├── .gitignore ├── .pylintrc ├── .vscode └── settings.json ├── Calc.py ├── LICENSE ├── MEPplot.code-workspace ├── README.md ├── README_CN.md ├── README_JP.md ├── Readme-figures ├── R1.png ├── R2.png ├── R3.png ├── R4.png ├── R5.png ├── R6.png └── R7.png ├── __pycache__ ├── Calc.cpython-37.pyc ├── Calc.cpython-38.pyc └── main.cpython-38.pyc ├── example ├── Circle-PES.txt ├── Rastrigin.txt └── muller.txt ├── main.py └── ui ├── GuessDia.ui ├── Logo.ico ├── Logo.png ├── Results.ui ├── about.ui └── main.ui /.gitignore: -------------------------------------------------------------------------------- 1 | .vscode 2 | .vscode/settings.json 3 | .vscode/settings.json 4 | .vscode/settings.json 5 | .pylintrc 6 | __pycache 7 | -------------------------------------------------------------------------------- /.pylintrc: -------------------------------------------------------------------------------- 1 | extension-pkg-whitelist=PyQt5 -------------------------------------------------------------------------------- /.vscode/settings.json: -------------------------------------------------------------------------------- 1 | { 2 | "python.pythonPath": "D:\\XinChen-workspace\\anaconda\\python.exe" 3 | } -------------------------------------------------------------------------------- /Calc.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from scipy.interpolate import interp1d 3 | def trans_back(x,y,trans): 4 | x = (x/trans[0][1])+trans[0][0] 5 | y = (y/trans[1][1])+trans[1][0] 6 | return x,y 7 | 8 | 9 | def InitBeads(Guess,f,nBeads): 10 | nGuess = len(Guess) 11 | ds = np.linspace(0,1,nGuess) 12 | ds[0] = 0 13 | 14 | if (np.max(Guess[:,0]) > 5): 15 | for bead in Guess: 16 | if bead[0] > 5: 17 | bead[0] = 4.0 18 | if (np.max(Guess[:,1]) > 5): 19 | for bead in Guess: 20 | if bead[1] > 5: 21 | bead[1] = 4.0 22 | if (np.min(Guess[:,0]) < 0): 23 | for bead in Guess: 24 | if bead[0] < 0: 25 | bead[0] = 1.0 26 | 27 | if (np.min(Guess[:,1]) < 0): 28 | for bead in Guess: 29 | if bead[1] < 0: 30 | bead[1] = 1.0 31 | 32 | for i in range(1,nGuess): 33 | ds[i] = ((Guess[i][0]-Guess[i-1][0])**2+(Guess[i][1]-Guess[i-1][1])**2)**0.5 34 | 35 | Sum = 0 36 | ds_cum= list(range(nGuess)) 37 | for i in range(nGuess): 38 | Sum = Sum + ds[i] 39 | ds_cum[i] = Sum 40 | 41 | DS = list(range(nGuess)) 42 | for i in range(len(ds_cum)): 43 | DS[i] = ds_cum[i]/Sum 44 | 45 | h = list(range(nBeads)) 46 | for i in range(nBeads): 47 | h[i] = h[i]/float(nBeads-1) 48 | 49 | x = list(range(nGuess)) 50 | y = list(range(nGuess)) 51 | for i in range(nGuess): 52 | x[i] = Guess[i][0] 53 | y[i] = Guess[i][1] 54 | 55 | interX = interp1d(DS,x,kind='slinear') 56 | interY = interp1d(DS,y,kind='slinear') 57 | 58 | S_new = list(range(nBeads)) 59 | 60 | X_new = interX(h) 61 | Y_new = interY(h) 62 | Z_new = f(X_new,Y_new) 63 | S_new = np.column_stack((X_new,Y_new)) 64 | 65 | 66 | return np.column_stack((S_new,Z_new)) 67 | 68 | def grad(beads,f): 69 | dx = 0.01 70 | dy = 0.01 71 | grad_x = (f(beads[:,0]-dx,beads[:,1])-beads[:,2])/dx 72 | grad_y = (f(beads[:,0],beads[:,1]-dy)-beads[:,2])/dy 73 | return grad_x,grad_y 74 | 75 | def walkdown(beads,step,f): 76 | nbeads = len(beads) 77 | gradientX, gradientY = grad(beads,f) 78 | factorX = 1.0 79 | factorY = 1.0 80 | if (max(gradientX*step) > 0.2): factorX = 0.2/(max(gradientX*step)) 81 | if (max(gradientY*step) > 0.2): factorY = 0.2/(max(gradientY*step)) 82 | beads[:,0] = beads[:,0] + gradientX*step*factorX 83 | beads[:,1] = beads[:,1] + gradientY*step*factorY 84 | if (np.max(beads[:,0]) > 5): 85 | for bead in beads: 86 | if bead[0] > 5: 87 | bead[0] = 4.0 88 | if (np.max(beads[:,1]) > 5): 89 | for bead in beads: 90 | if bead[1] > 5: 91 | bead[1] = 4.0 92 | if (np.min(beads[:,0]) < 0): 93 | for bead in beads: 94 | if bead[0] < 0: 95 | bead[0] = 1.0 96 | 97 | if (np.min(beads[:,1]) < 0): 98 | for bead in beads: 99 | if bead[1] < 0: 100 | bead[1] = 1.0 101 | 102 | beads[:,2] = f(beads[:,0],beads[:,1]) 103 | scale = 1 104 | if (factorX < 1 or factorY < 1): scale = 0.9 105 | if (factorX < 0.5 or factorY < 0.5): scale = 0.7 106 | if (factorX < 0.1 or factorY < 0.1): scale = 0.3 107 | if (factorX < 0.01 or factorY < 0.01): scale = 0.1 108 | if (factorX < 0.001 or factorY < 0.001): scale = 0.01 109 | if (factorX < 0.0001 or factorY < 0.0001 ): scale = 0.001 110 | if (factorX < 0.00001 or factorY < 0.00001) : scale = 0.0001 111 | 112 | return beads,scale 113 | 114 | def redist(beads,f): 115 | nbeads = len(beads) 116 | ds = np.linspace(0,1,nbeads) 117 | ds[0] = 0 118 | for i in range(1,nbeads): 119 | ds[i] = ((beads[i][0]-beads[i-1][0])**2+(beads[i][1]-beads[i-1][1])**2)**0.5 120 | 121 | Sum = 0 122 | ds_cum= list(range(nbeads)) 123 | for i in range(nbeads): 124 | Sum = Sum + ds[i] 125 | ds_cum[i] = Sum 126 | 127 | DS = list(range(nbeads)) 128 | for i in range(len(ds_cum)): 129 | DS[i] = ds_cum[i]/Sum 130 | 131 | h = list(range(nbeads)) 132 | for i in range(nbeads): 133 | h[i] = h[i]/float(nbeads-1) 134 | 135 | x = list(range(nbeads)) 136 | y = list(range(nbeads)) 137 | for i in range(nbeads): 138 | x[i] = beads[i][0] 139 | y[i] = beads[i][1] 140 | 141 | interX = interp1d(DS,x,kind='slinear') 142 | interY = interp1d(DS,y,kind='slinear') 143 | 144 | S_new = list(range(nbeads)) 145 | 146 | X_new = interX(h) 147 | Y_new = interY(h) 148 | Z_new = f(X_new,Y_new) 149 | S_new = np.column_stack((X_new,Y_new)) 150 | 151 | return np.column_stack((S_new,Z_new)) 152 | 153 | def calcDiff(beads,beads2): 154 | nbeads = len(beads) 155 | Sum = np.sum((beads[:,0]-beads2[:,0])**2+(beads[:,1]-beads2[:,1])**2)/nbeads 156 | diff = np.sqrt(Sum) 157 | return diff -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 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Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . -------------------------------------------------------------------------------- /MEPplot.code-workspace: -------------------------------------------------------------------------------- 1 | { 2 | "folders": [ 3 | { 4 | "path": "." 