假期简单复习的了一下LVTHW的部分内容，也顺便练习了一下吸附能的计算。练习例子是一篇小NC_Nat Commun_ 13, 6853 (2022)中的一个示例，引用量看起来还蛮高的

Nat Commun_ 13, 6853 (2022)

文章提出了PBE+D3/M06 混合计算方法，用于精准描述过渡金属表面吸附能和反应势垒，首先来试一下PBC边界条件下的PBE计算

VASP的周期性计算部分

文献中的例子比较多，选了一个经典的CO在Pt(111)晶面上的吸附。

¶建模

首先是建立模型，FCC的Pt晶胞来自于Material Studio中自带的例子，根据文献，本次结构的吸附气体覆盖度为 $\frac{1}{4}$ ，那么表面将会有4个Pt原子。
首先对Pt的FCC的惯用晶胞切一下，切出 111晶面，文献提到结构是four-layered slab，那么切的时候的thickness设置为4。
这样就得到了p( $1 \times 1$ )的原胞：
p(1*)
但此时表面的Pt原子只有一个，所以还需要扩胞成4个原子，这样才满足文献提到的 $\frac{1}{4}$ 的覆盖度，使用supercell功能扩成p( $2 \times 2$ )的胞：
p(22)
但此时还不是一个完整的晶胞，缺少PBC盒子，比如导出.cif文件会报错，需要添加真空层避免周期性镜像的相互作用，文献中的真空层是20埃的，添加真空层之后就是一个完整的晶胞了：
p(22 cell with vacuum)
纯净的表面构建完毕，接着构建吸附模型，这里的吸附类型是Top顶位吸附，添加碳原子和氧原子（不要加反了，确认谁是表面😢），确保Pt-C-O三个原子在一条直线上，Pt-C距离大概是1.85埃，C-O距离大概是1.15埃，不必在意是否有化学键连接，毕竟POSCAR结构文件中只记录了原子坐标：
吸附模型
最后构建一氧化碳模型，把一氧化碳分子放进一个空盒子就行，操作方法是首先建立一个空盒子（立方晶胞），盒子大小我设置的22埃，可能稍微有点大？k点用一个Gamma点就行。

¶计算

记录下几个关键点就行

计算流程
- 标准弛豫（几何优化）
- 静态计算
计算要点
- 开启自旋极化(ISPIN=2)
  - 虽然Pt和CO都是非磁性的，但是在高精度的计算中开启自旋极化有时会带来微小的能量差异，文献中开启了自旋极化
  - 对于本征非磁性的体系，开启自旋极化不会导致计算错误，可能的副作用是计算成本提高与收敛困难
- 不论是几何优化还是静态计算，确保ISIF=2即不改变晶胞体积
- 开启选择性动力学标记，在POSCAR第八行（Direct或Cartesian行上面）写入大写的S，根据文献，固定下面两层Pt，开放上面两层Pt以及表面的CO分子
- 计算时的结构是固体-真空……交替的结构，此slab模型是非对称的，z方向存在偶极，随之产生静电势，这会影响周期性边界条件，需要消除这种影响
  - 开启z方向上的偶极校正(IDIPOL=3)，修正z方向上的能量
  - 开启对势能和力的修正，LDIPOL=.TRUE.，副作用：显著减慢收敛到电子基态的速度
- 化学吸附强度毕竟不如化学键，为了准确描述这种弱相互作用（GGA-PBE泛函的描述不够准确）需要开启DFT-D3色散校正，高版本的vasp提供了不同DFT-D3实现形式，根据文献，使用BJ阻尼DFT-D3色散校正，参数为IVDW=12
- 平面波截断能ENCUT
  - 几何优化用500
  - 静态计算用700
- ISMEAR=2，文献中明确提到了：Partial occupations were obtained using the Methfessel-Paxton scheme of order 2 with a smearing of 0.2 eV，Methfessel-Paxton 方法（ISMEAR > 0）是专门为金属设计的。相比于 Gaussian (ISMEAR = 0)，它能让总能量关于K点的收敛速度更快。在计算CO的时候一定改回高斯展宽。
- k点选择
  - Gamma撒点
  - 几何优化 $4 \times 4 \times 1$ ，静态计算 $8 \times 8 \times 1$

