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--- exercise:uv [2014/05/16 04:07] – dpasserone
+++ exercises:2014_ethz_mmm:uv [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 12: / Line 12: @@
 </code>
-Then source your profile file, as well as loading the modules:
+Then source your profile file, as well as loading the modules, and copying this configuration file:
 <code>
 . ~/.bash_profile
 module load intel/12.1.2 open_mpi/1.6.5 python vmd
+cp ~danielep/.nwchemrc $HOME
 </code>
 Now you are able to run the **nwchem** code.
-Copy all files from the directory: ** /cluster/home03/matl/danielep/LECTURE6/EXERCISE_6.2 **.
+Download all files from the media manager: {{exercise_11.1.tar.gz|}}.
 ===== Calculation of the spectrum using linear response TDDFT =====
@@ Line 103: / Line 104: @@
 </code>
-<note important>  - List in a table the orbital energies for this system. Note that alpha and beta orbitals are listed, but they are degenerate in this case (alpha=beta). Search for the string "Occ." just after the title "Final Molecular Orbital Analysis". Note the character of the orbital (px, py, pz...) and the sign of the LUMO coefficients (comment).
+<note important>
+  - List in a table the orbital energies for this system. Note that alpha and beta orbitals are listed, but they are degenerate in this case (alpha=beta). Search for the string "Occ." just after the title "Final Molecular Orbital Analysis". Note the character of the orbital (px, py, pz...) and the sign of the LUMO coefficients (comment).
   - Visualize homo and lumo with vmd.
-  - The excitation spectrum corresponds to transitions between occupied and unoccupied states. Look for this information in the file, and compare it with the peaks in the plot.</note>
+  - The excitation spectrum corresponds to transitions between occupied and unoccupied states. Look for this information in the file, and compare it with the peaks in the plot.
+</note>
+===== Resonant ultraviolet excitation of water =====
+In this second part, we compute the time-dependent electron response to a quasi-monochromatic laser pulse tuned to a particular transition.
+The spectrum obtained with linear response TDDFT can be also calculated by exciting the system through a laser pulse with a specific polarization along x, y, or z.
+We will use the results of a calculation described [[http://www.nwchem-sw.org/index.php/Release62:RT-TDDFT|here]]. The total spectrum  (6-31G * */PBE0 gas-phase water) is the same as the one we calculated before. First, we consider the absorption spectrum (computed previously) but plotted for the three polarizations (x,y,z) rather then as a sum. The details are given in the previously cited link.
+{{ 730px-rt_tddft_h2o_resonant_spec_field.png?direct&300 |}}
+Say we are interested in the excitation near 10 eV. We can clearly see this is a z-polarized transition (green on curve). To selectively excite this we could use a continuous wave E-field, which has a delta-function, i.e., single frequency, bandwidth but since we are doing finite simulations we need a suitable envelope. The broader the envelope in time the narrower the excitation in frequency domain, but of course long simulations become costly so we need to put some thought into the choice of our envelope. In this case the peak of interest is spectrally isolated from other z-polarized peaks, so this is quite straightforward. The procedure is outlined below, and the corresponding frequency extent of the pulse is shown on the absorption figure in orange. Note that it only covers one excitation, i.e., the field selectively excites one mode. The full input deck is ** h2o_resonant.nw **.
+The relevant code section is:
+<code>
+rt_tddft
+  tmax 1000.0
+  dt 0.2
+  field "driver"
+    type gaussian
+    polarization z
+    frequency 0.3768  # = 10.25 eV
+    center 393.3
+    width 64.8
+    max 0.0001
+  end
+  excite "system" with "driver"
+ end
+task dft rt_tddft
+</code>
+Run now ** h2_resonant.nw ** on 4 cores:
+<code>
+bsub -n 4 -o resonant.out  mpirun nwchem resonant.nw
+</code>
+The run (follow with bpeek) will apply a field for a limited amount of time. This field will excite the system into a superposition of the ground state and the one excited state, which manifests as monochromatic oscillations. After the field has passed the dipole oscillations continue forever as there is no damping in the system.
+There are 5000 MD steps. It will take about 10 minutes. At the end, cubefiles for the density at each timestep will be generated.
+You can visualize the animation using vmd, using a script that cleans a bit (moving the cubes into another directory)
+<code>
+./createlist
+vmd -e animate.cube.vmd
+</code>
+What you will see is the electron density difference between the initial state and an instant along the trajectory.
+<note important>
+  - Plot from the output file the applied field: **grep -i Applied resonant.out | grep alpha > appl**
+  - Plot the z component of the induced dipole moment: **grep ipole resonant.out > dipole**
+  - Explain what you see in the vmd representation based on what you see on the previous plot
+</note>