5 | } 6 | ] 7 | } -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | 3 | # MEPplot 4 | [中文](README_CN.md) [日本語](README_JP.md) 5 | 6 | 7 | 8 | A GUI program for plotting minimal energy path on potential energy (or free energy) surface. This program is based on string method. Please refer to this paper (Phys. Rev. B **66**, 052301 – Published 12 August 2002) for details. 9 | 10 | 11 | 12 | 13 | ## Download and Installation 14 | 15 | Find the latest `.rar` file here: 16 | 17 | https://github.com/chenxin199261/MEPplot/releases 18 | 19 | or 20 | 21 | https://mega.nz/folder/hsVzVSKT#3IEzoJZzkmEQZJACTAEcMQ 22 | 23 | For users in mainland China (GitHub is slow), please use the following address: 24 | 25 | https://n459.com/file/30374101-473325811 （passwd: 111111） 26 | 27 | Download rar file and unzip the file. You will see 3 files. 28 | 29 | * MEPplot.bat : Entry of MEPplot, executable file. 30 | * example: Template PES. 31 | * main: Program files. 32 | 33 | 34 | 35 | ## Usage 36 | 37 | Double click the file `MEPplot.bat`. The following interface will be showed. Please follow the instructions step by step. 38 | 39 | R2 40 | 41 | #### 1. Prepare potential energy surface (PES) data file 42 | 43 | Your 2D PES file should be prepared in specific format strictly. The file contains 3 columns (X, Y and Energy) as following examples, 44 | 45 | ``` 46 | -0.88235 1.99224 30.64485 47 | 1.23646 -0.78346 420.58113 48 | 1.03326 0.21343 18.23895 49 | -1.28864 1.87634 23.34170 50 | 0.22373 0.08548 -79.56263 51 | 0.97433 0.60216 119.97031 52 | 0.03879 -0.50717 55.13104 53 | ... 54 | ``` 55 | 56 | Templates can also be found in example folder. 57 | 58 | 59 | 60 | #### 2. Load PES data file in and plot 2D PES 61 | 62 | Click `Open...` button at up-right corner and select your PES data file. The PES will be showed in `plot window` immediately. The auto-generated plot may not be perfect for locating minima and saddle points. The users need to adjust the relevant parameters in `PES plot control` panel. 63 | 64 | R3 65 | 66 | * **Max. V**: Maximum value in countour plot. Values larger than *Max. V* will be screened out. 67 | * **Min. V**: Minimum value. Values smaller than *Mix. V* will be screened out (Don't adjust it or you will miss the local minimas). 68 | * **Level**: Number of contour lines plotted on PES. 69 | * **Cmap**：Colormap styles. 70 | 71 | Click `Regenrate` button you will see the new PES figure. If you mess the plot setting up, just click `Reset plot`. 72 | 73 | 74 | 75 | #### 3. Search minimum energy path 76 | 77 | Firstly, users need to provide a initial guess string. An accurate initial guess string can be optimized to final result fast. The initial guess is defined by beads (at least 2 beads). Click `Guess beads` and provide the coordinates (X and Y) into dialog box, 78 | 79 | 80 | 81 | R4 82 | 83 | In this example, 4 beads are provided sequently to define a initial string. After clicking `OK`, the initial guess string is then plotted on PES in black solid line. 84 | 85 | R5 86 | 87 | The program provides defaulf values for the optimization parameters. You can use them directly. If converge fail, you can adjust the parameters for the optimization. 88 | 89 | R6 90 | 91 | * **No. of Beads**: Number of beads. It defines the the number of beads of the string. More beads more accuracy. 92 | * **Max. iter**: Maximum iteration number. If the optimization steps exceed the *Max. iter* value, the process will stop. 93 | * **Step size**: *Step size* value detemines the gradient decend step-size. 94 | 95 | 96 | 97 | Click `Run` button. The optimization process will start. Then, the initial guess string is optimized to minimum energy path. The optimization process can be visualized in plot window. The `Converged !` message in log panel means the optimization is successful. 98 | 99 | 100 | 101 | #### 4. Show results 102 | 103 | Finally, click `Show` button in `MEP searching` panel. You will see the final results. 104 | 105 | R7 106 | 107 | Click `Export data` button, the beads' coordinates and relevant energies of MEP can be exported in a file for further use. 108 | 109 | 110 | 111 | 112 | 113 | ## Tips 114 | 115 | 1. The initial guess beads will be updated to the latest optimized beads after one optimization process. Users can click run directly in the case of convergence failure. You need click `Guess beads` to generated new initial guess. 116 | 2. If the string vibrates, try to reduce the `step size` value. 117 | 3. If the beads on string move slowly, try to increase the `step size` value. 118 | 4. Negative `step size` value yields *maximum energy path* 119 | 120 | 121 | 122 | ## Dependency 123 | 124 | * pyqt5: 5.15 125 | * Matplotlib: 3.1.3 126 | * numpy: 1.15 127 | * scipy:1.5.4 128 | 129 | 130 | 131 | ## License 132 | 133 | MEPplot: A GUI program for plotting Minimal energy path on potential energy surface. 134 | Copyright (C) 2020 Xin Chen 135 | 136 | This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. 137 | 138 | This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. 139 | 140 | You should have received a copy of the GNU General Public License along with this program. If not, see . 141 | 142 | 143 | -------------------------------------------------------------------------------- /README_CN.md: -------------------------------------------------------------------------------- 1 | 2 | 3 | # MEPplot 4 | [English](README.md) [日本語](README_JP.md) 5 | 6 | 7 | 8 | 一个在势能面（自由能面）上绘制最小能量路径的程序。 本程序基于弦方法(string method)。 