Differences

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

--- exercises:2019_conexs_newcastle:ex3 [2019/09/07 09:35] – abussy
+++ exercises:2019_conexs_newcastle:ex3 [2019/09/10 16:49] – abussy
@@ Line 2: / Line 2: @@
-In this exercise we are going to compute near-edge X-ray absorption spectra of bulk MgS and MgO, performing all-electron calculations with GAPW method, using the Transition Potential approach.
+In this exercise we are going to compute near-edge X-ray absorption spectra of bulk MgS and MgO, performing all-electron calculations with GAPW method, using the Transition Potential and $\Delta$SCF approaches. Our goal is to identify differences in the electronic structure, and as a consequence in the K-edge absorption spectrum, of the magnesium due to the different anions it is bounded to. We are also going to analyze the influence of basis set quality in the calculations.
-Before start, it is recommended to create one directory for each system and, within the system directory, create the subfolders 'optimization', 'dscf' and 'xas'.
+Before starting, it is recommended to create one directory for each system (MgO and MgS) and, within the system's directory, create the subfolders 'optimization', 'dscf' and 'xas'.
-====Part 1: optimizing geometry====
+=====Part 1: optimizing geometry=====
 The first step of the calculation is to optimize the geometry of the systems you are going to work with. It is also possible to use experimental geometries if available.
-===MgO===
+====MgO====
 To start the calculation, download or copy the input ''MgO_opt.inp'' to the optimization folder in the work directory of MgO.
@@ Line 99: / Line 99: @@
 </code>
-Since we are going to perform calculations for bulk structures, and both systems have only two atoms in their unit cells, it is not necessary to have a separate .xyz file with the atomic positions. You can directly write the coordinates in the input file in the ''&COORD'' subsection.
+Since both systems have only two atoms in their unit cells it is not necessary to have a separate .xyz file with the atomic positions. To make it simple we are going to write the coordinates in the ''&COORD'' subsection of the input file.
 Do not forget to put in your work directory the files ''GTH_POTENTIALS'' and ''GTH_BASIS_SETS'', which contain the parameters for the pseudopotentials and basis sets used in the calculations.
-To run the calculation, type in your terminal:
+To run the calculation follow the instructions on the page [[exercises:2019_conexs_newcastle:ex0|Connecting to the HPC cluster]].
-<code>
-./cp2k.sopt -i MgO_opt.inp -o MgO_opt.out &
-</code>
 After the calculation is finished, you can check the files created in your directory. First open the output file ''MgO_opt.out'' and search for the following banner:
@@ Line 117: / Line 114: @@
 </code>
 If you found it, it means that the optimization of the geometry is done, and you can find the final atomic coordinates in the file ''MgO-pos-1.xyz''. You can visualize the optimized geometry using Avogadro or VESTA programs, for example.
 cp2k prints out the coordinates for each step of the calculation (they are indicated in the file by the index i, right below the number of atoms), so in order to use the optimized geometry in the following calculations, you should use the positions corresponding to the last iteration.
+It is also important to check for warnings in your output file. In the end of the file you can find the following banner:
-===MgS===
+<code>
+-------------------------------------------------------------------------------
+The number of warnings for this run is : 0
+-------------------------------------------------------------------------------
+</code>
+which means that the calculation ran without problems. If the number is different than 0, search for the warning messages through out the output file.
+====MgS====
 Now we are going to perform the same calculation, but for the MgS system. In order to do so, let's make some changes to the input file ''MgO_opt.inp''. You can either download the input file above again, and change its name no ''MgS_opt.inp'', or type in your terminal:
@@ Line 147: / Line 155: @@
 </code>
-These are the lengths of the vectors a, b and c of the MgS unit cell. Both systems have rhombohedral unit cells, so the angles $\alpha$, $\beta$ and $\gamma$ are the same.