收敛相对会慢一些：
吸附模型的几何优化
一共18个原子，用时如下：

(base) storm@X16:~/test/ads/ads/opt$ tail OUTCAR
                            User time (sec):    15699.993
                          System time (sec):      101.669
                         Elapsed time (sec):    16178.992

                   Maximum memory used (kb):      628856.
                   Average memory used (kb):          N/A

                          Minor page faults:      1405416
                          Major page faults:            0
                 Voluntary context switches:        14197

¶吸附能

根据文献，吸附能的计算公式为：

E_{adsorption} = E_{ads_slab} - E_{slab} - E_{CO}

能量的查看可以是OSZICAR的最后一行，比如：

[lalala728@wh-login01 ST]$ cat OSZICAR 
       N       E                     dE             d eps       ncg     rms          ort
SDA:   1    -0.147968374953E+02   -0.14797E+02    0.00000E+00    16   0.129E-07 0.000E+00
CGA:   2    -0.147968374962E+02   -0.96497E-09   -0.25614E-08    16   0.690E-08 0.834E-08
CGA:   3    -0.147968374956E+02    0.63460E-09   -0.10626E-08    16   0.437E-08 0.440E-08
CGA:   4    -0.147968374847E+02    0.10848E-07   -0.41650E-08    16   0.475E-07-0.591E-08
CGA:   5    -0.147968374883E+02   -0.36002E-08   -0.42707E-08    16   0.418E-09 0.790E-09
CGA:   6    -0.147968374886E+02   -0.28069E-09    0.55850E-11    16   0.266E-09 0.754E-10
   1 F= -.14808028E+02 E0= -.14808028E+02  d E =-.364215E-19

Methfessel-Paxton方法会引入非物理的熵项 ( $T Δ S$ )，其中：

F是自由能 (Free energy, 包含熵)。
$E_{0}$ 是外推到 0K 的能量 (Energy for sigma->0)
计算吸附能时，必须统一使用 $E_{0}$

我最初的计算为：

E = - 118.643 - (- 92.526) - (- 14.797) = - 11.32 eV

与文献相差了-1.86eV，这是一个比较大的误差。检查后发现纯净的slab以及一氧化碳分子在计算的时候没有开启DFT-D3色散校正，开启后结果变成了：

E = - 118.643 - (- 101.677) - (- 14.808) = - 2.185 eV

距离文献还有0.3 eV的差距，最后发现文献中开启了自旋极化，开启之后大约的确是复现成功了：

E = - 118.640 - (- 101.969) - (- 14.808) = - 1.863 eV \approx - 42.96 kcal/mol

接近文献中提到的：

The PBE+D3 predicted an adsorption energy of -42.9 kcal mol⁻¹ for CO at the top site of the surface…

量子化学计算部分

PBE+D3预测预测的吸附能与实验值仍有差距(-29.6 ± 3.4 kcal/mol)，用VASP做的PBE+D3 计算严重高估了吸附能，应当进行如下修正：

E_{ads}^{Final} = E_{Ads, PBC}^{P B E + D 3} + (E_{Ads, Cluster}^{M 06} - E_{A d s, C l u s t e r}^{P B E + D 3})

¶建模

取vasp几何优化之后的结构：

Symmetry-Unbuild Crystal，这样盒子就被删掉了，然后手动选中原子删除，顶层吸附位点周围六个Pt原子、次顶层三个原子，构建这样一个原子团簇：

¶计算结果

吸附能计算：

E_{Ads, Cluster}^{ω B 97 M - V} = - 0.07743 E h

E_{Ads, Cluster}^{P B E + D 3} = - 0.07925 E h

最终的吸附能：

E = - 1.863 e V + (- 0.07743 + 0.07925) \times 27.211386 (e V) = - 1.81347

这是第一次计算的结果，很顺利踩坑了，因为所有的自旋多重度都设置的一，关键在于自旋多重度的设置：

Multiplicity = 2 S + 1 = e_{α} - e_{β} + 1

∣ S_{1} ​ - S_{2} ​ - . . . - S_{10} ​ ∣\leq Multiplicity \leq | S_{1} ​ + S_{2} ​ + . . . + S 10 | ​

