== Total ==========
                        ===========================
Total q(V=0):          Infinity
Total q(bot):          Infinity
Total q(V=0)/NA:       Infinity
Total q(bot)/NA:       Infinity
Total CV:    240.342 J/mol/K    57.443 cal/mol/K
Total CP:    248.657 J/mol/K    59.430 cal/mol/K
Total S:    Infinity J/mol/K Infinity cal/mol/K -TS: -Infinity kcal/mol
Thermal correction to U: 405.455 kJ/mol    96.906 kcal/mol 0.154430 a.u.
Thermal correction to H: 407.934 kJ/mol    97.499 kcal/mol 0.155374 a.u.
Thermal correction to G:  -Infinity kJ/mol  -Infinity kcal/mol  -Infinity a.u.
Electronic energy:    -701.0371940 a.u.
Sum of electronic energy and ZPE, namely U/H/G at 0 K:    -700.8995304 a.u.
Sum of electronic energy and thermal correction to U:       -700.8827644 a.u.
Sum of electronic energy and thermal correction to H:       -700.8818202 a.u.
Sum of electronic energy and thermal correction to G:          -Infinity a.u.

sobereva · 发表于 Post on 2020-9-29 15:03:30

hzfish 发表于 2020-9-29 10:22
2.0.4版对Th点群还是有同样的问题。

===========================

请把你的文件上传，否则我没法测试
我这里测试过的都没问题

hzfish · 发表于 Post on 2020-9-29 16:28:48

sobereva 发表于 2020-9-29 15:03
请把你的文件上传，否则我没法测试
我这里测试过的都没问题

Th点群的例子。

sobereva · 发表于 Post on 2020-9-30 19:50:43

hzfish 发表于 2020-9-29 16:28
Th点群的例子。

是个bug，我已更新了Shermo官网上的2.0.5版修正了这个bug

hzfish · 发表于 Post on 2020-9-30 20:58:46

sobereva 发表于 2020-9-30 19:50
是个bug，我已更新了Shermo官网上的2.0.5版修正了这个bug

社长，其它高对称性点群是否一并测试过？

		自动登录 Automatic login	找回密码 Forget password
密码 Password			注册 Register

[辅助/分析程序] 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

评分 Rate

评分 Rate