Adsorption Site Study on Pt(111)
********************************

ReaxFF Catalysis AMS Driver Adsorption Binding sites PES Exploration
Surface

This tutorial shows how to use the PES exploration tools of the AMS
driver to examine oxygen adsorption sites on a Pt(111) surface using
the ReaxFF engine.


Structure Setup
===============

We will be using the following structure as basis for the subsequent
calculations.

   O     5.54003937   1.60484089   8.92740946
   Pt    8.31521714   4.80239136   7.78926430
   Pt    5.54298786   0.00160612   7.79128800
   Pt    6.92910250   2.40199874   7.79027615
   Pt   11.08707571   4.80244586   7.78854885
   Pt    8.31484643   0.00166062   7.79057254
   Pt    9.70096096   2.40178486   7.79068672
   Pt    5.54335868   4.80260524   7.78885374
   Pt    2.77112940   0.00182001   7.79087743
   Pt    4.15724404   2.40221263   7.78986559
   Pt    9.70154331   5.60130339   5.52585419
   Pt    6.92931403   0.80051815   5.52787789
   Pt    8.31542867   3.20091077   5.52686604
   Pt    4.15782639   5.60173116   5.52503306
   Pt    1.38559711   0.80094593   5.52705675
   Pt    2.77171175   3.20133854   5.52604491
   Pt    6.92968485   5.60151727   5.52544363
   Pt    4.15745557   0.80073204   5.52746732
   Pt    5.54357021   3.20112466   5.52645547
   Pt    6.92989639   4.00003668   3.26303536
   Pt    8.31601103   6.40042930   3.26202352
   Pt    5.54378174   1.59964406   3.26404721
   Pt    9.70175484   3.99982280   3.26344593
   Pt   11.08786948   6.40021541   3.26243408
   Pt    8.31564020   1.59943018   3.26445778
   Pt    4.15803792   4.00025057   3.26262480
   Pt    5.54415256   6.40064318   3.26161295
   Pt    2.77192328   1.59985795   3.26363664
   Pt    1.38639089   2.39871548   1.00094199
   Pt    5.54436409   4.79916260   0.99921469
   Pt    6.93024583   7.19969029   1.00043291
   Pt    4.15824945   2.39876998   1.00022653
   Pt    8.31622256   4.79894871   0.99962525
   Pt    9.70210429   7.19947641   1.00084348
   Pt    6.93010792   2.39855609   1.00063710
   Pt    2.77250564   4.79937648   0.99880412
   Pt    4.15838737   7.19990418   1.00002234
   VEC1  8.31557575   0.00000000   0.00000000
   VEC2  4.15778787   7.20149984   0.00000000

Hint:

  To build a custom crystal surface slab model, check out the Tutorial
  on Building Crystals and Slabs

   **1.** Open AMSinput
   **2.** Copy & paste the coordinates above into AMSinput.
   **3.** Switch to [image: ReaxFFPanel][image]
   **4.** Select **Task → PES Exploration**
   **5.** Select **Force-Field → OPt.ff**
   **6.** Select the Oxygen atom & press the **Pre-optimize** button, and choose to only optimize the selection
   **7.** Change to the regions panel **Model → Regions**
   **8.** Switch to a different perspective with **ctrl + 1**
   **9.** Select all Pt-atoms, then click on [image: AddButton][image] to create a new region
   **10.** Rename the new region to 'surface'
 [image]

   **11.** Change to **Model → Geometry Constraints and PES Scan**
   **12.** With all Pt-atoms still selected, click on [image: AddButton][image] **surface (fixed position)**


PES Exploration
===============

With the Pt(111) model in place, we can proceed to set up the rest of
the calculation parameters.

   **1.** Go to the **Main** panel and set **Task** to **PES Exploration**
   **2.** Go to the **Model → PES Exploration** panel
   **3.** Select **Job → Process Search**
   **4.** Enter **Num expeditions:** *50*
   **5.** Enter **Num explorers:** *8*
 [image]

   **6.** Click on **Structure comparison** [image: MoreBtn][image]
   **7.** Enter **Neighbor cutoff:** *5.0 Å*
   **8.** Click on **PES Exploration main panel** [image: MoreBtn][image]
 [image]

   **9.** Click on **Binding sites calculation** [image: MoreBtn][image]
   **10.** Select **Reference Region: → surface**
   **11.** Enter **Distance Difference:** *1.0 Å*
   **12.** Tick **Calculate**
   **13.** Click on **PES Exploration main panel** [image: MoreBtn][image]
 [image]

As we are only interested in finding binding sites, i.e. local minima
accessible by surface hopping reactions, we have to limit the barrier
heights allowed during the process search

   **14.** Click on **Saddle Search** [image: MoreBtn][image]
   **15.** Enter **Max Energy:** *4.0 eV*
 [image]


Computation & Results
=====================

We are now ready to start the calculation

   **16.** Click **File → Run**, save as e.g. *Pt111O_adsorptionSites.ams*

The calculation should take a couple of minutes, during which we can
monitor the discovery of new minima and transition states either from
[image: SCMMenu][image] **→ logfile**

[image]

The newly discovered states can also be inspected in [image:
SCMMenu][image] **→ Movie**

[image]

where we can see the nicely resolved energy differences between the
two different hollow sites on an fcc (111) surface. Note, that in the
case of oxygen adsorption, bridge sites act as transition states for
the hopping between different hollow sites, while top adsorption sites
are too high in energy to be reached in this process search run.

After the calculation is concluded, we return to [image:
SCMMenu][image] **→ Input** and click **Yes** in the prompt to
**create a new job and load binding sites**.

This displays the identified adsorption sites, which can be
individually selected from **Details → PES Exploration ... → PES
Exploration Binding Sites**

[image]