所以用单点能计算任务(PBE-D3/def2-TZVP)测试了一下自旋多重度，发现对于吸附团簇来讲，自旋多重度为3时能量最低，而对于裸团簇来讲，自旋多重度为7时能量最低，分别应用这两个自旋多重度进行计算，而闭壳层的CO自旋多重度自然是1，以下所有基于DFT方法计算的基组均为def2-TZVP。

首先试了一下 $ω B 97 M - V$

\begin{aligned} E_{Ads, Cluster}^{ω B 97 M - V} & = (- 1306.042338809542) - (- 1192.630891831586) - (- 113.338691492256) = - 0.072755485700 Eh \\ = - 1.97987630572 eV \\ = - 45.65475 kcal/mol \end{aligned}

\begin{aligned} E_{Ads, Cluster}^{PBE+D3} & = (- 1307.585520827298) - (- 1194.273378678571) - (- 113.234775522846) = - 0.077366625881 Eh \\ = - 2.10525313939 eV \\ = - 48.54829 kcal/mol \end{aligned}

如果使用 $ω B 97 M - V$ 做修正，那么最后算出的吸附能为：

\begin{aligned} E & = - 1.863 eV + (- 1.97987630572 eV) - (- 2.10525313939 eV) \\ = - 1.7376232 eV \\ = - 40.07115 kcal/mol \end{aligned}

里文献还有一些差异，再换成M06再试试：

\begin{aligned} E_{Ads, Cluster}^{M 06} & = (- 1307.117290599373) - (- 1193.751153760116) - (- 113.301440916919) = - 0.064695922338 Eh \\ = - 1.76047256862 eV \\ = - 40.5882421556 kcal/mol \end{aligned}

如果使用M06做修正，那么最后算出的吸附能为：

\begin{aligned} E & = - 1.863 eV + (- 1.76047256862 eV) - (- 2.10525313939 eV) \\ = - 1.5182194 eV \\ = - 35.0115 kcal/mol \end{aligned}

还是有比较大的差距，从补充信息里面发现作者似乎用的Spin 5，但是我扫描的结果却是裸团簇Spin 7的时候能量最低，抱着试一试的态度用M06泛函再扫了一次发现这次是Spin 5的时候能量最低。于是再Spin 5下再次进行了计算：

\begin{aligned} E_{ads}^{PBE} & = (- 1307.585521) - (- 1194.270302) - (- 113.234776) \\ = - 0.080443 Eh \\ = - 2.189 eV \end{aligned}

\begin{aligned} E_{ads}^{M 06} & = (- 1307.117291) - (- 1193.753296) - (- 113.301441) \\ = - 0.062554 Eh \\ = - 1.702 eV \end{aligned}

\begin{aligned} E_{ads}^{ω B 97 M - V} & = (- 1306.042339) - (- 1192.618183) - (- 113.338691) \\ = - 0.085465 Eh \\ = - 2.326 eV \end{aligned}

最终修正结果如下：

\begin{aligned} E_{Final}^{M 06} & = - 1.863 + [(- 1.702) - (- 2.189)] \\ = - 1.863 + 0.487 \\ = - 1.376 eV \\ \approx - 31.74 kcal / mol \end{aligned}

\begin{aligned} E_{Final}^{ω B 97 M - V} & = - 1.863 + [(- 2.326) - (- 2.189)] \\ = - 1.863 - 0.137 \\ = - 2.000 eV \\ \approx - 46.11 kcal / mol \end{aligned}

但是不太敢相信对于过渡金属团簇吸附能的计算，老泛函M06比 $ω B 97 M - V$ 更加优秀，遂使用DLPNO-CCSD(T)/def2-TZVPP级别再次计算了一下：

\begin{aligned} E_{Ads,Cluster}^{DLPNO-CCSD(T)} & = - 1303.19632675218 Eh - (- 1189.94842992788 Eh) - (- 113.158128734305 Eh) \\ = - 0.089768089995 Eh \\ = - 2.4426525664269465 eV \end{aligned}

如果使用DLPNO-CCSD(T)做修正，那么最后算出的吸附能为：

\begin{aligned} E & = - 1.863 eV + (- 2.4426525664269465 eV) - (- 2.189 eV) \\ = - 2.1166525664269465 eV \\ = - 48.81191316911517054185 kcal/mol \end{aligned}

