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--- howto:newtonx [2023/08/31 12:27] – [Brief theory recap] ahehn
+++ howto:newtonx [2023/08/31 14:09] – [A) Initial conditions and photoabsorption spectra] ahehn
@@ Line 17: / Line 17: @@
 The corresponding excited-state gradient is obtained setting up a variational Lagrangian and taking the derivative with respect to the nuclear coordinates $\mathbf{R}$ (see also https://www.cp2k.org/howto:tddft).
-By performing a TDDFPT computation, excitation energies $\Omega^M$, excited-state eigenvectors $\mathbf{X}^M$ and corresponding excited-state gradients $\nabla \Omega^M (\mathbf{R})$ are provided by CP2K. On the so-defined potential energy surfaces, the nuclei are propagated classically relying on the surface hopping code of NEWTONX,
+By performing a TDDFPT computation, excitation energies $\Omega^M (\mathbf{R}(t))$, excited-state eigenvectors $\mathbf{X}^M (\mathbf{R}(t))$ and corresponding excited-state gradients $\nabla \Omega^M (\mathbf{R}(t))$ are provided by CP2K. On the so-defined potential energy surfaces, the nuclei are propagated classically relying on the surface hopping code of NEWTONX,
 \begin{equation} \label{newtons_eom}
@@ Line 27: / Line 27: @@
 \end{equation}
-The coefficients $c^M$ of the total wave function $\Psi$ are obtained implying hopping probabilities $P_{M\rightarrow N}$ of Tully's surface hopping,
+The coefficients $c^M (t)$ of the total wave function $\Psi (\mathbf{R}(t))$ over all excited states $M$ are obtained implying hopping probabilities $P_{M\rightarrow N}$ of Tully's surface hopping,
 \begin{equation}\label{surface_hopping}
 \begin{aligned}
-%\Psi (\mathbf{R}(t)) &= \sum_{M} c^{M} (t) \Psi^M (\mathbf{R}(t)) \\
+\Psi (\mathbf{R}(t)) &= \sum_{M} c^{M} (t) \Psi^M (\mathbf{R}(t)) \\
-%i \frac{{\rm{d}} c^M (t)}{{\rm{d}} c^M (t)}{\rm{d}}t} &= \sum_N c^N (t) ( \delta_{MN} E_N (\mathbf{R}(t)) - i \sigma_{MN} (t)) \, , \\
+i \frac{{\rm{d}} c^M (t)}{{\rm{d}}t} &= \sum_N c^N (t) \left ( \delta_{MN} E_N (\mathbf{R}(t)) - i \sigma_{MN} (t) \right ) \, , \\
-P_{M \rightarrow N} &= {\rm{max}} [ 0, \frac{-2 \Delta t}{| c^M|^2} {\rm{Re}} (c^M c^{N \ast}) \sigma_{MN} ] \, .
+P_{M \rightarrow N} &= {\rm{max}} \left [ 0, \frac{-2 \Delta t}{| c^M|^2} {\rm{Re}} (c^M c^{N \ast}) \sigma_{MN} \right ] \, .
 \end{aligned}
 \end{equation}
-The therefore required non-adiabatic time derivative couplings $\sigma_{MN}$ can be obtained relying on semi-empirical models (Baeck-An; please cite Barbatti et al., //Open Research Europe// 1, 49 (2021).) or as numerical time derivative couplings (orbital time derivative (OD); please cite Ryabinkin et al., //J. Phys. Chem. Lett.// 6, 4200 (2015); Barbatti et al., //Molecules// 21, 1603 (2021).), with the corresponding molecular orbital overlap matrix $\mathbf{S}^{{\rm{\tiny{t-\Delta t,t}}}}$ being provided by CP2K,
+The therefore required non-adiabatic time derivative couplings $\sigma_{MN}$ can be obtained relying on semi-empirical models (Baeck-An; please cite Barbatti //et al.//, //Open Research Europe// 1, 49 (2021).) or as numerical time derivative couplings (orbital time derivative (OD); please cite Ryabinkin //et al.//, //J. Phys. Chem. Lett.// 6, 4200 (2015); Barbatti //et al.//, //Molecules// 21, 1603 (2021).), with the corresponding molecular orbital overlap matrix $\mathbf{S}^{{\rm{\tiny{t-\Delta t,t}}}}$ being provided by CP2K,
 \begin{equation}\label{ot_time_deriverative_couplings}
@@ Line 59: / Line 59: @@
 ===== A) Initial conditions and photoabsorption spectra =====
-The following tutorial to obtain photoabsorption spectra is based on https://vdv.dcf.mybluehost.me/nx/wp-content/uploads/2020/02/tutorial-2_2.pdf.
+The following tutorial to obtain photoabsorption spectra is based on section 2 of https://vdv.dcf.mybluehost.me/nx/wp-content/uploads/2020/02/tutorial-2_2.pdf.