+In order to deal with a smaller number of atoms, we are declaring the structures of MgO and MgS using the rhombhedral unit cell, so the lengths of the lattice vectors //a//, //b// and //c//, so as the angles $\alpha$, $\beta$ and $\gamma$, are the same.
+The last modification that needs to be done is regarding the atomic types. In this case we do not have oxygen in the system anymore, so the subsection ''&KIND O'' can be renamed ''&KIND S''. The only modification that needs to be done is in the keyword ''ELEMENT'', where ''O'' has to be replaced by ''S''.
+<note important>Even though we are not changing the name of the basis set or pseupotential used, cp2k will use the parameters for the sulfur atom now, since the ''ELEMENT'' type is different. However, it is important to check in the ''GTH_BASIS_SET'' and ''GTH_POTENTIALS'' files whether the names are the same for different atoms.</note>
+Now the input is ready and it can be run in the same way as before, just remember to change the file ''cp2k.sh''.
+After the calculation is finished, open the output file ''MgS_opt.out'' and look for the same banner as before. The optimized atomic positions are written in the file ''MgS-pos-1.xyz''.
+=====Part 2: XAS calculations=====
+To compute the absorption spectra, download or copy the input file bellow to the working directory. It is a general input that needs to be edited depending on which system you are working with.
+<code - MgX_xas.inp>
+&GLOBAL
+  PROJECT_NAME MgX ! TASK: change X to O or S
+  RUN_TYPE ENERGY
+  PRINT_LEVEL LOW
+  FLUSH_SHOULD_FLUSH .TRUE.
+&END GLOBAL
+&FORCE_EVAL
+  METHOD QS
+  &DFT
+    BASIS_SET_FILE_NAME  EMSL_BASIS_SETS ! basis set file with all-electron basis set
+    POTENTIAL_FILE_NAME  POTENTIAL ! file with parameters for all-electron calculations
+    UKS
+    &MGRID
+      NGRIDS 5
+      CUTOFF 400
+      REL_CUTOFF 60
+    &END MGRID
+    &QS
+      METHOD GAPW ! using GAPW for all-electron calculations
+      EXTRAPOLATION ASPC
+      EXTRAPOLATION_ORDER 3
+      MAP_CONSISTENT
+      EPS_DEFAULT 1.0E-10
+      ! algorithm to construct the atomic radial grid for GAPW
+      QUADRATURE   GC_LOG
+      ! parameters needed for the GAPW method, look at the manual for more details
+      EPSFIT       1.E-4 ! precision to give the extension of a hard gaussian
+      EPSISO       1.0E-12
+      EPSRHO0      1.E-8
+      LMAXN0       4
+      LMAXN1       6
+      ALPHA0_H     10 ! Exponent for hard compensation charge
+    &END QS
+    &SCF
+      MAX_SCF 30
+      EPS_SCF 1.0E-5
+      SCF_GUESS ATOMIC
+      ADDED_MOS 8
+      &MIXING
+         METHOD BROYDEN_MIXING
+         ALPHA 0.5
+      &END MIXING
+      &OUTER_SCF
+        EPS_SCF 1.0E-5
+        MAX_SCF 50
+      &END OUTER_SCF
+    &END SCF
+    &XC
+      &XC_FUNCTIONAL PBE
+      &END XC_FUNCTIONAL
+      &XC_GRID
+         XC_SMOOTH_RHO NN50
+         XC_DERIV NN50_SMOOTH
+      &END XC_GRID
+      &VDW_POTENTIAL
+        POTENTIAL_TYPE PAIR_POTENTIAL
+        &PAIR_POTENTIAL
+          PARAMETER_FILE_NAME dftd3.dat
+          TYPE DFTD3
+          REFERENCE_FUNCTIONAL PBE
+          R_CUTOFF [angstrom] 16
+        &END PAIR_POTENTIAL
+      &END VDW_POTENTIAL
+    &END XC
+    &XAS
+      RESTART .FALSE.