很顺利的翻车了，Pt的价电子排布是 $5 d^{9} 6 s^{1}$ ，体系是含有10个Pt的金属团簇，开壳层体系，可能是体系的多参考特征比较强，查看了一下输出文件果然是这样。
对于吸附模型，我的自旋多重度是5，那么自旋量子数 $S = \frac{(5 - 1)}{2} = 2$ ，总自旋量子数 $< S^{2} >= S (S + 1) = 6$ ，部分输出信息：

T1 diagnostic                              ...      0.045926612                              

<S**2>(linearized)                         ...      6.3661646 (ideal value:      6.0000000)
------------------------------------------------------------------------------------------------------
Expectation value of <S**2>     :     9.090611

Ideal value S*(S+1) for S=2.0   :     6.000000

Deviation                       :     3.090611

再看看裸团簇的：

T1 diagnostic                              ...      0.049390694                              
<S**2>(linearized)                         ...      6.4633603 (ideal value:      6.0000000)
------------------------------------------------------------------------------------------------------
Expectation value of <S**2>     :     9.286144
Ideal value S*(S+1) for S=2.0   :     6.000000
Deviation

最后看看闭壳层分子CO的：

1
2
3

Singles Norm <S|S>**1/2                    ...      0.058876257  
T1 diagnostic                              ...      0.018618307

很明显T1诊断给出的结果明显偏大，是多参考体系，这也是DLPNO-CCSD(T)结果不准确的原因，这么大的体系用多参考方法做计算也显然不现实！
至于DFT的结果：M06为什么能算准而其他诸如双杂化泛函翻车我也确实不太能解释，可能是泛函利用UKS 的对称性破缺修正了能量？？？
总结了一下各个泛函计算后的总自旋量子数的情况：

Structure	$< S^{2} >$ expectation	$< S^{2} >$ ideal	$< S^{2} >$ deviation	T $_{1}$ diagnostic	Method	Basis set
Cluster	7.42353	6	1.42353		B3LYP-D4	def2-QZVP
Cluster	7.42353	6	1.42353		B3LYP-D3BJ	def2-QZVP
Cluster	7.423529	6	1.423529		B3LYP	def2-QZVP
Ads cluster	6.645988	6	0.645988		B3LYP	def2-QZVP
Ads cluster	6.645988	6	0.645988		B3LYP-D3BJ	def2-QZVP
Cluster	9.286144	6	3.286144	0.049390694	DLPNO	def2-TZVPP
Ads cluster	9.090611	6	3.090611	0.045926612	DLPNO	def2-TZVPP
Cluster	6.830101	6	0.830101		M06	def2-QZVP
Cluster	6.763179	6	0.763179		M06	def2-TZVP
Ads cluster	6.31562	6	0.31562		M06	def2-QZVP
Cluster	6.649309	6	0.649309		PBE-D3BJ	def2-TZVP
Ads cluster	6.017272	6	0.017272		PBE-D3BJ	def2-TZVP
Cluster	7.91564	6	1.91564		PBE0	def2-TZVP
Ads cluster	7.030855	6	1.030855		PBE0	def2-QZVP
Cluster	8.338167	6	2.338167		PWPB95	def2-QZVP
Ads cluster	7.524001	6	1.524001		PWPB95	def2-QZVP
Cluster	8.338167	6	2.338167		PWPB95-D4	def2-QZVP
Ads cluster	7.524001	6	1.524001		PWPB95-D4	def2-QZVP
Ads cluster	7.533567	6	1.533567		R2SCAN0	def2-QZVP
Cluster	8.583892	6	2.583892		SCAN0	def2-QZVP
Ads cluster	7.467305	6	1.467305		SCAN0	def2-QZVP
Cluster	7.038397	6	1.038397		TPSS	def2-QZVP
Ads cluster	6.127104	6	0.127104		TPSS	def2-QZVP
Cluster	8.190075	6	2.190075		TPSS0-D4	def2-QZVP
Ads cluster	7.133094	6	1.133094		TPSS0-D4	def2-QZVP
Cluster	7.11102	6	1.11102		TPSSh	def2-QZVP
Ads cluster	6.624638	6	0.624638		TPSSh	def2-QZVP
Cluster	8.22399	6	2.22399		wB97M-V	def2-QZVP
Cluster	8.074089	6	2.074089		wB97M-V	def2-TZVP
Monoxide molecule				0.020036319	DLPNO-CCSD(T)	def2-TZVPP

