Differences

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--- exercises:2019_conexs_newcastle:ex4 [2019/09/11 12:52] – [Part 1: PDOS and spectra broadening of liquid water] abussy
+++ exercises:2019_conexs_newcastle:ex4 [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 301: / Line 301: @@
 <code>
 module load Anaconda3/5.0.1
+</code>
+and then typing
+<code>
+python pdos_conv.py
 </code>
 Note that you might have to change the parameters at the top of the file to get pleasing results. If a new window with the plot does not open, it is also saved in the current directory as "pdos.png".
 <code - pdos_conv.py>
 import numpy as np
-import matplotlib.pyplot as plt
 import os
+import matplotlib as mpl
+mpl.use('Agg')
+import matplotlib.pyplot as plt
 # Parameters
@@ Line 399: / Line 405: @@
 &END MOTION
 </code>
-The parameters in the MD section has been selected to finish in a few minut, but feel free to experiment with different values. To not print too much, also modify the &PDOS section to
+The parameters in the MD section has been selected to finish in a few minutes, but feel free to experiment with different values and get a feel for how they work. To not print too much, also modify the &PDOS section to
 <code>
 &PDOS
@@ Line 409: / Line 415: @@
 &END PDOS
 </code>
-which means that we only print the PDOS every third step, as well as appending the specta instead of overwriting them.
+which means that we only print the PDOS every third step, as well as appending the spectra instead of overwriting them.
 When you have finished the calculation, you should have created some new files, including
@@ Line 417: / Line 423: @@
 <code - pdos_conv_md.py>
 import numpy as np
-import matplotlib.pyplot as plt
 import os
+import matplotlib as mpl
+mpl.use('Agg')
+import matplotlib.pyplot as plt
 # Parameters
-FWHM = 0.3   # Full width half maximum
+FWHM = 0.4   # Full width half maximum
 Emin=-16.    # Starting energy
 Emax= 4.     # -----