-For the electronic-structure calculation with CP2K, a ''cp2k.inp'' and ''cp2k.par'' file as well as a coordinate file named ''coord.cp2k'' has to be provided in a subdirectory called JOB_AD, with ''cp2k.inp'' including all required print sections stated above. Furthermore, to generate the initial conditions, the ''initqp_input'' file requires to specify ''iprog = 10'' for CP2K and ''file_nmodes = cp2k.eig'' to refer to the corresponding output file comprising the normal modes provided by CP2K. All other keywords are to be chosen as outlined in the corresponding NEWTONX tutorial.
+For the electronic-structure calculation with CP2K, a ''cp2k.inp'' and ''cp2k.par'' file as well as a coordinate file named ''coord.cp2k'' has to be provided in a subdirectory called ''JOB_AD''. Furthermore, a vibrational analysis computation has to be performed to provide cartesian normal modes, with the input file including the corresponding ''NAMD print'' section.
-Examplary input files for computing the absorption spectrum of a water molecule are given below:
+Examplary input files for computing the absorption spectrum as well as for performing a vibrational analysis for a single water molecule with CP2K are given below:
-<code - h2o_cp2k.inp>
+<code - cp2k_excitedstates.inp>
+&GLOBAL
+  PROJECT excited_states_for_h2o
+  RUN_TYPE ENERGY
+  PREFERRED_DIAG_LIBRARY SL
+  PRINT_LEVEL medium
+&END GLOBAL
+&FORCE_EVAL
+ &PRINT                      # print statement for ground-state or excited-state forces
+  &FORCES
+  &END FORCES
+ &END PRINT
+ METHOD Quickstep
+ &PROPERTIES
+  &TDDFPT                    # TDDFPT input section to compute 10 excited states
+   &DIPOLE_MOMENTS
+    DIPOLE_FORM LENGTH
+   &END DIPOLE_MOMENTS
+   KERNEL FULL
+   NSTATES 10
+   MAX_ITER   100
+   MAX_KV 20
+   CONVERGENCE [eV] 1.0e-5
+   RKS_TRIPLETS F
+   &PRINT                     # NAMD print section to print excited-state eigenvectors
+    &NAMD_PRINT
+     PRINT_VIRTUALS T
+     PRINT_PHASES T
+    &END NAMD_PRINT
+   &END PRINT
+  &END TDDFPT
+ &END PROPERTIES
+  &DFT
+    &QS
+      METHOD GAPW
+     EPS_DEFAULT 1.0E-17
+    &END QS
+    &SCF
+      SCF_GUESS restart
+      &OT
+        PRECONDITIONER FULL_ALL
+        MINIMIZER DIIS
+      &END OT
+      &OUTER_SCF
+        MAX_SCF 900
+        EPS_SCF 1.0E-7
+      &END OUTER_SCF
+      MAX_SCF 10
+      EPS_SCF 1.0E-7
+    &END SCF
+    POTENTIAL_FILE_NAME POTENTIAL
+    BASIS_SET_FILE_NAME EMSL_BASIS_SETS
+    &MGRID
+      CUTOFF 1000
+      REL_CUTOFF 100
+      NGRIDS 5
+    &END MGRID
+    &POISSON
+      PERIODIC NONE
+      PSOLVER MT
+    &END
+    &XC
+     &XC_FUNCTIONAL PBE
+     &END XC_FUNCTIONAL
+    &END XC
+  &END DFT
+  &SUBSYS
+    &CELL
+      ABC 8.0 8.0 8.0
+      PERIODIC NONE
+    &END CELL
+                                    # Coordinates are provided externally for the interface
+     &COORD
+      @include coord.cp2k
+     &END COORD
+    &TOPOLOGY
+     &CENTER_COORDINATES T
+     &END
+     NATOMS 3                       # specifying number of atoms for NEWTONX
+     CONNECTIVITY OFF
+    &END TOPOLOGY
+    &KIND H
+      BASIS_SET 6-311Gxx
+      POTENTIAL ALL
+    &END KIND
+    &KIND O
+      BASIS_SET 6-311Gxx
+      POTENTIAL ALL
+    &END KIND
+  &END SUBSYS
+&END FORCE_EVAL
+</code>
+<code - cp2k_vib.inp>
+&GLOBAL
+  PROJECT normal_modes_for_h2o
+  RUN_TYPE VIBRATIONAL_ANALYSIS      #computing normal modes to generate initial conditions
+  PREFERRED_DIAG_LIBRARY SL
+  PRINT_LEVEL medium
+&END GLOBAL
+&FORCE_EVAL
+ &PRINT
+  &FORCES
+  &END FORCES
+ &END PRINT
+  METHOD Quickstep
+  &DFT
+    &QS
+      METHOD GAPW                   # GAPW enables comparison with all-electron molecular program codes like Turbomole
+      EPS_DEFAULT 1.0E-17
+    &END QS
+    &SCF
+      SCF_GUESS restart
+      &OT
+        PRECONDITIONER FULL_ALL
+        MINIMIZER DIIS