关键词的写法

在做DLPNO-CCSD(T)之前，也考虑过是BSSE的误差，文献也明确提到了，于是采用更大的基组def2-QZVP尽可能消除BSSE误差，依然是除了M06和B3LYP基本都翻车，算是一些无用功，整理的数据如下。

Function/basis	Ads cluster (Spin 5)	Bare cluster (Spin 5)	Monoxide molecule (Spin 1)	Ads (eV)	Final (eV)	Final (kcal/mol)
PBE-D3	-1307.585521	-1194.270302	-113.2347755	-2.188925172	-1.862925172	-42.9607311
M06	-1307.117291	-1193.753296	-113.3014409	-1.702131353	-1.376131353	-31.73482752
$ω$ B97M-V	-1306.042339	-1192.618183	-113.3386915	-2.325552839	-1.999552839	-46.11148807
DLPNO-CCSD(T)/def2-TZVPP	-1303.196327	-1189.94843	-113.1581287	-2.442652566	-2.116652566	-48.81191317
MN15	-1305.158483	-1191.836939	-113.2438128	-2.115127547	-1.789127547	-41.25889145
TPSS	-1307.01858	-1193.574495	-113.3744827	-1.893916048	-1.567916048	-36.15755519
TPSSh	-1306.786495	-1193.353985	-113.3595549	-1.985171262	-1.659171262	-38.26198255
TPSS0-D4	-1306.546916	-1193.130064	-113.3384528	-2.133283227	-1.807283227	-41.67757776
PWPB95-D4	-1305.271685	-1191.889498	-113.2960491	-2.343871299	-2.017871299	-46.53392825
PWPB95	-1305.258767	-1191.879864	-113.2957172	-2.263550789	-1.937550789	-44.681665
B3LYP-D3(BJ)	-1306.846736	-1193.460863	-113.3110755	-2.035295218	-1.709295218	-39.41788608
B3LYP-D4	-1306.829099	-1193.444594	-113.3109833	-2.000579197	-1.674579197	-38.61730339
B3LYP	-1306.71305	-1193.34303	-113.3103477	-1.623736953	-1.297736953	-29.92698211
PBE0	-1306.828955	-1193.524534	-113.2310197	-1.997280784	-1.671280784	-38.54123904
R2SCAN0	-1306.822109	-1193.461035	-113.2803062	-2.197761086	-1.871761086	-43.16449523
SCAN0	-1306.730149	-1193.367917	-113.2889399	-1.994327977	-1.668327977	-38.47314465
M06	-1307.143993	-1193.772441	-113.3088975	-1.704861915	-1.378861915	-31.79779673
MN15	error	error	-113.304667	#VALUE!	#VALUE!	#VALUE!
PWPB95 D4	-1305.773859	-1192.388853	-113.3078275	-2.100087022	-1.774087022	-40.91204342
PWPB95	-1305.760942	-1192.379219	-113.2957172	-2.3402638	-2.0142638	-46.45073607
R2SCAN0	-1306.855674	-1193.501377	-113.285907	-1.860946472	-1.534946472	-35.39724709
SCAN0	-1306.766073	-1193.399823	-113.2948917	-1.941713495	-1.615713495	-37.25980735
TPSS	-1307.056197	-1193.60716	-113.3802364	-1.872120731	-1.546120731	-35.65493556
TPSSh	-1306.822915	-1193.386111	-113.3651449	-1.949888753	-1.623888753	-37.44833614
TPSS0-D4	-1306.58189	-1193.161494	-113.3438373	-2.083233109	-1.757233109	-40.52337699
wB97M-V	WAIT	-1192.651556	-113.3442127	#VALUE!	#VALUE!	#VALUE!
B3LYP	-1306.742404	-1193.366257	-113.3168517	-1.613450558	-1.287450558	-29.68976857
B3LYP-D3(BJ)	-1306.876089	-1193.48409	-113.3175795	-2.025008731	-1.699008731	-39.18067044
B3LYP-D4	-1306.858452	-1193.467821	-113.3174873	-1.990292607	-1.664292607	-38.38008537

虽然做了很多探索（无用功😢，当个笑话罢），但也算成功走流程、复现了文献✌️。

Old is gold? May be for the case?