+      METHOD TP_HH ! transition potential half core hole
+      DIPOLE_FORM VELOCITY
+      STATE_TYPE 1s ! excitation from 1s orbital (K-edge calculation)
+      ATOMS_LIST 1 2 ! calculate absorption for 1st and 2nd atoms in the &COORD subsection
+      ADDED_MOS 8
+      &SCF
+         EPS_SCF 1.0E-5
+         MAX_SCF 200
+         &MIXING
+            METHOD BROYDEN_MIXING
+            ALPHA 0.5
+         &END MIXING
+         &SMEAR
+           ELECTRONIC_TEMPERATURE [K] 300
+           METHOD FERMI_DIRAC
+           &END SMEAR
+      &END SCF
+      &LOCALIZE
+      &END LOCALIZE
+      &PRINT
+         &PROGRAM_RUN_INFO
+         &END PROGRAM_RUN_INFO
+         &RESTART
+             FILENAME ./MgX ! TASK: change X to O or S
+             &EACH
+               XAS_SCF 20
+             &END EACH
+             ADD_LAST NUMERIC
+         &END RESTART
+         &XAS_SPECTRUM
+           FILENAME ./MgX ! TASK: change X to O or S
+         &END XAS_SPECTRUM
+         &XES_SPECTRUM
+           FILENAME ./MgX ! TASK: change X to O or S
+         &END XES_SPECTRUM
+      &END PRINT
+    &END XAS
+  &END DFT
+  &SUBSYS
+    &COORD
+      X   x(X)   y(X)   z(X)
+      Mg  x(Mg)  y(Mg)  z(Mg)
+    &END COORD
+    &CELL
+      PERIODIC XYZ
+      ALPHA_BETA_GAMMA 60 60 60
+      ABC A B C
+    &END CELL
+    &KIND Mg
+      ELEMENT Mg
+      BASIS_SET Ahlrichs-pVDZ
+      POTENTIAL ALL ! all-electron calculations
+      LEBEDEV_GRID 80
+      RADIAL_GRID 200
+    &END KIND
+    &KIND X ! TASK: change X to O or S
+      ELEMENT X ! TASK: change X to O or S
+      BASIS_SET Ahlrichs-pVDZ
+      POTENTIAL ALL ! all-electron calculations
+      LEBEDEV_GRID 80
+      RADIAL_GRID 200
+    &END KIND
+  &END SUBSYS
+&END FORCE_EVAL
+</code>
+====MgS====
+To compute the absorption spectra for the bulk MgS, first rename the input file changing the ''X'' to ''S''. It can be done by typing in the terminal:
+<code>
+cp MgX_xas.inp MgS_xas.inp
+</code>
+Now change all the ''X''s in the input file to ''S''s. Move the new input file to the correct working directory.
+The next step is to add the optimized coordinates of the system, that you can find them in the ''.xyz'' file written by the program after the geometry optimization. Use the last iteration step values, and write them in the ''&COORD'' subsection. The final step is to add the correct values for the lattice vectors. You can copy it from the geometry optimization input file.
+<note important>At this time we are using cartesian coordinates to indicate the position of the atoms, so the keyword ''SCALED'' should be removed.</note>
+To run this calculation proceed as you did before.
+This calculation should take longer than the geometry optimization to run. Once it is finished, check the number of warnings and if the calculation converged. Sometimes it does not converge within the maximum number of iterations we set in the input file. If this is the case, you can increase the number using the keyword ''MAX_SCF''.
+You can check in the working directory that some files were created. The absorption energies and intensities (oscillator strength) are written in the files named ''MgS-xas_at1_st1.spectrum'' and ''MgS-xas_at2_st1.spectrum'', where the first one corresponds to the atom 1 in your input file, and the second one to atom number 2.
