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--- exercises:2017_ethz_mmm:c2h2_pdga [2017/05/05 09:09] – dpasserone
+++ exercises:2017_ethz_mmm:c2h2_pdga [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 14: / Line 14: @@
 ===== 1. Task: Familiarize yourself  =====
 The coordinates of the optimized configuration are provided to you as ''S_M.opt.xyz'' (S stands for "Substrate", M for "Molecule", opt for "optimized"). Visualize the geometry with VMD and familiarize yourself with the system.
-<!--
 ===== 2. Task: Bond induced density differences =====
 Compute the density difference induced by the adsorption bonding.
-For this you will have to run three separate energy calculations:
+For this you will have to run three separate energy calculations, using the *.ene.inp files.
-  - combined system bound in the first mode (file ''mode1.xyz'')
+  - combined system  (file ''S_M.opt.xyz'')
-  - lone acetic acid molecule (just remove slab's coordinates from ''mode1.xyz'')
+  - lone acetylene (file ''M.S_M.xyz'')
-  - lone TiO$_2$ slab (just remove the acid's coordinates from ''mode1.xyz'')
+  - lone slab (file ''S.S_M.xyz'')
 In order to output the electronic densities as cube files, your input file has to contain the following snipped:
@@ Line 33: / Line 33: @@
 <note tip>
-The calculations involving the large TiO$_2$ slab should be run on 16 nodes with ''bsub  -n 16''.
+The calculations involving the slab should be run on at least 16 cores with ''qsub run -v INP=prefix''. Check the  ''run'' file for the number of nodes.
 </note>
-To process the cube files we are going to use the [[tools:cubecruncher | cubecruncher]] tool. It is part of CP2K, but not installed on euler.
+To process the cube files we are going to use the [[tools:cubecruncher | cubecruncher]] tool. It is part of CP2K and is in your exercise directory.
-Therefore, you'll have to download and compile it yourself:
 <code>
-you@eulerX ~$ svn checkout http://svn.code.sf.net/p/cp2k/code/trunk/cp2k/tools/cubecruncher
+you@eulerX ~$ ./cubecruncher.x -i S_M-ELECTRON_DENSITY-1_0.cube -subtract S-ELECTRON_DENSITY-1_0.cube -o tmp.cube
-you@eulerX ~$ cd cubecruncher
+you@eulerX ~$ ./cubecruncher.x -i tmp.cube -subtract M-ELECTRON_DENSITY-1_0.cube -o Delta_ads.cube
-you@eulerX ~$ make
-you@eulerX ~$ ./cubecruncher.x -help
-</code>
-Now subtract the densities of the lone systems from the bonded system:
-<code>
-you@eulerX ~$ ./cubecruncher.x -i mode1-ELECTRON_DENSITY-1_0.cube -subtract mode1_acid-ELECTRON_DENSITY-1_0.cube -o tmp.cube
-you@eulerX ~$ ./cubecruncher.x -i tmp.cube -subtract mode1_slab-ELECTRON_DENSITY-1_0.cube -o mode1_delta.cube
 </code>
@@ Line 54: / Line 45: @@
 The generated cube file is not aligned with the simulation cell. Center the cube file with the cubecruncher.x tool:
 <code>
-you@eulerX ~$ ./cubecruncher.x -center geo -i mode1_delta.cube -o mode1_delta-centered.cube
+you@eulerX ~$ ./cubecruncher.x -center geo -i Delta_ads.cube -o Delta_ads-centered.cube
 </code>
-You can visualize the resulting file ''mode1_delta-centered.cube'' with VMD. This has been covered in a [[mo_ethene| previous exercise]].
+You can visualize the resulting file ''delta_ads-centered.cube'' with VMD. This has been covered in a [[reaction_energy_2017| previous exercise]].
 What you get should look similar to this:
@@ Line 63: / Line 54: @@
 ===== 3. Task: Bonding energies  =====
-Compute the binding energy for both binding modes:
+Compute the binding energy:
 \[ E_\text{binding}=\sum E_\text{products} - \sum E_\text{reactants} \]
-For this you will need the energy values of four systems:
+For this you will need the energy values of three systems:
-  - lone acetic acid molecule (run geometry optimization, use energy of last step)
+  - lone acetylene 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)
+  - lone  slab  (you can use the already geometry optimized coordinates from ''S.opt.xyz'' at the end of the exercise)
-  - combined system bound in the first mode (can be reused from previous task)
+  - combined system adsorbed (can be reused from previous task)
-  - combined system bound in the second mode (file ''mode2.xyz'')
 <note important>
-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
+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.
-[[geometry_optimization|previous exercise]].
 </note>
 ===== Questions =====
-  * Sketch briefly the two binding modes.
+  * Sketch briefly the geometry of the molecule **when adsorbed** and **in the gas phase**.
-  * Report the system energy for the two binding modes, lone slab, and lone acid molecule.
+  * Report the system energy for the bonded system, lone slab, and lone molecule.
-  * Which binding mode is more stable?
+  * Can you estimate the contribution due to the geometry relaxation?