UMA模型验证

BTW，后面在huggingface上申请了一下Meta家的UMA模型： A Family of Universal Models for Atoms进行推理，尝试计算吸附能：
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计算准确度非常不错，使用的uma-m-1p1.pt模型进行推理，所有计算任务在自己的笔记本电脑上完成：

storm@storm ~ $ fastfetch    
        -/oyddmdhs+:.                 storm@storm  
    -odNMMMMMMMMNNmhy+-`              -----------  
  -yNMMMMMMMMMMMNNNmmdhy+-            OS: Gentoo Linux x86_64  
`omMMMMMMMMMMMMNmdmmmmddhhy/`         Host: X16 (1)  
omMMMMMMMMMMMNhhyyyohmdddhhhdo`       Kernel: Linux 6.18.12-gentoo-gentoo-dist  
.ydMMMMMMMMMMdhs++so/smdddhhhhdm+`    Uptime: 9 mins  
oyhdmNMMMMMMMNdyooydmddddhhhhyhNd.    Packages: 1501 (emerge)  
 :oyhhdNNMMMMMMMNNNmmdddhhhhhyymMh    Shell: bash 5.3.9  
   .:+sydNMMMMMNNNmmmdddhhhhhhmMmy    Display (BOE0A0B): 2560x1600 @ 1.25x in 16", 165 Hz [Built-in]  
      /mMMMMMMNNNmmmdddhhhhhmMNhs:    DE: KDE Plasma 6.5.5  
   `oNMMMMMMMNNNmmmddddhhdmMNhs+`     WM: KWin (Wayland)  
 `sNMMMMMMMMNNNmmmdddddmNMmhs/.       WM Theme: Sweet-Dark-transparent  
/NMMMMMMMMNNNNmmmdddmNMNdso:`         Theme: Breeze (WhiteSurDark) [Qt], Breeze-Dark [GTK2], Breeze [GTK3]  
+MMMMMMMNNNNNmmmmdmNMNdso/-           Icons: Tela-circle-purple-light [Qt], Tela-circle-purple-light [GTK2/3/4]  
yMMNNNNNNNmmmmmNNMmhs+/-`             Font: Noto Sans (10pt) [Qt], Noto Sans (10pt) [GTK2/3/4]  
/hMMNNNNNNNNMNdhs++/-`                Cursor: Oxygen_White (24px)  
`/ohdmmddhys+++/:.`                   Terminal: konsole 25.8.3  
 `-//////:--.                         CPU: AMD Ryzen 7 7840HS (16) @ 5.14 GHz  
                                      GPU: AMD Radeon 780M Graphics [Integrated]  
                                      Memory: 5.81 GiB / 30.52 GiB (19%)  
                                      Swap: 0 B / 16.00 GiB (0%)  
                                      Disk (/): 200.38 GiB / 234.00 GiB (86%) - btrfs  
                                      Disk (/run/media/storm/Data): 593.09 GiB / 701.87 GiB (85%) - ntfs3  
                                      Local IP (wlp2s0): 192.168.2.135/24  
                                      Battery (BASE-BAT): 99% [AC Connected]  
                                      Locale: zh_CN.UTF-8

尽管有的预设明显不合理，但还是分别是用了如下预设进行吸附能的计算并统计时间：

oc20: use this for catalysis
omat: use this for inorganic materials
omol: use this for molecules
odac: use this for MOFs
omc: use this for molecular crystals
完整的oc20预设计算日志如下：

(fairchem) storm@storm ~/claudecode/fairchem/uma/temp $ time python ../examples/adsorption_energy.py --adsorbed ads_POSCAR --gas CO_POSCAR --surface surfac  
e_POSCAR --model ../uma-m-1p1.pt --task oc20  
============================================================  
ADSORPTION ENERGY CALCULATION  
============================================================  
  