更多细节，请参考如下论文 (Phys. Rev. B **66**, 052301 – Published 12 August 2002) 9 | 10 | 11 | 12 | 13 | 14 | ## 下载与安装 15 | 16 | 在如下链接里找到 `.rar` 文件： 17 | 18 | https://github.com/chenxin199261/MEPplot/releases 19 | 20 | 或者 21 | 22 | https://mega.nz/folder/hsVzVSKT#3IEzoJZzkmEQZJACTAEcMQ 23 | 24 | 对于身处中国大陆的用户 (GitHub非常慢), 请用如下链接下载: 25 | 26 | https://n459.com/file/30374101-473325811 （提取码;111111） 27 | 28 | 下载rar文件并解压， 你会得到如下三个文件， 29 | 30 | * MEPplot.bat :MEPplot程序的入口, 可执行脚本. 31 | * example: 势能面模板. 32 | * main: 程序文件. 33 | 34 | ## 用法 35 | 36 | 点击二进制文件 `MEPplot.exe`。 你会看到如下界面。 请跟随指引一步步完成绘制。 37 | 38 | R2 39 | 40 | #### 1. 准备势能面数据文件 41 | 42 | 你的二维势能面文件应该遵循严格格式，文件包含三列 (X坐标, Y坐标 和能量）。如下： 43 | 44 | ``` 45 | -0.88235 1.99224 30.64485 46 | 1.23646 -0.78346 420.58113 47 | 1.03326 0.21343 18.23895 48 | -1.28864 1.87634 23.34170 49 | 0.22373 0.08548 -79.56263 50 | 0.97433 0.60216 119.97031 51 | 0.03879 -0.50717 55.13104 52 | ... 53 | ``` 54 | 55 | 模板也可以在example文件夹中找到。 56 | 57 | 58 | 59 | #### 2. 载入势能面数据文件并且绘制二维势能面 60 | 61 | 点击右上角的`Open...` 按钮并选择你的势能面文件。势能面会立即出现在 `plot window` 中。自动生成的图像可能并不适宜观察到最低点与鞍点。用户需要修改 `PES plot control` 面板中的相关参数。 62 | 63 | R3 64 | 65 | * **Max. V**: 等高面中的最大值。大于 *Max. V* 的数据点会被屏蔽掉。. 66 | * **Min. V**: 等高面中的最小值。小于 *Mix. V* 的数据点会被屏蔽掉。 (不要修改、否则你会看不到最小值点) 67 | * **Level**: 势能面上的等高线数目. 68 | * **Cmap**：图形风格. 69 | 70 | 点击 `Regenrate` 按钮你会看到新的势能面。如果你把它们弄乱了， 点击`Reset plot`。 71 | 72 | 73 | 74 | #### 3. 寻找能量最低路径 75 | 76 | 首先，用户需要提供”弦“的初始猜测。准确的初始猜测能让你更快得到结果。可以通过珠子来定义”弦“ (最少两个珠子)。 点击 `Guess beads`，并在如下对话框中输入初始猜测珠子的坐标（X、Y）。 77 | 78 | 79 | 80 | R4 81 | 82 | 在本例中， 我们用四个珠子来定义初始”弦“。 点击`OK`， 初始弦（黑实线）会在势能面上被绘制。 83 | 84 | R5 85 | 86 | 本程序会提供优化最低能量路径的默认参数。建议您直接使用默认参数。 如果收敛失败， 你可以调整这些参数。 87 | 88 | R6 89 | 90 | * **No. of Beads**: 珠子的数目。 这里定义了弦上有多少个珠子， 珠子越多越精确。 91 | * **Max. iter**: 最大迭代数目。如果优化迭代步数超过 *Max. iter* 值， 优化进程便会停止。 92 | * **Step size**: *Step size* 值决定了梯度下降的步长。 93 | 94 | 95 | 96 | 点击 `Run` ， 优化过程会开始。 初始猜测的”弦“会被优化为最低能量路径。优化过程可以在绘图窗口中可视化。 当你在记录窗口看到 `Converged !` ，意味着优化结束并且得到了最低能量路径。 97 | 98 | 99 | 100 | #### 4. 显示结果 101 | 102 | 最后, 在 `MEP searching` 界面点击 `Show` 按钮。 你会看到如下结果。 103 | 104 | R7 105 | 106 | 点击`Export data` 按钮，最低能量路径上珠子的坐标以及对应的能里会被输出到一个文件中来进行后续应用。 107 | 108 | 109 | 110 | 111 | 112 | ## 技巧 113 | 114 | 1. 当完成一轮优化后，未收敛（或收敛）的珠子会被设定为初始猜测。用户可以继续点击`run` 以使优化过程收敛。 你也可以点击 `Guess beads` 来生成新的初始猜测。 115 | 2. 如果”弦“不停振荡， 尝试减小 `step size` 数值。 116 | 3. 如果”弦“上珠子移动十分慢， 试着增大 `step size` 数值。 117 | 4. 负的 `step size` 值，可以得到”最高“能量路径。 118 | 119 | 120 | 121 | ## 依赖关系 122 | 123 | * pyqt5: 5.15 124 | * Matplotlib: 3.1.3 125 | * numpy: 1.15 126 | * scipy:1.5.4 127 | 128 | 129 | 130 | ## License 131 | 132 | MEPplot: A GUI program for plotting Minimal energy path on potential energy surface. 133 | Copyright (C) 2020 Xin Chen 134 | 135 | This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. 136 | 137 | This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. 138 | 139 | You should have received a copy of the GNU General Public License along with this program. If not, see . -------------------------------------------------------------------------------- /README_JP.md: -------------------------------------------------------------------------------- 1 | # MEPplot 2 | [English](README.md) [中文](README_CN.md) 3 | 4 | 5 | 6 | 潜在的なエネルギー面（自由エネルギー面）に最小エネルギーの経路を描くプログラム。 このプログラムはstring法に基づいています(string method)。 詳細については、以下の論文を参照してください。 (Phys. Rev. B **66**, 052301 – Published 12 August 2002) 7 | 8 | ## ダウンロードダウンロード安装 9 | 10 | 次のリンクにあります `.rar` ファイル： 11 | 12 | https://github.com/chenxin199261/MEPplot/releases 13 | 14 | 中国本土のユーザー向け (GitHub非常に遅い), ダウンロードするには、次のリンクを使用してください: 15 | 16 | https://n459.com/file/30374101-473325811 （passwd:111111） 17 | 18 | ダウンロードrarファイルと解凍， 次の3つのファイルを取得します， 19 | 20 | * MEPplot.bat :MEPplotプログラムエントリ、実行可能なスクリプト,実行可能なスクリプト 21 | * example: 潜在的なエネルギー表面テンプレート. 22 | * main: プログラムファイル. 23 | 24 | ## 使用法 25 | 26 | スクリプトファイルをクリックします `MEPplot.bat`。 次のインターフェイスが表示されます。ガイドに従ってステップバイステップで描画を完了してください。 27 | 28 | R2 29 | 30 | #### 1.潜在的なエネルギー表面データファイルを準備します 31 | 32 | 2Dポテンシャルエネルギーサーフェスファイルは、厳密な形式に従う必要があります，ファイルには3つの列（X座標、Y座標、エネルギー）が含まれています。次のように： 33 | 34 | ``` 35 | -0.88235 1.99224 30.64485 36 | 1.23646 -0.78346 420.58113 37 | 1.03326 0.21343 18.23895 38 | -1.28864 1.87634 23.34170 39 | 0.22373 0.08548 -79.56263 40 | 0.97433 0.60216 119.97031 41 | 0.03879 -0.50717 55.13104 42 | ... 43 | ``` 44 | 45 | テンプレートは、サンプルフォルダにもあります。 46 | 47 | #### 2. PESデータファイルをロードして2DPESをプロットします 48 | 49 | クリック `Open...` 右上隅のボタン PESデータファイルを選択します. PESはで表示されます `plot window` すぐに. 自動生成されたプロットは、最小点と鞍点を見つけるのに完全ではない場合があります. ユーザーは、関連するパラメータを調整する必要があります `PES plot control` パネル. 50 | 51 | R3 52 | 53 | * **Max. V**: カウントプロットの最大値. より大きい値 *Max. V* 選別されます. 54 | * **Min. V**: 最小値. より小さい値 *Min. V* 選別されます (調整しないでください。調整しないと、ローカルミニマを見逃してしまいます). 55 | * **Level**: PESにプロットされた等高線の数. 56 | * **Cmap**：カラーマップスタイル. 57 | 58 | クリック `Regenrate` ボタン新しいPESの図が表示されます. プロットの設定を台無しにした場合, クリックするだけ `Reset plot`. 59 | 60 | 61 | 62 | #### 3. 最小エネルギー経路を検索する 63 | 64 | まず、 ユーザーは最初の推測を提供する必要がありますストリング。 正確な初期推定ストリングは、最終結果にすばやく最適化できます。 最初の推測はビーズ（少なくとも2つのビーズ）によって定義されます。 クリック `Guess beads` 座標（XとY）をダイアログボックスに入力し、 65 | 66 | 67 | 68 | R4 69 | 70 | この例では、最初のストリングを定義するために4つのビーズが連続して提供されています。 「OK」をクリックすると、最初の推測文字列がPESに黒い実線でプロットされます。 71 | 72 | R5 73 | 74 | プログラムは、最適化パラメーターのデフォルト値を提供します。直接使用できます。収束に失敗した場合は、最適化のためにパラメーターを調整できます。 75 | 76 | R6 77 | 78 | * **No. of Beads**: ビーズの数。文字列のビーズの数を定義します。より多くのビーズより多くの精度。 79 | * **Max. iter**: 最大反復回数。最適化ステップが。 最大反復回数。最適化ステップが Maxを超える場合。 iter 値の場合、プロセスは停止します。 80 | * **Step size**: *Step size* 値は、勾配の降順のステップサイズを決定します。 81 | 82 | 83 | 84 | クリック `Run` ボタン、 最適化プロセスが開始されます。 次に、最初の推測文字列が最小エネルギーパスに最適化されます。 最適化プロセスは、プロットウィンドウで視覚化できます。ログパネルの `Converged !` メッセージは、最適化が成功したことを意味します。 85 | 86 | 87 | 88 | #### 4. 結果を示す 89 | 90 | 最終的に、クリック `Show` ボタン に `MEP searching` パネル。最終結果が表示されます。 91 | 92 | R7 93 | 94 | クリック`Export data` ボタン、 ビーズの座標とMEPの関連エネルギーは、さらに使用するためにファイルにエクスポートできます。 95 | 96 | 97 | 98 | ## チップ 99 | 100 | 1. 