   * Briefly report the bond induced density difference on the system.
@@ Line 89: / Line 78: @@
 <note warning>
-The provided [[wp>XYZ_file_format|XYZ-files]] can not be included into CP2K's input directly. You have to convert them to ''.coord'' files by removing the first line, which states the number of atoms, and the following empty comment line.
+The provided files are all in the directory ''/home/psd/Exercise_9''. Change the name of the xyz file accordingly in the input files.
 </note>
-<code - mode1.inp>
+<code - S_M.inp>
-&GLOBAL
-  ! change name for each different run performed
-  PROJECT mode1
-  RUN_TYPE ENERGY
-&END GLOBAL
 &FORCE_EVAL
   METHOD Quickstep
   &DFT
+  &PRINT
-    &PRINT
+    &E_DENSITY_CUBE
-       &E_DENSITY_CUBE        !  section to print the electronic density of the system (Task 2)
+    &END E_DENSITY_CUBE
-       &END E_DENSITY_CUBE
+  &END
+    BASIS_SET_FILE_NAME ./BR
+    POTENTIAL_FILE_NAME ./GR
+    &QS
+      EPS_DEFAULT 1.0E-10
+      METHOD GPW
+      EXTRAPOLATION ASPC
+      EXTRAPOLATION_ORDER 3
+    &END QS
+    &MGRID
+      CUTOFF 400
+      NGRIDS 5
     &END
+    &SCF
-    BASIS_SET_FILE_NAME BASIS_SETS
+      MAX_SCF 20
-    ! This keyword refers the input to an external basis file, which has to be in the same directory as this input file
+      SCF_GUESS RESTART
-    POTENTIAL_FILE_NAME POTENTIALS
+      EPS_SCF 1.0E-5
-    ! This keyword refers the input to an external potential file, which has to be in the same directory as this input file
-    &SCF                                      ! Ensures convergence of SCF and simulations stability. This section should not be changed
-      MAX_SCF 50
       &OT
-        PRECONDITIONER FULL_SINGLE_INVERSE
+        PRECONDITIONER  FULL_SINGLE_INVERSE
-      &END OT
+        MINIMIZER  CG
+      &END
       &OUTER_SCF
-        MAX_SCF 10
+        MAX_SCF 50
+        EPS_SCF 1.0E-5
+      &END
+      &PRINT
+        &RESTART
+          &EACH
+            GEO_OPT 2
+          &END
+          ADD_LAST NUMERIC
+          FILENAME RESTART
+        &END
+        &RESTART_HISTORY OFF
+        &END
       &END
     &END SCF
     &XC
       &XC_FUNCTIONAL PBE
       &END XC_FUNCTIONAL
     &END XC
   &END DFT
   &SUBSYS
     &CELL
-      ABC 10.2270 11.3460 20.000
+A [angstrom] 14.08557 0 0
+B [angstrom] 0 12.1985 0
+C [angstrom] 0.000000      0.000000    15.0
     &END CELL
-    &COORD
+    &TOPOLOGY
+     COORD_FILE_NAME ./S_M.opt.xyz
-! Here you either manually insert the coordinates of the system (as usual) OR use the @INCLUDE statement like this:
+     COORDINATE xyz
-@INCLUDE 'mode1.coord'        ! The mode1.coord file must be present in the same directory as the input.
+    &END
-                              ! The file should be similar to an *.xyz file but without the total number of atoms at the beginning
+    &KIND Pd
+      BASIS_SET DZVP-MOLOPT-SR-GTH-q18
-   &END COORD
+      POTENTIAL GTH-PBE-q18
-    &KIND H                                 ! All basis sets and potentials are looked up in the external files specified above.
+    &END KIND
-      BASIS_SET DZVP-MOLOPT-GTH             ! search in the external basis file (specified above) the one named DZVP-MOLOPT-GTH for H.
+    &KIND Ga
-      POTENTIAL GTH-PBE-q1                  ! search in the external potential file (specified above) the one named GTH-PBE-q1 for H.
+      BASIS_SET DZVP-MOLOPT-SR-GTH-q13
+      POTENTIAL GTH-PBE-q13
     &END KIND
     &KIND C
-      BASIS_SET DZVP-MOLOPT-GTH
+      BASIS_SET TZV2P-MOLOPT-GTH
       POTENTIAL GTH-PBE-q4
     &END KIND
-    &KIND O
+    &KIND H
-      BASIS_SET DZVP-MOLOPT-GTH
+      BASIS_SET TZV2P-MOLOPT-GTH
-      POTENTIAL GTH-PBE-q6
+      POTENTIAL GTH-PBE-q1
-    &END KIND
-    &KIND Ti
-      BASIS_SET DZVP-MOLOPT-SR-GTH
-      POTENTIAL GTH-PBE-q12
     &END KIND
   &END SUBSYS
 &END FORCE_EVAL
+&GLOBAL
+  PRINT_LEVEL LOW
+  PROJECT S_M
+  RUN_TYPE ENERGY
+&END GLOBAL
 </code>
+<!--
 <code - POTENTIALS>
 ################################################################################