1. Calculating adsorbed system energy...  
System: COPt16  
Atoms: 18  
Loading model: ../uma-m-1p1.pt  
  
--------------------------------------------------------------------------------  
SINGLE POINT CALCULATION  
--------------------------------------------------------------------------------  
 Cell: 5.5492 x 5.5492 x 26.7964 Å  
 Cell: 5.5492 x 5.5492 x 26.7964 Å  
 PBC: [ True  True  True]  
 Volume: 714.61 Å³  
WARNING:root:If 'dataset_list' is provided in the config, the code assumes that each dataset maps to itself. Please use 'dataset_mapping' as 'dataset_list'  
is deprecated and will be removed in the future.  
 Calculating energy and forces...  
 Calculating stress...  
 Energy: -98.817862 eV  
 Calculation completed in 1.50 s  
 OUTCAR written to: results/OUTCAR  
 JSON results written to: results/uma_results.json  
 CONTCAR written to: results/CONTCAR  
  
================================================================================  
SUMMARY  
================================================================================  
Total energy:         -98.81786186 eV  
Energy per atom:       -5.48988121 eV/atom  
Max force:              0.52008080 eV/Å  
RMS force:              0.21199445 eV/Å  
Pressure:               1.96439230 GPa  
Calculation time:             1.50 s  
================================================================================  
  Energy: -98.817862 eV  
  
2. Calculating gas molecule energy...  
System: CO  
Atoms: 2  
Loading model: ../uma-m-1p1.pt  
  
--------------------------------------------------------------------------------  
SINGLE POINT CALCULATION  
--------------------------------------------------------------------------------  
 Cell: 17.0000 x 17.0000 x 17.0000 Å  
 Cell: 17.0000 x 17.0000 x 17.0000 Å  
 PBC: [ True  True  True]  
 Volume: 4913.00 Å³  
WARNING:root:If 'dataset_list' is provided in the config, the code assumes that each dataset maps to itself. Please use 'dataset_mapping' as 'dataset_list'  
is deprecated and will be removed in the future.  
 Calculating energy and forces...  
 Calculating stress...  
 Energy: -14.437472 eV  
 Calculation completed in 0.60 s  
 OUTCAR written to: results/OUTCAR  
 JSON results written to: results/uma_results.json  
 CONTCAR written to: results/CONTCAR  
  
================================================================================  
SUMMARY  
================================================================================  
Total energy:         -14.43747178 eV  
Energy per atom:       -7.21873589 eV/atom  
Max force:              0.57697660 eV/Å  
RMS force:              0.57697660 eV/Å  
Pressure:               0.00717079 GPa  
Calculation time:             0.60 s  
================================================================================  
  Energy: -14.437472 eV  
  
3. Calculating clean surface energy...  
System: Pt16  
Atoms: 16  
Loading model: ../uma-m-1p1.pt  
  
--------------------------------------------------------------------------------  
SINGLE POINT CALCULATION  
--------------------------------------------------------------------------------  
 Cell: 5.5492 x 5.5492 x 26.7964 Å  
 Cell: 5.5492 x 5.5492 x 26.7964 Å  
 PBC: [ True  True  True]  
 Volume: 714.61 Å³  
WARNING:root:If 'dataset_list' is provided in the config, the code assumes that each dataset maps to itself. Please use 'dataset_mapping' as 'dataset_list'  
is deprecated and will be removed in the future.  
 Calculating energy and forces...  
 Calculating stress...  
 Energy: -83.144463 eV  
 Calculation completed in 1.49 s  
 OUTCAR written to: results/OUTCAR  
 JSON results written to: results/uma_results.json  
 CONTCAR written to: results/CONTCAR  
  
================================================================================  
SUMMARY  
================================================================================  
Total energy:         -83.14446262 eV  
Energy per atom:       -5.19652891 eV/atom  
Max force:              0.41771099 eV/Å  
RMS force:              0.21009526 eV/Å  
Pressure:               1.22113061 GPa  
Calculation time:             1.49 s  
================================================================================  
  Energy: -83.144463 eV  
  
------------------------------------------------------------  
Adsorption Energy: -1.235927 eV  
============================================================  
  
============================================================  
CALCULATION COMPLETE  
============================================================  
  
Energy Components:  
 Adsorbed system:    -98.817862 eV  
 Gas molecule:       -14.437472 eV  
 Clean surface:      -83.144463 eV  
  