最初の推測ビーズは、1回の最適化プロセスの後、最新の最適化されたビーズに更新されます。収束に失敗した場合、ユーザーは[実行]をクリックして直接実行できます。クリックする必要があります `Guess beads` 新しい初期推測を生成します。 101 | 2. 弦が振動する場合、 削減してみてください `step size` 値。 102 | 3. ストリング上のビーズがゆっくり動く場合、増加してみてください `step size` 値。 103 | 4. 負`step size`値取得する *maximum energy path* 104 | 105 | -------------------------------------------------------------------------------- /Readme-figures/R1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XinChenQC/MEPplot/8f68c0606b7ea7c27676442d9e7909320de25864/Readme-figures/R1.png -------------------------------------------------------------------------------- /Readme-figures/R2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XinChenQC/MEPplot/8f68c0606b7ea7c27676442d9e7909320de25864/Readme-figures/R2.png -------------------------------------------------------------------------------- /Readme-figures/R3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XinChenQC/MEPplot/8f68c0606b7ea7c27676442d9e7909320de25864/Readme-figures/R3.png -------------------------------------------------------------------------------- /Readme-figures/R4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XinChenQC/MEPplot/8f68c0606b7ea7c27676442d9e7909320de25864/Readme-figures/R4.png -------------------------------------------------------------------------------- /Readme-figures/R5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XinChenQC/MEPplot/8f68c0606b7ea7c27676442d9e7909320de25864/Readme-figures/R5.png -------------------------------------------------------------------------------- /Readme-figures/R6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XinChenQC/MEPplot/8f68c0606b7ea7c27676442d9e7909320de25864/Readme-figures/R6.png -------------------------------------------------------------------------------- /Readme-figures/R7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XinChenQC/MEPplot/8f68c0606b7ea7c27676442d9e7909320de25864/Readme-figures/R7.png -------------------------------------------------------------------------------- /__pycache__/Calc.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XinChenQC/MEPplot/8f68c0606b7ea7c27676442d9e7909320de25864/__pycache__/Calc.cpython-37.pyc -------------------------------------------------------------------------------- /__pycache__/Calc.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XinChenQC/MEPplot/8f68c0606b7ea7c27676442d9e7909320de25864/__pycache__/Calc.cpython-38.pyc -------------------------------------------------------------------------------- /__pycache__/main.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XinChenQC/MEPplot/8f68c0606b7ea7c27676442d9e7909320de25864/__pycache__/main.cpython-38.pyc -------------------------------------------------------------------------------- /main.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from scipy.interpolate import griddata,interp2d,SmoothBivariateSpline,CloughTocher2DInterpolator 3 | import sys 4 | from os import environ 5 | from io import StringIO 6 | import time 7 | from copy import deepcopy 8 | # PyQt5 9 | from PyQt5.uic import loadUi 10 | from PyQt5.QtWidgets import QApplication,QWidget,QGroupBox,QLabel 11 | from PyQt5.QtWidgets import QPushButton,QTextBrowser,QFileDialog 12 | from PyQt5.QtWidgets import QVBoxLayout 13 | from PyQt5.QtCore import QFile,Qt 14 | from PyQt5.QtGui import QIcon 15 | # matplotlib 16 | import matplotlib 17 | matplotlib.use('Qt5Agg') 18 | from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg, NavigationToolbar2QT as NavigationToolbar 19 | from matplotlib.figure import Figure 20 | #import matplotlib.pyplot as plt 21 | from Calc import * 22 | 23 | 24 | import ctypes 25 | myappid = 'mycompany.myproduct.subproduct.version' # arbitrary string 26 | ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid) 27 | 28 | if hasattr(Qt, 'AA_EnableHighDpiScaling'): 29 | QApplication.setAttribute(Qt.AA_EnableHighDpiScaling, True) 30 | 31 | if hasattr(Qt, 'AA_UseHighDpiPixmaps'): 32 | QApplication.setAttribute(Qt.AA_UseHighDpiPixmaps, True) 33 | 34 | 35 | ## Global PES and MEP variables 36 | PESdata = 0 # Original PES data provided by User [2D array, 3*N_points] 37 | MaxValueInit = 1.0 # Maximum value of PES 38 | MinValueInit = 0.0 # Minimum value of PES 39 | xi = 0 # Initial interpolated Grid data X 100 [Grid_data] 40 | yi = 0 # Initial interpolated Grid data Y 100 [Grid_data] 41 | zi = 0 # Initial interpolated Grid data Z 100 [Grid_data] 42 | Guess_beads = 0 # initGuess Beads [2D array, 2*N_guessbeads] 43 | 44 | stepsize=1.00 # Optimize stepsize 45 | max_iter=60 # maximum interation 46 | nbeads=50 # Number of beads 47 | 48 | regul_scale = [[0,1],[0,1]] # regularization factors for X and Y. 49 | xi_r = 0 # Regularized interpolated Grid data X 100 [Grid_data] 50 | yi_r = 0 # Regularized interpolated Grid data Y 100 [Grid_data] 51 | Guess_beads_r = 0 # Regularized Beads [2D array, 2*N_guessbeads] 52 | 53 | PES_f = None # Fitted function for PES 54 | 55 | beads = None 56 | ## Matplotlib Canvas initialization main Windows. 57 | class MplCanvas(FigureCanvasQTAgg): 58 | def __init__(self, parent=None, width=5, height=4, dpi=100): 59 | self.fig = Figure(figsize=(width, height), dpi=dpi, constrained_layout=True) 60 | #plt.ion() 61 | self.axes = self.fig.add_subplot(1,1,1) 62 | super(MplCanvas, self).__init__(self.fig) 63 | def draw_beads(self,beads_x, beads_y): 64 | line = self.axes.plot(beads_x, beads_y,'o-',color='r',markersize=1.3,lw=1) 65 | #plt.pause(0.1) 66 | self.fig.canvas.flush_events() 67 | self.draw() 68 | line.pop(0).remove() 69 | 70 | ## Matplotlib Canvas initialization Result Windows, plot PES. 71 | class MplCanvas2(FigureCanvasQTAgg): 72 | def __init__(self, parent=None, width=5, height=4, dpi=100): 73 | self.fig = Figure(figsize=(width, height), dpi=dpi, constrained_layout=True) 74 | #plt.ion() 75 | self.axes = self.fig.add_subplot(1,1,1) 76 | super(MplCanvas2, self).