Differences

This shows you the differences between two versions of the page.

--- exercises:2015_pitt:gga [2015/02/26 13:56] – further updates vondele
+++ exercises:2015_pitt:gga [2015/03/02 15:54] – [Required Files] vondele
@@ Line 87: / Line 87: @@
 {{ exercises:2015_ethz_mmm:dye_tio_bonding_density.png?300 |}}
-===== 3. Task: Bonding energies  =====
+===== 3. Task: relative stabilities  =====
-Compute the binding energy for both binding modes:
-\[ E_\text{binding}=\sum E_\text{products} - \sum E_\text{reactants} \]
+In order to compute the relative stability of mode1 and mode2, both configurations need to be geometry optimized.
-For this you will need the energy values of four systems:
+To do so, turn off the generation of cubes (''&E_DENSITY_CUBE OFF'') in mode1.inp, change to ''RUN_TYPE GEO_OPT'' and adjust the project name. Create and run a similar input file for mode2.
-  - lone acetic acid molecule (run geometry optimization, use energy of last step)
-  - lone TiO$_2$ slab  (you can use the already geometry optimized coordinates from ''relaxed_slab.xyz'' at the end of the exercise)
-  - combined system bound in the first mode (can be reused from previous task)
-  - combined system bound in the second mode (file ''mode2.xyz'')
-<note important>
+input topics:
-You can not reuse the energy values for the lone sub-systems from the previous task. Since the unbound subsystems might relax into a different geometry, they have to be geometry optimized first. This has been covered in a
+  * BFGS vs LBFGS
-[[geometry_optimization|previous exercise]].
+  * EPS_SCF, CUTOFF, MAX_DR, ..
-</note>
+output topics:
+  * ''Informations at step''
+  * Trajectory ''MODE1_GEO-pos-1.xyz''
+Compare the final energies (''ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.):''), and determine which mode is most stable. Does this agree with the values in table 1 of the manuscript cited ?
+===== 4. Task: ab initio molecular dynamics  =====
+<note>This task is optional, and can be done near the end if time is available. Ab initio MD will be briefly discussed in a next exercise.</note>
+Perform a short ab initio molecular dynamics simulation of the system (~1000 steps, ~0.5ps) by changing to ''RUN_TYPE MD''. After a couple of hours the job should be finished. Now analyze the OH distance in VMD. A possible outcome is :
+{{exercises:2015_pitt:acetic_acid_mode1_md.png?600 |}}
+What can you say about the hydrogen bond to the surface, relative acidity of the two oxygens ?
+Note that, in order to be statistically relevant, longer trajectories should be employed, and surface slab thickness will play an important role. Also compare to Fig. 7 of the paper referenced.
+====== Required Files ======
+(right) click on the filename to download to your local machine.
-===== Required Files =====
 <code - mode1.inp>
 &GLOBAL
@@ Line 127: / Line 138: @@
     &MGRID
        ! PW cutoff ... depends on the element (basis) too small cutoffs lead to the eggbox effect.
-       ! certain calculations (e.g. geometry optimization, vibrational frequencies, NPT and cell optimizations, need higher cutoffs)
+       ! certain calculations (e.g. geometry optimization, vibrational frequencies,
+       ! NPT and cell optimizations, need higher cutoffs)
        CUTOFF [Ry] 400
     &END
     &QS
-       METHOD GPW  ! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme).
+       ! use the GPW method (i.e. pseudopotential based calculations with the Gaussian and Plane Waves scheme).
-       EPS_DEFAULT 1.0E-10 ! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron, sets reasonable values for all other thresholds
+       METHOD GPW
-       EXTRAPOLATION ASPC ! used for MD, the method used to generate the initial guess.
+       ! default threshold for numerics ~ roughly numerical accuracy of the total energy per electron,
+       ! sets reasonable values for all other thresholds.
+       EPS_DEFAULT 1.0E-10
+       ! used for MD, the method used to generate the initial guess.
+       EXTRAPOLATION ASPC
     &END
@@ Line 191: / Line 207: @@
     &END CELL
-    ! atom coordinates can be in the &COORD section, or provided as an external file.
+    ! atom coordinates can be in the &COORD section,
+    ! or provided as an external file.
     &TOPOLOGY
       COORD_FILE_NAME mode1.xyz
@@ Line 197: / Line 214: @@
     &END
-    ! MOLOPT basis sets are fairly costly, but in the 'DZVP-MOLOPT-SR-GTH' available for all elements
+    ! MOLOPT basis sets are fairly costly,
-    ! their contracted nature makes them suitable for condensed and gas phase systems alike.
+    ! but in the 'DZVP-MOLOPT-SR-GTH' available for all elements
+    ! their contracted nature makes them suitable
+    ! for condensed and gas phase systems alike.
     &KIND H
       BASIS_SET DZVP-MOLOPT-SR-GTH
@@ Line 231: / Line 250: @@
    TEMPERATURE [K] 300
    TIMESTEP [fs] 0.5
-   STEPS 100
+   STEPS 1000
    # GLE thermostat as generated at http://epfl-cosmo.github.io/gle4md
    # GLE provides an effective NVT sampling.