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Transition State Calculation with Nudged Elastic Band (NEB) Method

The Nudged Elastic Band (NEB) method is used in computational chemistry to find saddle points and minimum energy pathways for reactions. It calculates diffusion paths, diffusion barriers, and transition states. The NEB calculation involves optimizing the reaction pathway through a series of intermediate structures. Key parameters such as optimization method, force convergence criteria, and image insertion are specified in the input file. The output includes information on energy barriers, distances between images, and angles along the pathway. Additional steps for continuation of the NEB calculation are also provided.

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Transition State Calculation with Nudged Elastic Band (NEB) Method

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  1. 过渡态计算(NEB) 版本: PWmat/2023.11.24

  2. 过渡态计算(NEB) • 爬坡弹性能带法(Nudged Elastic Band)是一种 已知反应物和产物来寻找鞍点(saddle point)和最 小路径(MEP)的方法。 • 用NEB可以计算其扩散路径或者扩散势垒,过渡态。 • 目前大多数第一性原理计算软件都是通过爬坡弹性 能带法计算反应路径 0.30 IMTH-1 0.25 0.20 ΔE (eV) 0.15 0.10 0.05 0.00 0 1 2 3 4 5 6 image

  3. 过渡态计算(NEB) • atom.config: initial: final:

  4. 过渡态计算(NEB) • etot.input: 2 2 JOB = NEB IN.PSP1 = C.SG15.PBE.UPF IN.PSP2 = Li.SG15.PBE.UPF IN.ATOM = atom_initial.config NEB_DETAIL = 5, 100, 0.02, 5, 0.1, 1, -7946.02, -7946.02, 1, atom_final.config Ecut = 50 Ecut2 = 200 MP_N123 = 3 3 1 0 0 0 2 XCFUNCTIONAL = PBE SYS_TYPE = 2 IN.RELAXOPT = T #optional #2表示关闭对称性 #设置 Fermi-Dirac 函数中的 kT 为 0.2 eV ,常用于金属性体系计算 注:SYS_TYPE 的优先级低于关键词FERMIDE、SCF_ITER0_1/2/3,详细内容可参考Manual

  5. 过渡态计算(NEB) NEB_DETAIL=IMTH, NSTEP, FORCE_TOL, NIMAGE, AK, TYPE_SPRING, E0, EN, ITYPE_AT2, ATOM2.CONFIG 1. IMTH:优化方法 2. NSTEP:最大NEB优化步数 3. FORCE_TOL:力收敛标准(eV/Å) 4. NIMAGE:插入构象数量 5. AK:弹性力大小 6. TYPE_SPRING:弹性力类型(决定使用NEB 还是CI-NEB计算,详见手册Manual) 7. E0/EN:初态、末态的总能 8. ITYPE_AT2:是否续算 9. ATOM2.CONFIG:末态结构文件

  6. 过渡态计算(NEB) • 其他与原子弛豫有关的关键词可在IN.RELAXOPT设置: 例如:IMTH=5时,采用LBFGS优化方法,推荐使用较小的原子移动步长, 改善该方法下能量可能出现跳变的情况。 在etot.input中设置IN.RELAXOPT=T 创建IN.RELAXOPT文件,设置RELAX_MAXMOVE=0.5(默认值为1) 详细内容可参考Manual : http://www.pwmat.com/pwmat-resource/Manual_cn.pdf

  7. 过渡态计算(NEB) • 主要输出文件 • MOVEMENT: 每个 每个image的轨迹 的轨迹 • NEB.BARRIER : NEB势垒和路径 势垒和路径

  8. 过渡态计算(NEB) • NEB.BARRIER: iter= 0 Etot(eV),dist(Bohr),angle(cos(th)) 0 -0.79461092436916E+04 0.775111E+00 0.000000E+00 ... 6 -0.79461092430510E+04 0.000000E+00 0.000000E+00 ... iter= 28 Etot(eV),dist(Bohr),angle(cos(th)) 0 -0.79461092436916E+04 0.929461E+00 0.000000E+00 1 -0.79460399971247E+04 0.879733E+00 0.552177E+00 2 -0.79458891505418E+04 0.811118E+00 0.976190E+00 3 -0.79458271588755E+04 0.812727E+00 0.982278E+00 4 -0.79458890518680E+04 0.883907E+00 0.974868E+00 5 -0.79460402519750E+04 0.930987E+00 0.542413E+00 6 -0.79461092430510E+04 0.000000E+00 0.000000E+00

  9. 过渡态计算(NEB) • NEB.BARRIER(用最后一步的数据绘图): iter= 28 Etot(eV),dist(Bohr),angle(cos(th)) 0 -0.79461092436916E+04 0.929461E+00 0.000000E+00 1 -0.79460399971247E+04 0.879733E+00 0.552177E+00 2 -0.79458891505418E+04 0.811118E+00 0.976190E+00 3 -0.79458271588755E+04 0.812727E+00 0.982278E+00 4 -0.79458890518680E+04 0.883907E+00 0.974868E+00 5 -0.79460402519750E+04 0.930987E+00 0.542413E+00 6 -0.79461092430510E+04 0.000000E+00 0.000000E+00 1. iter: :NEB步数 2. Etot: :每个构象的 每个构象的总 3. dist: :两个构象之 两个构象之间 4. angle: :R(image + 1) − R(image)和 − 1)之 之间 间的 的夹 夹角余弦 角余弦值 步数 总能 能 间所有原子移 所有原子移动 动的平均距离 的平均距离 和R(image) − R(image 值

  10. 过渡态计算(NEB)——续算 • etot.input: 2 2 JOB = NEB IN.PSP1 = C.SG15.PBE.UPF IN.PSP2 = Li.SG15.PBE.UPF IN.ATOM = atom_initial.config NEB_DETAIL = 5, 100, 0.02, 5, 0.1, 1, -7946.02, -7946.02, 2, atom_final.config Ecut = 50 Ecut2 = 200 MP_N123 = 3 3 1 0 0 0 2 XCFUNCTIONAL = PBE SYS_TYPE = 2 IN.RELAXOPT = T #optional 还需将上一步NEB计算得到的MOVEMENT文件中,最后一步计算的N+2个结构信息拷贝到 atom_final.config文件中。

  11. 上机操作 案例文件获取: 方式1:点击下载到本地 example14 方式2:Mcloud用户直接在线拷贝:/share/public/examples-slurmPBS/example14 注:案例将输入文件和部分输出文件分别放置在inputs和relative_outputs文件夹中 注册Mcloud领取上机机时: https://mcloud.lonxun.com

  12. 北京市海淀区学清路8号科技财富中心A座908室 400-618-6006 support@pwmat.com 微信公众号: pwmat1

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