CP2K Open Source Molecular Dynamics

User Tools

Site Tools

Trace:
howto:newtonx

Differences

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

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
howto:newtonx [2023/08/31 12:28] – [Brief theory recap] ahehnhowto:newtonx [2024/01/03 13:09] (current) – oschuett
Line 1: Line 1:
-====== How to run NAMD computations using the CP2K-NEWTONX interface ====== +This page has been moved to: https://manual.cp2k.org/trunk/methods/sampling/newton-x.html
- +
-This is a short tutorial on how to use the CP2K-NEWTONX interface to a) generate initial conditions to compute photoabsorption spectra and b) to run non-adiabatic dynamics simulations using orbital derivative couplings. A more comprehensive tutorial on all NEWTONX features, including a documentation of the required specifications for the CP2K interface, can be found on the NEWTONX homepage, https://newtonx.org/documentation-tutorials/. +
- +
-===== Brief theory recap ===== +
- +
-The interface enables to use electronic-structure data from CP2K and combine it with the surface hopping module of NEWTONX. Excitation energies $\Omega^M$ and excited-state eigenvectors $\mathbf{X}^M$ to describe the excited state $M$ are provided by CP2K, relying on the Tamm-Dancoff eigenvalue problem, +
- +
-\begin{equation} \label{tda_equation} +
-\begin{aligned} +
-      \mathbf{A} \mathbf{X}^M &= \Omega^M \mathbf{S} \mathbf{X}^M \, , \\ +
-      \sum_{\kappa k} [ F_{\mu \kappa \sigma} \delta_{ik} - F_{ik \sigma} S_{\mu \kappa} ] X^M_{\kappa k \sigma} + \sum_{\lambda} K_{\mu \lambda \sigma} [\mathbf{D}^{{\rm{\tiny{X}}}M}] C_{\lambda i \sigma} &=  \sum_{\kappa} \Omega^M S_{\mu \kappa} X^M_{\kappa i \sigma} \, ,  +
-    \end{aligned} +
-\end{equation} +
- +
-with $\mathbf{S}$ representing the conventional atomic-orbital overlap matrix, $\mathbf{F}$ the Kohn-Sham matrix, $\mathbf{K}$ the kernel comprising -- depending on the chosen functional -- Coulomb, exchange and exchange-correlation contributions, and $\mathbf{C}$ the molecular orbital coefficients. $\mu, \nu, \dots$ denote atomic orbitals, $i, j, \dots$ occupied molecular orbitals.  +
-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, +
- +
-\begin{equation} \label{newtons_eom} +
-\begin{aligned} +
-\mathbf{R}(t + \Delta t) &= \mathbf{R} (t) + \mathbf{v} (t) \Delta t + \frac{1}{2} \mathbf{a}(t) \Delta t^2  \, ,\\ +
-\mathbf{v} (t + \Delta t) &= \mathbf{v} (t) + \frac{1}{2} (\mathbf{a} (t) + \mathbf{a} (t+ \Delta t) ) \Delta t  \, , \\ +
-\mathbf{a} (t) &= - \frac{1}{m} \nabla \Omega^M (\mathbf{R}(t)) \, . +
-\end{aligned} +
-\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, +
- +
-\begin{equation}\label{surface_hopping} +
-\begin{aligned} +
-\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)) \, , \\ +
-P_{M \rightarrow N} &= {\rm{max}} [ 0, \frac{-2 \Delta t}{| c^M|^2} {\rm{Re}} (c^M c^{N \ast}) \sigma_{MN} ] \, . +
-\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, +
- +
-\begin{equation}\label{ot_time_deriverative_couplings} +
-\begin{aligned} +
-\sigma_{MN}^{{\rm{\tiny{OD}}}} &= \sum_{ia} X_{ia}^{M} \frac{\partial }{\partial t} X_{ia}^N + \sum_{iab} X_{ia}^M X_{ib}^N  S_{ab}^{{\rm{\tiny{t-\Delta t,t}}}} - \sum_{ija} P_{ij} X_{ia}^M X_{ja}^N +
- S_{ji}^{{\rm{\tiny{t-\Delta t,t}}}} \\ +
-S_{pq}^{{\rm{\tiny{t - \Delta t , t}}}} &= \frac{\langle \phi_i (\mathbf{R}(t- \Delta t )) | \phi_j (\mathbf{R} (t)) \rangle}{\Delta t} \, . +
-\end{aligned} +
-\end{equation} +
-$a,b, \dots$ denote virtual molecular orbitals. +
- +
-===== General input setup ===== +
- +
-The input sections for TDDFPT energy and gradient computations are described in the CP2K tutorial https://www.cp2k.org/howto:tddft. +
-To furthermore provide the required CP2K output, subsequently read in by NEWTONX, the following print statements have to be added to the CP2K input files: +
-  * ''FORCE_EVAL/PRINT/FORCES'': prints the excited-state forces +
-  * ''TDDFPT/PRINT/NAMD_PRINT'' with keyword option ''PRINT_PHASES'': prints the excited-state eigenvectors in MO format as well as the corresponding phases. +
-  * ''VIBRATIONAL_ANALYSIS/PRINT/NAMD_PRINT'': prints normal modes to generate initial conditions +
