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Guide to PWmat for Lattice Optimization and Atomic Relaxation

Learn how to perform lattice optimization and atomic relaxation using PWmat software. Explore examples, parameters, and output files for different relaxation scenarios. Understand how to modify atom.config and etot.input files to customize relaxation requirements. Dive into potential energy surface calculations, Vander Waals corrections, and various optimization methods. Perfect for users interested in computational materials science.

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Guide to PWmat for Lattice Optimization and Atomic Relaxation

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  1. 晶格优化和原子弛豫计算(RELAX) 版本: PWmat/2023.11.24

  2. 弛豫( RELAX ) 不同的弛豫要求主要通过修改atom.config和etot.input两个 文件的参数来完成,案例: • (固定)晶格优化和原子弛豫 • (部分)原子弛豫 • 带电体系优化

  3. 晶格优化和原子弛豫(RELAX) • atom.config: 4 LATTICE 2.46596583 0.00000000 0.00000000 -1.23298291 2.13558905 0.00000000 0.00000000 0.00000000 6.41151115 POSITION 6 0.00000000 0.00000000 0.75000000 1 1 1 6 0.66667000 0.33333000 0.75000000 1 1 1 6 0.00000000 0.00000000 0.25000000 1 1 1 6 0.33333000 0.66667000 0.25000000 1 1 1 #原子沿a,b,c 3个方 向,是(1)/否(0)可 以弛豫

  4. 晶格优化和原子弛豫(RELAX) 注:二维材料可以固定晶格优化,在atom.config中设置 4 LATTICE 2.46596583 0.00000000 0.00000000 -1.23298291 2.13558905 0.00000000 0.00000000 0.00000000 6.41151115 POSITION 6 0.00000000 0.00000000 0.75000000 1 1 1 6 0.66667000 0.33333000 0.75000000 1 1 1 6 0.00000000 0.00000000 0.25000000 1 1 1 6 0.33333000 0.66667000 0.25000000 1 1 1 STRESS_MASK 1 1 0 #固定c轴方向的晶格优化,但是原子仍 可以沿c轴弛豫 1 1 0 0 0 0

  5. 晶格优化和原子弛豫(RELAX) • etot.input: 1 4 JOB = RELAX IN.PSP1 = C.SG15.PBE.UPF IN.ATOM = atom.config RELAX_DETAIL = 1 100 0.01 1 0.02 VDW = DFT-D2 Ecut = 70 Ecut2 = 280 MP_N123 = 12 12 4 0 0 0 二维材料进行范德华修正

  6. 晶格优化和原子弛豫(RELAX) RELAX_DETAIL=IMTH NSTEP FORCE_TOL ISTRESS TOL_STRESS 1. IMTH表示优化方法 • IMTH=1(default), conjugated gradient; • IMTH=2, BFGS method; • IMTH=3, steepest decent; • IMTH=4, preconditioned conjugate gradient; • IMTH=5, Limited-memory BFGS method; • IMTH=6, FIRE: Fast Inertial Relaxation Engine.

  7. 晶格优化和原子弛豫(RELAX) RELAX_DETAIL=IMTH NSTEP FORCE_TOL ISTRESS TOL_STRESS 2. NSTEP表示弛豫的最大步数 3. FORCE_TOL表示弛豫的收敛标准(eV/Å) 4. ISTRESS表示是否进行晶格优化 5. TOL_STRESS表示晶格优化的标准(eV/Natom)

  8. 晶格优化和原子弛豫(RELAX) • 主要输出文件 • final.config : 弛豫后的结构 弛豫后的结构 • RELAXSTEPS : RELAX每步情况 每步情况 • MOVEMENT : 轨迹 轨迹