__init__(self.fig) 77 | 78 | ## Matplotlib Canvas initialization Result Windows, plot curve. 79 | class MplCanvas3(FigureCanvasQTAgg): 80 | def __init__(self, parent=None, width=5, height=4, dpi=100): 81 | self.fig = Figure(figsize=(width, height), dpi=dpi, constrained_layout=True) 82 | #plt.ion() 83 | self.axes = self.fig.add_subplot(1,1,1) 84 | super(MplCanvas3, self).__init__(self.fig) 85 | 86 | ## Result Class 87 | class ResultBox(QWidget): 88 | def __init__(self,maxV=MaxValueInit,minV=MinValueInit,level=20,Cmap='bwr'): 89 | global xi,yi,zi,nbeads 90 | super(ResultBox,self).__init__() 91 | loadUi("ui/Results.ui",self) 92 | self.Canvas1 = MplCanvas2(self.PES_result, width=6, height=6, dpi=100) 93 | toolbar = NavigationToolbar(self.Canvas1,self.PES_result) 94 | layout = QVBoxLayout() 95 | layout.addWidget(toolbar) 96 | layout.addWidget(self.Canvas1) 97 | self.PES_result.setLayout(layout) 98 | 99 | 100 | self.Canvas2 = MplCanvas3(self.Curv_result, width=6, height=6, dpi=100) 101 | toolbar = NavigationToolbar(self.Canvas2,self.Curv_result) 102 | layout = QVBoxLayout() 103 | layout.addWidget(toolbar) 104 | layout.addWidget(self.Canvas2) 105 | self.Curv_result.setLayout(layout) 106 | 107 | ## Click to export results. 108 | self.exportRes.clicked.connect(self.save_result) 109 | 110 | ## Plot PES and MEP on left 111 | self.Canvas1.axes.contour( 112 | xi,yi,zi,vmax=maxV,vmin=minV, 113 | linewidths=0.5,colors='k',levels=np.linspace(minV,maxV,level)) 114 | 115 | cf = self.Canvas1.axes.contourf( 116 | xi,yi,zi,vmax=maxV,vmin=minV, 117 | levels=np.linspace(minV,maxV,140),cmap=Cmap) 118 | 119 | self.cb = self.Canvas1.axes.figure.colorbar(mappable=cf) 120 | beads_tx, beads_ty = trans_back(beads[:,0],beads[:,1],regul_scale) 121 | self.Canvas1.axes.plot(beads_tx, beads_ty,'-',color='r',lw=1.8) 122 | self.Canvas1.draw() 123 | 124 | ## Plot Curve on right 125 | Energy = PES_f(beads[:,0],beads[:,1]) 126 | x = np.linspace(1,len(Energy),len(Energy)) 127 | if(len(Energy) < 100): ms =2 128 | if(len(Energy) > 100 and len(Energy) < 300): ms =1.5 129 | if(len(Energy) > 300 ): ms =1 130 | ## Prepare beads output file: 131 | self.beadsText = "" 132 | for ibead in range(len(Energy)): 133 | self.beadsText = self.beadsText+" "+str(beads_tx[ibead])+" "+str(beads_ty[ibead])+" "+str(Energy[ibead])+" \n" 134 | self.Canvas2.axes.plot(x,Energy,'o-',color='black',markersize=ms) 135 | self.Canvas2.axes.set_xlabel('xlabel') 136 | self.Canvas2.axes.set_ylabel('ylabel') 137 | self.Canvas2.draw() 138 | 139 | def save_result(self): 140 | name = QFileDialog.getSaveFileName(self, 'Export beads') 141 | if (len(name[0]) == 0): return 142 | file = open(name[0],'w') 143 | #text = self.beadsText.toPlainText() 144 | file.write(self.beadsText) 145 | file.close() 146 | self.exported.setText("Exported !") 147 | 148 | ## About box Class 149 | class AboutBox(QWidget): 150 | def __init__(self): 151 | global xi,yi,zi,nbeads 152 | super(AboutBox,self).__init__() 153 | loadUi("ui/about.ui",self) 154 | 155 | class NavigationToolbarCus(NavigationToolbar): 156 | # only display the buttons we need 157 | toolitems = [t for t in NavigationToolbar.toolitems if 158 | t[0] in ('Home', 'Pan', 'Zoom')] 159 | 160 | 161 | ## Guess beads input Class 162 | class GuessBox(QWidget): 163 | def __init__(self,CanvasIn,LableIn,BrowserIn): 164 | super(GuessBox,self).__init__() 165 | loadUi("ui/GuessDia.ui",self) 166 | ## Initial Click events 167 | self.Click() 168 | self.Canvas = CanvasIn 169 | self.label2 = LableIn 170 | self.browser = BrowserIn 171 | 172 | def Click(self): 173 | self.ok.clicked.connect(self.okReadin) 174 | self.reset.clicked.connect(self.resetData) 175 | def okReadin(self): 176 | global Guess_beads 177 | text = self.data.toPlainText() 178 | f = StringIO(text) 179 | try: 180 | Guess_beads = np.loadtxt(f) 181 | if (len(Guess_beads) == 0): 182 | self.browser.append("No beads") 183 | return 184 | if Guess_beads.ndim == 1: 185 | self.browser.append("At least 2 guess beads") 186 | return 187 | self.Canvas.axes.plot(Guess_beads[:,0],Guess_beads[:,1],'o-',color='k') 188 | self.Canvas.draw() 189 | self.label2.setText("Guess finished") 190 | except: 191 | self.browser.append("Guess beads input format error") 192 | 193 | self.close() 194 | def resetData(self): 195 | self.data.clear() 196 | 197 | 198 | class MainWindow(QWidget): 199 | cb = None 200 | def __init__(self): 201 | super(MainWindow,self).__init__() 202 | loadUi("ui/main.ui",self) 203 | ## Initial Click events 204 | self.Click() 205 | 206 | ## Canvas define 207 | self.Canvas = MplCanvas(self.plotWindows, width=6, height=6, dpi=100) 208 | toolbar = NavigationToolbarCus(self.Canvas,self.plotWindows) 209 | layout = QVBoxLayout() 210 | layout.addWidget(toolbar) 211 | layout.addWidget(self.Canvas) 212 | self.plotWindows.setLayout(layout) 213 | self.setWindowIcon(QIcon('ui/Logo.ico')) 214 | ## Initial Guess InputBox 215 | self.guessb = GuessBox(self.Canvas,self.label2,self.outBrowser) 216 | 217 | def Click(self): 218 | self.openB.clicked.connect(self.readFile) 219 | self.Rgen.clicked.connect(self.plotReGen) 220 | self.Rset.clicked.connect(self.plotReset) 221 | self.run.clicked.connect(self.runMEPsearch) 222 | self.guessinp.clicked.connect(self.plotGuessDot) 223 | self.showResult.clicked.connect(self.showRes) 224 | self.about.clicked.connect(self.showAbout) 225 | 226 | def readFile(self): 227 | global PESdata,MaxValueInit,MinValueInit 228 | fileName = QFileDialog.getOpenFileName(self, "Read PES", "../","File (*.dat *.txt)") 229 | if (len(fileName[0]) == 0): return 230 | self.outBrowser.append("Potential energy surface file selected: "+fileName[0]) 231 | 232 | self.label.setText("File loaded") 233 | self.PESfile = fileName 234 | PESfile = open(fileName[0],'r') 235 | # Process The Data 236 | PESdata = np.loadtxt(PESfile) 237 | maxD = np.max(PESdata[:,2]) 238 | minD = np.min(PESdata[:,2]) 239 | MaxValueInit = maxD 240 | MinValueInit = minD 241 | 242 | self.outBrowser.append(" \n==== Information of the surface ====") 243 | self.outBrowser.append(" Xrange: "+str(round(np.min(PESdata[:,0]),4))\ 244 | +" to "+str(round(np.max(PESdata[:,0]),4))) 245 | 246 | self.outBrowser.append(" Yrange: "+str(round(np.min(PESdata[:,1]),4))\ 247 | +" to "+str(round(np.max(PESdata[:,1]),4))) 248 | self.outBrowser.append(" Maximum Value: "+str(round(maxD,4))) 249 | self.outBrowser.append(" Minimum Value: "+str(round(minD,4))) 250 | self.outBrowser.append(" ========================") 251 | 252 | self.Vmax.setText(str(round(maxD,3))) 253 | self.Vmin.setText(str(round(minD,3))) 254 | self.Level.setText(str(24)) 255 | self.plotPES_int() 256 | 257 | # Initial plot 258 | def plotPES_int(self): 259 | global PESdata,MaxValueInit,MinValueInit,xi,yi,zi,FuncInter 260 | if(self.cb != None ): self.cb.remove() 261 | self.Canvas.axes.clear() 262 | X_max = np.max(PESdata[:,0]) 263 | X_min = np.min(PESdata[:,0]) 264 | Y_max = np.max(PESdata[:,1]) 265 | Y_min = np.min(PESdata[:,1]) 266 | xi = np.linspace(X_min,X_max,300) 267 | yi = np.linspace(Y_min,Y_max,300) 268 | zi = griddata((PESdata[:,0],PESdata[:,1]),PESdata[:,2], 269 | (xi[None,:],yi[:,None]),method='cubic') 270 | 271 | self.Canvas.axes.contour(xi,yi,zi, 272 | levels=24,linewidths=0.5,colors='k') 273 | 274 | cf = self.Canvas.axes.contourf(xi,yi,zi, 275 | levels=140,cmap="bwr") 276 | # Get color bar 277 | self.cb = self.Canvas.axes.figure.colorbar(mappable=cf) 278 | self.Canvas.draw() 279 | 280 | # Regenerate plot 281 | def plotReGen(self): 282 | global PESdata,MaxValueInit,MinValueInit,xi,yi,zi 283 | if (type(PESdata) is int): 284 | return 285 | self.cb.remove() 286 | self.Canvas.axes.clear() 287 | self.Canvas.draw() 288 | try: 289 | maxV = float(self.Vmax.text()) 290 | minV = float(self.Vmin.text()) 291 | level = int(self.Level.text()) 292 | except: 293 | maxV = MaxValueInit 294 | minV = MinValueInit 295 | level = 12 296 | self.Vmax.setText(str(round(MaxValueInit,3))) 297 | self.Vmin.setText(str(round(MinValueInit,3))) 298 | self.Level.setText(str(12)) 299 | Cmap = self.cmap.currentText() 300 | 301 | self.Canvas.axes.contour( 302 | xi,yi,zi,vmax=maxV,vmin=minV, 303 | linewidths=0.5,colors='k',levels=np.linspace(minV,maxV,level)) 304 | 305 | cf = self.Canvas.axes.contourf( 306 | xi,yi,zi,vmax=maxV,vmin=minV, 307 | levels=np.linspace(minV,maxV,140),cmap=Cmap) 308 | 309 | self.cb = self.Canvas.axes.figure.colorbar(mappable=cf) 310 | self.Canvas.draw() 311 | 312 | # Plot Guess dot on Canvas 313 | def plotGuessDot(self): 314 | global Guess_beads,stepsize,max_iter,nbeads 315 | 316 | self.plotReGen() 317 | self.guessb.show() 318 | self.Nbeads.setText(str(50)) 319 | 320 | stepsize = 3.0/((MaxValueInit-MinValueInit)) 321 | max_iter = 60 322 | nbeads = 50 323 | 324 | self.Stepsize.setText(str(round(stepsize,3))) 325 | self.Maxiter.setText(str(80)) 326 | #self.cb.remove() 327 | 328 | # Show results 329 | def showRes(self): 330 | if (type(PESdata) is int): 331 | self.outBrowser.append(" Error ! No potential energy surface data !") 332 | return 333 | 334 | if (beads is None): 335 | self.outBrowser.append(" Error ! No optimized beads") 336 | return 337 | 338 | maxV = float(self.Vmax.text()) 339 | minV = float(self.Vmin.text()) 340 | level = int(self.Level.text()) 341 | Cmap = self.cmap.currentText() 342 | self.resultb = ResultBox(maxV,minV,level,Cmap) 343 | self.resultb.show() 344 | # Show about 345 | 346 | def showAbout(self): 347 | self.aboutb = AboutBox() 348 | self.aboutb.show() 349 | 350 | def plotReset(self): 351 | global PESdata,MaxValueInit,MinValueInit,xi,yi,zi 352 | if (type(PESdata) is int): 353 | return 354 | self.cb.remove() 355 | self.Canvas.axes.clear() 356 | self.Canvas.draw() 357 | 358 | self.Vmax.setText(str(round(MaxValueInit,3))) 359 | self.Vmin.setText(str(round(MinValueInit,3))) 360 | self.Level.setText(str(12)) 361 | #self.cb.remove() 362 | Cmap = self.cmap.currentText() 363 | self.Canvas.axes.contour( 364 | xi,yi,zi,vmax=MaxValueInit,vmin=MinValueInit, 365 | linewidths=0.5,colors='k',levels=np.linspace(MinValueInit,MaxValueInit,12)) 366 | 367 | cf = self.Canvas.axes.contourf( 368 | xi,yi,zi,vmax=MaxValueInit,vmin=MinValueInit, 369 | levels=np.linspace(MinValueInit,MaxValueInit,140),cmap=Cmap) 370 | 371 | self.cb = self.Canvas.axes.figure.colorbar(mappable=cf) 372 | self.Canvas.draw() 373 | 374 | def runMEPsearch(self): 375 | global Guess_beads,stepsize,max_iter,nbeads,regul_scale,\ 376 | xi_r,yi_r,Guess_beads_r,PES_f,beads 377 | ## Read MEP optimization options. 378 | if (type(PESdata) is int): 379 | self.outBrowser.append(" Error ! No potential energy surface data !") 380 | return 381 | 382 | if (type(Guess_beads) is int): 383 | self.outBrowser.append(" Warnning ! No initial guess beads !") 