-It should furthermore be noted that cartesian coordinates have to be provided in terms of the external file "coord.cp2k" and that the number of atoms has to be specified in the CP2K input file in the SUBSYS section. +
- +
-===== 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. +
-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. +
- +
-Examplary input files for computing the absorption spectrum of a water molecule are given below: +
-<code - h2o_cp2k.inp> +
- +
-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. +
- +
-<code cp2k> +
-Cartesian normal modes (1/sqrt(amu)) +
- +
-        0.00        0.00        0.00        0.00        0.00        0.00     1523.92     3851.12 +
- +
-      0.0000     -0.0492      0.0001     -0.1268      0.5632     -0.0083      0.0000     -0.0000 +
-     -0.0886      0.0000     -0.0000     -0.0169      0.0047      0.5777      0.0000     -0.0000 +
-     -0.0000     -0.0000     -0.0000      0.5630      0.1269      0.0155     -0.0715      0.0487 +
-      0.0001      0.3905     -0.0004     -0.1267      0.5632     -0.0082     -0.4184     -0.5910 +
-      0.7043      0.0008      0.7071     -0.0162      0.0040      0.5768      0.0000      0.0000 +
-     -0.0001     -0.5885      0.0007      0.5630      0.1270      0.0155      0.5678     -0.3867 +
-      0.0000      0.3905     -0.0004     -0.1267      0.5632     -0.0083      0.4184      0.5910 +
-      0.7043     -0.0009     -0.7071     -0.0170      0.0051      0.5768      0.0000      0.0000 +
-     -0.0000      0.5885     -0.0007      0.5630      0.1269      0.0154      0.5678     -0.3867 +
- +
-     3986.44 +
- +
-      0.0712 +
-     -0.0000 +
-      0.0000 +
-     -0.5650 +
-      0.0000 +
-     -0.4222 +
-     -0.5650 +
-      0.0000 +
-      0.4222 +
- +
-Mass weighted normal modes +
-Frequencies will be multiplied by ANH_F =    1.00000 +
- +
-        0.00        0.00        0.00        0.00        0.00        0.00     1523.92     3851.12 +
- +
-      0.0001     -0.1967      0.0006     -0.5069      2.2526     -0.0330      0.0000     -0.0000 +
-     -0.3543      0.0000     -0.0000     -0.0677      0.0186      2.3104      0.0000     -0.0000 +
-     -0.0001     -0.0000     -0.0002      2.2517      0.5077      0.0619     -0.2861      0.1949 +
-      0.0001      0.3920     -0.0004     -0.1272      0.5654     -0.0083     -0.4200     -0.5933 +
-      0.7071      0.0008      0.7099     -0.0162      0.0040      0.5791      0.0000      0.0000 +
-     -0.0001     -0.5908      0.0007      0.5652      0.1275      0.0155      0.5700     -0.3882 +
-      0.0000      0.3921     -0.0004     -0.1272      0.5654     -0.0083      0.4200      0.5933 +
-      0.7071     -0.0009     -0.7099     -0.0171      0.0051      0.5790      0.0000      0.0000 +
-     -0.0000      0.5908     -0.0007      0.5652      0.1274      0.0155      0.5700     -0.3882 +
- +
-     3986.44 +
- +
-      0.2847 +
-     -0.0000 +
-      0.0000 +
-     -0.5672 +
-      0.0000 +
-     -0.4238 +
-     -0.5672 +
-      0.0000 +
-      0.4238 +
-</code> +
- +
-The thereon based initial conditions are summarized in the output files dubbed "final_output", comprising geometries and velocities, as examplarily given below, +
- +
-<code cp2k> +
- Initial condition =     1 +
- Geometry in COLUMBUS and NX input format: +
- o     8.0    5.00630777    5.00000001    4.46399957   15.99491464 +
- h     1.0    6.37684065    5.00000128    5.50815661    1.00782504 +
- h     1.0    3.52303474    5.00000149    5.58297278    1.00782504 +
- Velocity in NX input format: +
-   -0.000089112    0.000000000   -0.000020915 +
-    0.000417197    0.000000002    0.000694479 +
-    0.000997296    0.000000013   -0.000362483 +
- Epot of initial state (eV):    0.0865  Epot of final state (eV):     19.0799 +
- Vertical excitation (eV):     18.9935  Is Ev in the required range? YES +
- Ekin of initial state (eV):    0.0479  Etot of initial state (eV):    0.1343 +
- Oscillator strength:           0.1221 +
- State:                         10 +
-</code> +
- +
-Moreover, the output file ''cross-section.dat'' comprises the data points of the computing photoabsorption spectrum, as shown below. +
-  +
- +
-===== B) Non-adiabatic dynamics using orbital determinant derivatives ===== +
-                                                                             +
howto/newtonx.1693484882.txt.gz · Last modified: 2023/08/31 12:28 by ahehn