  9. 晶格优化和原子弛豫(RELAX) • final.config: 4 atoms,Iteration = 13, Etot,Ep,Ek = -0.6210525330E+03 -0.6210525330E+03 0.0000000000E+00, Average Force= 0.59222E-02, Max force= 0.88894E-02 Lattice vector (Angstrom), stress(eV) 0.2457107053E+01 0.8717252798E-04 -0.3842910741E-18 stress: -0.516864E-01 0.818701E-02 0.000000E+00 -0.1228478028E+01 0.2127960710E+01 -0.4707389663E-19 stress: 0.818701E-02 -0.422328E-01 0.000000E+00 -0.1002525004E-17 -0.7206765261E-18 0.6342490987E+01 stress: 0.000000E+00 -0.147513E-17 -0.292400E-01 Position, move_x, move_y, move_z 6 0.999978148 0.000021852 0.750000000 1 1 1 6 0.666690737 0.333309263 0.750000000 1 1 1 6 0.000021852 0.999978148 0.250000000 1 1 1 6 0.333309263 0.666690737 0.250000000 1 1 1 Force 6 -0.008889429 0.005132314 0.000000000 6 0.008877254 -0.005125285 0.000000000 6 0.008889429 -0.005132314 0.000000000 6 -0.008877254 0.005125285 0.000000000 STRESS_MASK 1.00000000000000 1.00000000000000 1.00000000000000 1.00000000000000 1.00000000000000 1.00000000000000 1.00000000000000 1.00000000000000 1.00000000000000 第13步离子步的总能,势能,动能,平均受力,最大受力信息 晶格受力信息 原子受力信息 注:final.config可以作为续算的初始结构文件

  10. 晶格优化和原子弛豫(RELAX) • RELAXSTEPS: It= -1 CORR E= -0.6210490073237E+03 Av_F= 0.39E-03 M_F= 0.59E-03 Av_e= 0.23E+00 dE= 0.7E-05 dRho= 0.2E-03 SCF= 13 dL= 0.00E+00 d_AL= 0.00E+00 p*F= 0.00E+00 p*F0= 0.00E+00 Fch= 0.00E+00 It= 0 NEW E= -0.6210508020456E+03 Av_F= 0.15E-02 M_F= 0.22E-02 Av_e= 0.15E+00 dE= 0.1E-05 dRho= 0.6E-04 SCF= 4 dL= 0.62E-04 d_AL= 0.21E-01 p*F= 0.51E-02 p*F0= -0.14E-02 Fch= -0.15E+05 It= 1 CORR E= -0.6210520488984E+03 Av_F= 0.71E-03 M_F= 0.11E-02 Av_e= 0.26E-01 dE= 0.8E-04 dRho= 0.7E-05 SCF= 3 dL= 0.38E-04 d_AL= 0.84E-02 p*F= 0.25E-02 p*F0= -0.14E-02 Fch= -0.14E+06 It= 2 CORR E= -0.6210520494058E+03 Av_F= 0.72E-03 M_F= 0.11E-02 Av_e= 0.26E-01 dE= 0.4E-06 dRho= 0.7E-05 SCF= 2 dL= 0.38E-04 d_AL= 0.40E-04 p*F= 0.25E-02 p*F0= -0.14E-02 Fch= -0.14E+06 ... It= 12 *END E= -0.6210525330363E+03 Av_F= 0.59E-02 M_F= 0.89E-02 Av_e= 0.13E-01 dE= 0.1E-03 dRho= 0.2E-04 SCF= 3 dL= 0.12E-02 d_AL= 0.58E-02 p*F= -0.21E-01 p*F0= -0.15E+00 Fch= 0.94E+00 1. It:离子优化的步数 2. NEW:表示该步力的搜索方向改变; CORR:表示该步力的搜索方向跟其上NEW步时候的方向是一致的 3. E:该离子步体系的总能 4. Av_F:该步每个原子的平均受力大小 5. M_F:该步所有原子受力的最大值 6. dE, dRho:该离子步自洽的最后一步与上一步差值的绝对值 7. SCF:该离子步包含的自洽步数 8. dL:离子步移动的步长 9. p*F:原子受力沿搜索方向的投影值 注:最后一步出现*END,代表正常运行结束