+      &END OT
+      &OUTER_SCF
+        MAX_SCF 900
+        EPS_SCF 1.0E-7
+      &END OUTER_SCF
+      MAX_SCF 10
+      EPS_SCF 1.0E-7
+    &END SCF
+    POTENTIAL_FILE_NAME POTENTIAL
+    BASIS_SET_FILE_NAME EMSL_BASIS_SETS
+    &MGRID
+      CUTOFF 1000
+      REL_CUTOFF 100
+      NGRIDS 5
+    &END MGRID
+    &POISSON
+      PERIODIC NONE
+      PSOLVER MT
+    &END
+    &XC
+     &XC_FUNCTIONAL PBE
+     &END XC_FUNCTIONAL
+    &END XC
+  &END DFT
+  &SUBSYS
+    &CELL
+      ABC 8.0 8.0 8.0
+      PERIODIC NONE
+    &END CELL
+                                    # coordinates must be provided as external file for NEWTONX
+     &COORD
+     @include coord.cp2k
+     &END COORD
+     &TOPOLOGY
+      &CENTER_COORDINATES T
+      &END
+      NATOMS 3
+      CONNECTIVITY OFF
+     &END TOPOLOGY
+     &KIND H
+      BASIS_SET 6-311Gxx
+      POTENTIAL ALL
+     &END KIND
+     &KIND O
+      BASIS_SET 6-311Gxx
+      POTENTIAL ALL
+     &END KIND
+  &END SUBSYS
+&END FORCE_EVAL
+&VIBRATIONAL_ANALYSIS
+ &PRINT
+  &NAMD_PRINT                      # keyword to enable printing of cartesian normal modes
+  &END NAMD_PRINT
+ &END PRINT
+ DX 0.001
+&END VIBRATIONAL_ANALYSIS
+</code>
+The input file ''cp2k.par'' includes all specifications regarding the executable and parallelization setup.
+<code - cp2k.par>
+ parallel = 16
+ exec = cp2k.psmp
+</code>
+Furthermore, a ''initqp_input'' file has to be generated for NEWTONX following the instructions given in the NEWTONX tutorial. Specifications for CP2K in the ''initqp_input'' file are the following:
+  * The file comprising the normal modes of the CP2K frequency computation -- for the above input provided as ''normal_modes_for_h2o-VIBRATIONS-1.eig''-- has to be specified as ''file_nmodes = normal_modes_for_h2o-VIBRATIONS-1.eig''.
+  * The electronic structure program has to be specified as CP2K by defining ''iprog = 10''.
+<code - initqp_input>
+&dat
+ nact = 2
+ iprog = 10
+ numat = 3
+ npoints = 500
+ file_geom = geom
+ file_nmodes = normal_modes_for_h2o-VIBRATIONS-1.eig
+ anh_f = 1
+ rescale = n
+ temp = 0
+ ics_flg = n
+ chk_e = 1
+ nis = 1
+ nfs = 11
+ kvert = 1
+ de = 100
+ prog = 14
+ iseed = 0
+ lvprt = 1
+/
+</code>
-The resulting output file of the initcond.pl script of NEWTONX states that the read-in cartesian normal modes are first transfered to mass-weighted normal modes.
+After providing the excited-state CP2K computation based on input file ''h2o_cp2k.inp'' in the subdirectory ''JOB_AD'', the normal modes ''normal_modes_for_h2o-VIBRATIONS-1.eig'' of the frequency computation and the ''initqp_input'' file for NEWTONX, the script initcond.pl of NEWTONX can be executed to generate initial conditions. The resulting initcond-output file of NEWTONX, it is first stated that the read-in cartesian normal modes are transferred to mass-weighted normal modes.
 <code cp2k>
@@ Line 122: / Line 326: @@
 </code>
-The thereon based initial conditions are summarized in the output files dubbed "final_output", comprising geometries and velocities, as examplarily given below,
+The thereon based initial conditions are summarized in external output files for each state, dubbed "final_output_XXX", comprising information on the various geometries and velocities as examplarily given below:
 <code cp2k>
@@ Line 141: / Line 345: @@
 </code>
-Moreover, the output file ''cross-section.dat'' comprises the data points of the computing photoabsorption spectrum, as shown below.
+Based on the initial conditions, the broadened photoabsorption spectrum can be computed with the nxinp script. As outlined in section 2.7 of the cited NEWTONX tutorial, the so-obtained output file ''cross-section.dat'' comprises the data points of the computed photoabsorption spectrum as visualized below:
 ===== B) Non-adiabatic dynamics using orbital determinant derivatives =====