384 | return 385 | 386 | try: 387 | stepsize = float(self.Stepsize.text()) 388 | max_iter = int(self.Maxiter.text()) 389 | nbeads = int(self.Nbeads.text()) 390 | except: 391 | stepsize = 3.0/((MaxValueInit-MinValueInit)) 392 | max_iter = 80 393 | nbeads = 50 394 | self.Stepsize.setText(str(round(stepsize,3))) 395 | self.Maxiter.setText(str(max_iter)) 396 | self.Nbeads.setText(str(50)) 397 | 398 | 399 | ## Regularization data: 400 | self.outBrowser.append(" ================= \n Optimization start\n ================= ") 401 | regul_scale[0][0] = np.amin(PESdata[:,0]) 402 | regul_scale[0][1] = 5.0/(np.amax(PESdata[:,0]) - np.amin(PESdata[:,0])) 403 | 404 | regul_scale[1][0] = np.amin(PESdata[:,1]) 405 | regul_scale[1][1] = 5.0/(np.amax(PESdata[:,1]) - np.amin(PESdata[:,1])) 406 | 407 | xi_r = (PESdata[:,0]-regul_scale[0][0])*regul_scale[0][1] 408 | yi_r = (PESdata[:,1]-regul_scale[1][0])*regul_scale[1][1] 409 | 410 | Guess_beads_r = deepcopy(Guess_beads) 411 | Guess_beads_r[:,0] = (Guess_beads[:,0]-regul_scale[0][0])*regul_scale[0][1] 412 | Guess_beads_r[:,1] = (Guess_beads[:,1]-regul_scale[1][0])*regul_scale[1][1] 413 | 414 | PES_f = CloughTocher2DInterpolator(np.column_stack((xi_r,yi_r)),PESdata[:,2]) 415 | ## 1. Generate string 416 | beads = InitBeads(Guess_beads_r,PES_f,nbeads) 417 | self.plotReGen() 418 | beads_tx, beads_ty = trans_back(beads[:,0],beads[:,1],regul_scale) 419 | line = self.Canvas.axes.plot(beads_tx, beads_ty,'o-',color='k',markersize=1) 420 | 421 | self.Canvas.draw() 422 | line.pop(0).remove() 423 | ## 2. optimaztion loop 424 | beads_old = deepcopy(beads) 425 | diff = 1 426 | Conv_flag = 0 427 | for i in range(max_iter): 428 | if (i == 1 and diff < 0.5*10**-3 ): stepsize =stepsize*100 429 | #if (i == 1 and diff < 0.04 and diff > 0.004): stepsize =stepsize*100 430 | if (i == 45 and diff > 0.1 ): stepsize =stepsize*0.1 431 | if (i == 50 and diff > 0.05 ): stepsize =stepsize*0.1 432 | if (i > 55 and i < 58 and diff > 0.02 ): stepsize =stepsize*0.1 433 | #if (i > 65 and i < 68 and diff > 0.005 ): stepsize =stepsize*0.5 434 | beads,scale_step = walkdown(beads,stepsize,PES_f) 435 | beads = redist(beads,PES_f) 436 | diff = calcDiff(beads,beads_old) 437 | stepsize =stepsize*scale_step 438 | if (i%5 == 0): 439 | self.outBrowser.append("iteration number: " \ 440 | +str(i)+" Diff: "+ str(round(diff,6))\ 441 | +" stepsize: "+str(round(stepsize,6))) 442 | #print("iteration number: ",i,"Diff: ",diff," step: ",stepsize) 443 | if(diff<0.5*10**-3 and i >10): 444 | self.outBrowser.append(" Converged ! ") 445 | Conv_flag = 1 446 | break 447 | 448 | beads_old = deepcopy(beads) 449 | beads_tx, beads_ty = trans_back(beads[:,0],beads[:,1],regul_scale) 450 | #line = self.Canvas.axes.plot(beads_tx, beads_ty,'o-',color='r',markersize=1,lw=0.5) 451 | self.Canvas.draw_beads(beads_tx, beads_ty) 452 | time.sleep(0.2) 453 | #self.Canvas.draw() 454 | if (Conv_flag ==0 ): 455 | self.outBrowser.append(" Converge Failed ! ") 456 | Guess_beads = deepcopy(beads) 457 | Guess_beads[:,0],Guess_beads[:,1] = trans_back(beads[:,0],beads[:,1],regul_scale) 458 | beads_tx, beads_ty = trans_back(beads[:,0],beads[:,1],regul_scale) 459 | self.Canvas.axes.plot(beads_tx, beads_ty,'-',color='r',lw=1.8) 460 | self.Canvas.draw() 461 | 462 | 463 | ## RecoverData 464 | if __name__ == "__main__": 465 | app = QApplication(sys.argv) 466 | demo1 = MainWindow() 467 | demo1.show() 468 | sys.exit(app.exec_()) 469 | time.sleep(50) 470 | input("Press enter to end!") -------------------------------------------------------------------------------- /ui/GuessDia.ui: -------------------------------------------------------------------------------- 1 | 2 | 3 | Form 4 | 5 | 6 | 7 | 0 8 | 0 9 | 190 10 | 340 11 | 12 | 13 | 14 | 15 | 190 16 | 340 17 | 18 | 19 | 20 | 21 | 202 22 | 350 23 | 24 | 25 | 26 | Guess beads 27 | 28 | 29 | 30 | 31 | 20 32 | 290 33 | 61 34 | 23 35 | 36 | 37 | 38 | PointingHandCursor 39 | 40 | 41 | OK 42 | 43 | 44 | 45 | 46 | 47 | 90 48 | 290 49 | 71 50 | 23 51 | 52 | 53 | 54 | PointingHandCursor 55 | 56 | 57 | reset 58 | 59 | 60 | 61 | 62 | 63 | 20 64 | 10 65 | 141 66 | 271 67 | 68 | 69 | 70 | IBeamCursor 71 | 72 | 73 | 74 | 75 | 76 | 77 | -------------------------------------------------------------------------------- /ui/Logo.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XinChenQC/MEPplot/8f68c0606b7ea7c27676442d9e7909320de25864/ui/Logo.ico -------------------------------------------------------------------------------- /ui/Logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/XinChenQC/MEPplot/8f68c0606b7ea7c27676442d9e7909320de25864/ui/Logo.png -------------------------------------------------------------------------------- /ui/Results.ui: -------------------------------------------------------------------------------- 1 | 2 | 3 | Form 4 | 5 | 6 | 7 | 0 8 | 0 9 | 1000 10 | 530 11 | 12 | 13 | 14 | 15 | 1000 16 | 510 17 | 18 | 19 | 20 | 21 | 1100 22 | 530 23 | 24 | 25 | 26 | Results 27 | 28 | 29 | 30 | 31 | 19 32 | 9 33 | 951 34 | 451 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 472 43 | 449 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 472 53 | 449 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 780 64 | 470 65 | 101 66 | 31 67 | 68 | 69 | 70 | Export data 71 | 72 | 73 | 74 | 75 | 76 | 900 77 | 480 78 | 61 79 | 21 80 | 81 | 82 | 83 | 84 | Times New Roman 85 | 11 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | -------------------------------------------------------------------------------- /ui/about.ui: -------------------------------------------------------------------------------- 1 | 2 | 3 | aboutPage 4 | 5 | 6 | 7 | 0 8 | 0 9 | 530 10 | 360 11 | 12 | 13 | 14 | 15 | 530 16 | 360 17 | 18 | 19 | 20 | 21 | 530 22 | 360 23 | 24 | 25 | 26 | About 27 | 28 | 29 | 30 | 31 | 10 32 | 90 33 | 520 34 | 250 35 | 36 | 37 | 38 | 39 | 520 40 | 250 41 | 42 | 43 | 44 | 45 | 525 46 | 260 47 | 48 | 49 | 50 | IBeamCursor 51 | 52 | 53 | 0 54 | 55 | 56 | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> 57 | <html><head><meta name="qrichtext" content="1" /><style type="text/css"> 58 | p, li { white-space: pre-wrap; } 59 | </style></head><body style=" font-family:'SimSun'; font-size:9pt; font-weight:400; font-style:normal;"> 60 | <p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">MEPplot: A GUI program for plotting Minimal energy path on potential energy surface. </p> 61 | <p align="justify" style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p> 62 | <p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Copyright (C) 2020 Xin Chen</p> 63 | <p align="justify" style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p> 64 | <p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.