  11. 晶格优化和原子弛豫(RELAX) 提取RELAXSTEP中的列数据,查看弛豫过程的收敛信息(分隔符号为空格): • 方法1:通过gnuplot命令画图(先输入gnuplot进入命令行模式) 输入gnuplot进入命令行模式 plot ‘RELAXSTEPS’ u 2:5 w lp 查看能量变化 plot ‘RELAXSTEPS’ u 2:9 w lp 查看最大受力变化 • 方法2:通过gawk命令从RELAXATEPS中提取信息: 能量变化信息保存在E.dat文件中 gawk ‘{print $2,$5}’ RELAXSTEPS > E.dat 最大受力变化信息保存在M_F.dat文件中 gawk ‘{print $2,$9}’ RELAXSTEPS > M_F.dat

  12. 晶格优化和原子弛豫(RELAX) • MOVEMENT轨迹文件: 4 atoms,Iteration = 0, Etot,Ep,Ek = -0.6210490073E+03 -0.6210490073E+03 0.0000000000E+00, Average Force= 0.39399E-03, Max force= 0.59218E-03 ... Position (normalized), move_x, move_y, move_z ... Force (-force, eV/Angstrom) ... Velocity (bohr/fs) ... 32 atoms,Iteration (fs) = 0.2000000000E+01, Etot,Ep,Ek (eV) = -0.1391638513E+06 -0.1391663385E+06 0.2487282733E+01, SCF = 4 ... 可以把MOVEMENT转换成.xsf格式文件查看弛豫的轨迹动画 命令行:convert_from_config.x MOVEMENT

  13. 上机操作 案例文件获取: 方式1:点击下载到本地 example06 方式2:Mcloud用户直接在线拷贝:/share/public/examples-slurmPBS/example06 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

  14. 部分原子弛豫(RELAX) • atom.config: 2 LATTICE 0.00000000 2.73899206 2.73899206 2.73899206 0.00000000 2.73899206 2.73899206 2.73899206 0.00000000 POSITION 14 0.00000000 0.00000000 0.00000000 0 0 0 14 0.25000000 0.23000000 0.25000000 1 1 1

  15. 部分原子弛豫(RELAX) • etot.input: 1 4 JOB = RELAX IN.PSP1 = Si.SG15.PBE.UPF IN.ATOM = atom.config RELAX_DETAIL = 1 100 0.005 Ecut = 50 Ecut2 = 200 MP_N123 = 9 9 9 0 0 0 #不设置晶格优化参数,默认不优化晶格

  16. 上机操作 案例文件获取: 方式1:点击下载到本地 example05 方式2:Mcloud用户直接在线拷贝:/share/public/examples-slurmPBS/example05 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

  17. 带电体系优化(RELAX) 35个B原子,36个N原子,1个C原子 B.SG15.PBE.UPF: z_valence=" 3.00" C.SG15.PBE.UPF: z_valence=" 4.00" N.SG15.PBE.UPF: z_valence=" 5.00" 中性体系电子数:35*3+36*5+1*4=289

  18. 带电体系优化(RELAX) • etot.input: 中性体系电子数:35*3+36*5+1*4=289 4 1 JOB = RELAX NUM_ELECTRON = 288 IN.PSP1 = B.SG15.PBE.UPF IN.PSP2 = C.SG15.PBE.UPF IN.PSP3 = N.SG15.PBE.UPF IN.ATOM = atom.config RELAX_DETAIL = 1 100 0.01 Ecut = 50 Ecut2 = 200 MP_N123 = 1 1 1 0 0 0 体系为+1价

  19. 上机操作 案例文件获取: 方式1:点击下载到本地 example08 方式2:Mcloud用户直接在线拷贝:/share/public/examples-slurmPBS/example08 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

  20. 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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