Initial commit

.idea/.gitignore

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+# Default ignored files
+/shelf/
+/workspace.xml

.idea/AMM.iml

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+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$">
+      <excludeFolder url="file://$MODULE_DIR$/venv" />
+    </content>
+    <orderEntry type="jdk" jdkName="Python 3.8 (AMM)" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>

.idea/inspectionProfiles/profiles_settings.xml

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+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

.idea/misc.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.8 (AMM)" project-jdk-type="Python SDK" />
+</project>

.idea/modules.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/AMM.iml" filepath="$PROJECT_DIR$/.idea/AMM.iml" />
+    </modules>
+  </component>
+</project>

.idea/vcs.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>

exspectrum

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+# Excitation spectrum ; written at 2021-12-23 18:00:19
+#     Exc.     energy (Eh)   energy (eV)   energy (cm-1)   energy (nm)     Osc.(vel)      Osc.(len) 
+       1 a        0.081632       2.22132       17916.184       558.155     0.59324546     0.63875147
+       2 a        0.097816       2.66170       21468.087       465.808     0.01013849     0.01104033
+       3 a        0.101932       2.77371       22371.482       446.998     0.18173513     0.19477660
+       4 a        0.119431       3.24989       26212.132       381.503     0.64359780     0.65859697
+       5 a        0.121826       3.31506       26737.749       374.003     0.07358580     0.07053363
+       6 a        0.124153       3.37836       27248.345       366.995     0.58084889     0.60692493
+       7 a        0.133071       3.62104       29205.673       342.399     0.44634456     0.45611903
+       8 a        0.136025       3.70142       29853.943       334.964     0.01543649     0.01724145
+       9 a        0.138425       3.76673       30380.708       329.156     0.06870782     0.06655899
+      10 a        0.139343       3.79172       30582.302       326.986     0.09547385     0.09610700
+      11 a        0.139697       3.80135       30659.928       326.159     0.31050776     0.32244116
+      12 a        0.141117       3.83998       30971.558       322.877     0.04646558     0.04287950
+      13 a        0.143354       3.90086       31462.590       317.838     0.00140278     0.00117080
+      14 a        0.143957       3.91727       31594.889       316.507     0.07233739     0.07315710
+      15 a        0.144246       3.92514       31658.403       315.872     0.00752599     0.00818926
+      16 a        0.144772       3.93944       31773.723       314.725     0.00168315     0.00167697
+      17 a        0.145201       3.95111       31867.834       313.796     0.00226231     0.00201420
+      18 a        0.145758       3.96629       31990.274       312.595     0.00003515     0.00003452
+      19 a        0.146169       3.97747       32080.469       311.716     0.00837502     0.00898456
+      20 a        0.146494       3.98631       32151.783       311.025     0.00974370     0.00905770
+      21 a        0.148519       4.04140       32596.061       306.786     0.23894747     0.26006671
+      22 a        0.149195       4.05981       32744.572       305.394     0.01999536     0.02004168
+      23 a        0.149254       4.06140       32757.367       305.275     0.00860917     0.00890324
+      24 a        0.149750       4.07490       32866.276       304.263     0.02541908     0.02508246
+      25 a        0.151961       4.13507       33351.586       299.836     0.00081672     0.00066642
+      26 a        0.152157       4.14040       33394.610       299.450     0.00012992     0.00013872
+      27 a        0.152234       4.14249       33411.414       299.299     0.00004462     0.00004261
+      28 a        0.153115       4.16647       33604.808       297.576     0.03615181     0.04035899
+      29 a        0.153534       4.17787       33696.766       296.764     0.00006776     0.00007273
+      30 a        0.154251       4.19738       33854.151       295.385     0.03348557     0.03561208

exspectrum_plotter.py

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+"""
+Turbomole-Spectrum-Plotter
+(c) 2022 Lukas Schank
+
+This script will run through all subfolders of the given folder and plot excitation spectra of TDDFT calculations.
+"""
+
+import sys
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+from pathlib import Path
+
+
+def exspectrum_plotter(data_folder: str, output_folder: str):
+
+    # convert input to path objects
+    data_folder = Path(data_folder)
+    output_folder = Path(output_folder)
+    if not output_folder.exists():
+        output_folder.mkdir()
+
+    # convert data to plot
+    for data_file in data_folder.glob('**/exspectrum'):  # path.glob iterates through given folder for pattern
+        # read data
+        rawdata = pd.read_csv(
+            data_file,
+            sep='\s+',  # seperator is one or more spaces
+            skiprows=2,  # skip header rows
+            header=None  # prevent getting first numbers as header
+        )
+        data_energy = np.array(rawdata.iloc[:, 3])
+        data_osc_strength = np.array(rawdata.iloc[:, 6])
+
+        # calculate gauss broadening for spectrum
+        def gauss_spectrum(energy, osc_strength, sigma, gauss_energy_range):
+            gauss_osc_strength = []
+            for E_i in gauss_energy_range:
+                tot = 0
+                for E_j, osc in zip(energy, osc_strength):
+                    tot += osc * np.exp(-(((E_j - E_i) / sigma) ** 2))
+                gauss_osc_strength.append(tot)
+            return gauss_osc_strength
+
+        calc_energy_range = np.linspace(0, 6, num=500, endpoint=True)  # x values for calculated spectrum
+        calc_sigma = 0.15  # std for gauss broadening
+        calc_osc_strength = gauss_spectrum(data_energy, data_osc_strength, calc_sigma, calc_energy_range)
+
+        # create plot
+        fig, ax = plt.subplots(dpi=300, figsize=(6, 4))
+        ax.plot(calc_energy_range, calc_osc_strength, "-k")  # plot calculated spectrum
+        for plt_energy, plt_osc_strength in zip(data_energy, data_osc_strength):
+            ax.plot((plt_energy, plt_energy), (0, plt_osc_strength), c="k")  # plot lines from data
+        ax.set_xlabel("Energy / eV", fontsize=16)
+        ax.set_ylabel("Osc. Strength / a.u.", fontsize=16)
+        ax.xaxis.set_tick_params(labelsize=14, width=1.5)
+        ax.yaxis.set_tick_params(labelsize=14, width=1.5)
+        for axis in ['top', 'bottom', 'left', 'right']:
+            ax.spines[axis].set_linewidth(1.5)
+        ax.set_xlim(1.5, 5)
+        plt.tight_layout()
+
+        # save plot
+        data_name = Path(data_file)
+        output_name = data_name.parts[data_folder.parts.__len__()]
+        for name in data_name.parts[(data_folder.parts.__len__() + 1):]:
+            output_name += "_" + name
+        output_name += ".pdf"  # change here for pdf or png output
+        output_path = output_folder / output_name
+        plt.savefig(output_path)
+        plt.close(fig)  # close plot
+
+
+# getting commandline input and pass it to function
+if __name__ == "__main__":
+    a = str(sys.argv[1])
+    b = str(sys.argv[2])
+    exspectrum_plotter(a, b)
+
+# python exspectrum_plotter.py "C:\Path\to\Calculations" "C:\path\to\results"