</p> 65 | <p align="justify" style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p> 66 | <p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.</p> 67 | <p align="justify" style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p> 68 | <p align="justify" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.</p> 69 | <p align="justify" style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p></body></html> 70 | 71 | 72 | 73 | 74 | 75 | 76 | -------------------------------------------------------------------------------- /ui/main.ui: -------------------------------------------------------------------------------- 1 | 2 | 3 | Form 4 | 5 | 6 | 7 | 0 8 | 0 9 | 771 10 | 755 11 | 12 | 13 | 14 | 15 | 771 16 | 600 17 | 18 | 19 | 20 | 21 | 800 22 | 755 23 | 24 | 25 | 26 | 27 | Times New Roman 28 | 29 | 30 | 31 | false 32 | 33 | 34 | MEP Plot 35 | 36 | 37 | false 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 10 46 | 20 47 | 741 48 | 701 49 | 50 | 51 | 52 | 53 | 54 | 55 | 3 56 | 57 | 58 | 59 | 60 | true 61 | 62 | 63 | 64 | 0 65 | 0 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 1 74 | 75 | 76 | 77 | 78 | 1 79 | 80 | 81 | 82 | 83 | 84 | Times New Roman 85 | 10 86 | 87 | 88 | 89 | PointingHandCursor 90 | 91 | 92 | Open... 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | Times New Roman 101 | 8 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 | 114 | 115 | 0 116 | 0 117 | 118 | 119 | 120 | 121 | Times New Roman 122 | 123 | 124 | 125 | Plot setting 126 | 127 | 128 | 129 | 130 | 10 131 | 20 132 | 231 133 | 156 134 | 135 | 136 | 137 | 138 | 139 | 140 | true 141 | 142 | 143 | 144 | Times New Roman 145 | 10 146 | 147 | 148 | 149 | Max. V 150 | 151 | 152 | 153 | 154 | 155 | 156 | 157 | Times New Roman 158 | 10 159 | 160 | 161 | 162 | Cmap 163 | 164 | 165 | 166 | 167 | 168 | 169 | 170 | Times New Roman 171 | 10 172 | 173 | 174 | 175 | Level 176 | 177 | 178 | 179 | 180 | 181 | 182 | 183 | Times New Roman 184 | 10 185 | 186 | 187 | 188 | Min. V 189 | 190 | 191 | 192 | 193 | 194 | 195 | 196 | 197 | 198 | 199 | 200 | 201 | 202 | 203 | 204 | 205 | Times New Roman 206 | 10 207 | 208 | 209 | 210 | 211 | bwr 212 | 213 | 214 | 215 | 216 | jet 217 | 218 | 219 | 220 | 221 | rainbow 222 | 223 | 224 | 225 | 226 | 227 | 228 | 229 | 230 | Times New Roman 231 | 9 232 | 233 | 234 | 235 | PointingHandCursor 236 | 237 | 238 | Reset plot 239 | 240 | 241 | 242 | 243 | 244 | 245 | 246 | Times New Roman 247 | 9 248 | 249 | 250 | 251 | PointingHandCursor 252 | 253 | 254 | Regenerate 255 | 256 | 257 | 258 | 259 | 260 | 261 | 262 | 263 | 264 | 265 | 266 | 0 267 | 0 268 | 269 | 270 | 271 | 272 | Times New Roman 273 | true 274 | 275 | 276 | 277 | MEP searching 278 | 279 | 280 | false 281 | 282 | 283 | false 284 | 285 | 286 | 287 | 288 | 10 289 | 20 290 | 242 291 | 163 292 | 293 | 294 | 295 | 296 | 297 | 298 | 299 | Times New Roman 300 | 10 301 | 302 | 303 | 304 | Max. iter. 305 | 306 | 307 | 308 | 309 | 310 | 311 | 312 | 0 313 | 0 314 | 315 | 316 | 317 | 318 | 319 | 320 | 321 | 322 | 323 | 324 | 325 | Times New Roman 326 | 10 327 | 328 | 329 | 330 | No. of Beads: 331 | 332 | 333 | 334 | 335 | 336 | 337 | 338 | Times New Roman 339 | 10 340 | 341 | 342 | 343 | Step size: 344 | 345 | 346 | 347 | 348 | 349 | 350 | 351 | 352 | 353 | 354 | 6 355 | 5 356 | 357 | 358 | 359 | 360 | Times New Roman 361 | 10 362 | false 363 | 364 | 365 | 366 | PointingHandCursor 367 | 368 | 369 | Guess beads 370 | 371 | 372 | 373 | 374 | 375 | 376 | 377 | Times New Roman 378 | 9 379 | 380 | 381 | 382 | PointingHandCursor 383 | 384 | 385 | Run 386 | 387 | 388 | 389 | 390 | 391 | 392 | 393 | Times New Roman 394 | 9 395 | 396 | 397 | 398 | PointingHandCursor 399 | 400 | 401 | Show 402 | 403 | 404 | 405 | 406 | 407 | 408 | 409 | 8 410 | 411 | 412 | 413 | 414 | 415 | 416 | 417 | 418 | 419 | 420 | 421 | 422 | 423 | 424 | 425 | 426 | 427 | 428 | 429 | 430 | 431 | 432 | 433 | 690 434 | 730 435 | 61 436 | 21 437 | 438 | 439 | 440 | 441 | 442 | 443 | 444 | 445 | 0 446 | 85 447 | 255 448 | 449 | 450 | 451 | 452 | 453 | 454 | 0 455 | 85 456 | 255 457 | 458 | 459 | 460 | 461 | 462 | 463 | 0 464 | 85 465 | 255 466 | 467 | 468 | 469 | 470 | 471 | 472 | 0 473 | 85 474 | 255 475 | 476 | 477 | 478 | 479 | 480 | 481 | 482 | 483 | 0 484 | 85 485 | 255 486 | 487 | 488 | 489 | 490 | 491 | 492 | 0 493 | 85 494 | 255 495 | 496 | 497 | 498 | 499 | 500 | 501 | 0 502 | 85 503 | 255 504 | 505 | 506 | 507 | 508 | 509 | 510 | 0 511 | 85 512 | 255 513 | 514 | 515 | 516 | 517 | 518 | 519 | 520 | 521 | 120 522 | 120 523 | 120 524 | 525 | 526 | 527 | 528 | 529 | 530 | 120 531 | 120 532 | 120 533 | 534 | 535 | 536 | 537 | 538 | 539 | 120 540 | 120 541 | 120 542 | 543 | 544 | 545 | 546 | 547 | 548 | 0 549 | 85 550 | 255 551 | 552 | 553 | 554 | 555 | 556 | 557 | 558 | 559 | Times New Roman 560 | 9 561 | 50 562 | false 563 | false 564 | true 565 | 566 | 567 | 568 | PointingHandCursor 569 | 570 | 571 | font: 9pt "Times New Roman"; 572 | text-decoration: underline; 573 | 574 | 575 | About 576 | 577 | 578 | true 579 | 580 | 581 | 582 | 583 | 584 | 430 585 | 730 586 | 261 587 | 21 588 | 589 | 590 | 591 | 592 | 593 | 594 | 595 | 596 | 597 | 598 | 599 | Times New Roman 600 | 9 601 | 50 602 | false 603 | false 604 | true 605 | 606 | 607 | 608 | PointingHandCursor 609 | 610 | 611 | font: 9pt "Times New Roman"; 612 | text-decoration: underline; 613 | 614 | 615 | <html><head/><body><p><a href="https://github.com/chenxin199261/MEPplot"><span style=" font-family:'Times News Roman'; text-decoration: underline; color:#0000ff;">https://github.com/chenxin199261/MEPplot</span></a></p></body></html> 616 | 617 | 618 | true 619 | 620 | 621 | 622 | 623 | 624 | 625 | --------------------------------------------------------------------------------