Adsorption Energy:  
 E_ads =    -1.235927 eV  
 E_ads =     -28.5011 kcal/mol  
 E_ads =    -119.2485 kJ/mol  
  
real    0m57.502s  
user    1m14.811s  
sys     0m47.895s

omat、omol、odac、omc的计算结果分别如下：

================================================================================  
SUMMARY FOR omat
================================================================================  
Total energy:         -93.03783162 eV  
Energy per atom:       -5.81486448 eV/atom  
Max force:              0.24742778 eV/Å  
RMS force:              0.12906978 eV/Å  
Pressure:              -0.36038849 GPa  
Calculation time:             1.21 s  
================================================================================  
  Energy: -93.037832 eV  
  
------------------------------------------------------------  
Adsorption Energy: -1.760454 eV  
============================================================  
  
============================================================  
CALCULATION COMPLETE  
============================================================  
  
Energy Components:  
 Adsorbed system:   -109.462288 eV  
 Gas molecule:       -14.664002 eV  
 Clean surface:      -93.037832 eV  
  
Adsorption Energy:  
 E_ads =    -1.760454 eV  
 E_ads =     -40.5969 kcal/mol  
 E_ads =    -169.8574 kJ/mol  
  
real    0m49.194s  
user    1m11.338s  
sys     0m42.796s

================================================================================  
SUMMARY FOR omol
================================================================================  
Total energy:         -85.15865324 eV  
Energy per atom:       -5.32241583 eV/atom  
Max force:              0.35174352 eV/Å  
RMS force:              0.18068850 eV/Å  
Pressure:               0.46252662 GPa  
Calculation time:             1.18 s  
================================================================================  
  Energy: -85.158653 eV  
  
------------------------------------------------------------  
Adsorption Energy: -3.437631 eV  
============================================================  
  
============================================================  
CALCULATION COMPLETE  
============================================================  
  
Energy Components:  
 Adsorbed system:   -103.436992 eV  
 Gas molecule:       -14.840708 eV  
 Clean surface:      -85.158653 eV  
  
Adsorption Energy:  
 E_ads =    -3.437631 eV  
 E_ads =     -79.2735 kcal/mol  
 E_ads =    -331.6799 kJ/mol  
  
real    0m49.001s  
user    1m9.737s  
sys     0m42.362s

================================================================================  
SUMMARY FOR odac
================================================================================  
Total energy:         -85.15865324 eV  
Energy per atom:       -5.32241583 eV/atom  
Max force:              0.35174355 eV/Å  
RMS force:              0.18068850 eV/Å  
Pressure:               0.46252671 GPa  
Calculation time:             1.24 s  
================================================================================  
  Energy: -85.158653 eV  
  
------------------------------------------------------------  
Adsorption Energy: -3.437631 eV  
============================================================  
  
============================================================  
CALCULATION COMPLETE  
============================================================  
  
Energy Components:  
 Adsorbed system:   -103.436992 eV  
 Gas molecule:       -14.840708 eV  
 Clean surface:      -85.158653 eV  
  
Adsorption Energy:  
 E_ads =    -3.437631 eV  
 E_ads =     -79.2735 kcal/mol  
 E_ads =    -331.6799 kJ/mol  
  
real    0m49.999s  
user    1m12.139s  
sys     0m42.648s

================================================================================  
SUMMARY FOR omc
================================================================================  
Total energy:         -94.23304826 eV  
Energy per atom:       -5.88956552 eV/atom  
Max force:              0.35484159 eV/Å  
RMS force:              0.17868795 eV/Å  
Pressure:               0.27917987 GPa  
Calculation time:             1.42 s  
================================================================================  
  Energy: -94.233048 eV  
  
------------------------------------------------------------  
Adsorption Energy: -4.091944 eV  
============================================================  
  
============================================================  
CALCULATION COMPLETE  
============================================================  
  
Energy Components:  
 Adsorbed system:   -113.270863 eV  
 Gas molecule:       -14.945870 eV  
 Clean surface:      -94.233048 eV  
  
Adsorption Energy:  
 E_ads =    -4.091944 eV  
 E_ads =     -94.3623 kcal/mol  
 E_ads =    -394.8112 kJ/mol  
  
real    0m49.479s  
user    1m12.847s  
sys     0m44.418s