+The file looks like
+<code>
+  Absorption spectrum for atom      1, index of excited core MO is     2, # of lines      9
+    531.57449433      0.00000000      0.00000019     -0.00000002      0.00000000   0.00000
+    549.96927153      0.31337224      0.18092555      0.12793369      0.14730324   0.00000
+    550.01480014     -0.22208298      0.24828653      0.19285978      0.14816194   0.00000
+    550.01480014     -0.00815280      0.23149701     -0.30741602      0.14816194   0.00000
+    574.27304606     -0.84466734      0.95907128      0.71266966      2.14117868   0.00000
+    574.27304607     -0.01626535      0.86344807     -1.18125846      2.14117868   0.00000
+    574.27591527      1.19525241      0.69008026      0.48796033      2.14294438   0.00000
+    694.86428215      0.00000000     -0.00000010     -0.00000012      0.00000000   0.00000
+</code>
+and the first column corresponds to the index of the KS virtual state, the second to the energy in eV, the third, fourth and fifth to the intensities projected onto x, y and z, respectively, and in the sixth column you can find the norm of the absorption intensity, which is the quantity we are interested at.
+To convolute the spectra with gaussian functions, download the files {{exercises:2019_conexs_newcastle:lib_tools.zip}} and extract them in the same directory as the output files. Now run the script typing in the terminal:
+<code>
+./get_average_spectrum.sh
+</code>
+As an output you are going to get two files: ''spectrum.inp'' and ''spectrum.out''. The first one contains the same information as the ''Mgs-xas_at1_st1.spectrum'' file, and in the second one you will find you absorption spectrum for atom 1. Change the name of the files to ''S_K-edge.inp'' and ''S_K-edge.out'', for example. You can now plot both absorption intensities from the file ''S_K-edge.inp'' and the convoluted spectrum from the file ''S_K-edge.out''. From the first one only the second and sixth columns need to be plotted.
+In order to obtain the spectrum for atom 2, you can open the file ''get_average_spectrum.sh'', and replace ''at1'' by ''at2'' in the line ''for i in $(ls ${DIR}/*xas_at2*spectrum)''. Run the script again and you will obtain the same two files again, but now with the absorption intensities and spectrum of atom 2. Change their names to ''Mg_K-edge.inp'' and ''Mg_K-edge.out'', and plot the
+absorption spectrum.
+=====Part 3: $\Delta$SCF calculations=====
+Now, to finally finish the calculation, we need to get the an accurate energy for the first transition. In order to do that, we need to perform a $\Delta$SCF calculation. Copy the input file of the previous step to the 'dscf' directory. Change its name to ''MgX_dscf.inp'', where ''X'' can be again ''S'' or ''O''. The only thing that needs to be changed in the input file is the keyword ''METHOD'' in the ''&XAS'' section.  Use now
+<code>
+      METHOD DSCF
+</code>
+instead of ''TP_HH'', and you can run the calculation in the same way as you did before.
+After the calculation is done, look for the message
+<code>
+Ionization potential of the excited atom:                  -92.73815588900608
+</code>
+in the output file. The energy is given in Hartree, and to convert it to electron volts multiply the value by 27.211. This is the energy of the first transition, and you can use this value to rigidly shift your absorption spectrum.
+=====Part 4: Changing basis set=====
+Before performing the XAS calculations for the MgO system and compare the Mg absorption spectra, you can try to change the basis set you are using to run the absorption calculations to analyze differences it can bring to the description of the process. Try to perform the calculations using:
+  * pc-0 (smaller basis set)
+  * pob-TZVP (basis set for solid-state calculations)
+  * DZVP-all
+  * Ahlrichs-def2-SVP
+<note> In this exercise we have obtained absorption spectra using a simple basis set, in order to performed the calculations on small machines and using a limited time. Therefore, careful tests on basis set size, XC functional etc have to be carried out for production runs to get more reliable spectra. </note>
-The last modification that needs to be done is regarding the atomic types. In this case we do not have oxygen in the system anymore, so the subsection ''&KIND O'' can be replaced by ''&KIND S''. Since O and S are in the same group of the periodic table,
-====Part 2: XAS calculations====
-====Part 3: $\Delta$SCF calculations====