SHARC Manual
User Manual:
Open the PDF directly: View PDF
Page Count: 159 [warning: Documents this large are best viewed by clicking the View PDF Link!]
- Title Page
- Contact
- Contents
- Introduction
- Installation
- Execution
- Input files
- Output files
- Interfaces
- Auxilliary Scripts
- Wigner Distribution Sampling: wigner.py
- Amber Trajectory Sampling: amber_to_initconds.py
- Sharc Trajectory Sampling: sharctraj_to_initconds.py
- Setup of Initial Calculations: setup_init.py
- Excitation Selection: excite.py
- Setup of Trajectories: setup_traj.py
- Laser field generation: laser.x
- Calculation of Absorption Spectra: spectrum.py
- File transfer: retrieve.sh
- Data Extractor: data_extractor.x
- Plotting the Extracted Data: make_gnuscript.py
- Ensemble Diagnostics Tool: diagnostics.py
- Calculation of Ensemble Populations: populations.py
- Calculation of Numbers of Hops: transition.py
- Fitting population data to kinetic models: make_fitscript.py
- Estimating Errors of Fits: bootstrap.py
- Obtaining Special Geometries: crossing.py
- Internal Coordinates Analysis: geo.py
- Essential Dynamics Analysis: trajana_essdyn.py
- Normal Mode Analysis: trajana_nma.py
- General Data Analysis: data_collector.py
- Optimizations: orca_External and setup_orca_opt.py
- Single Point Calculations: setup_single_point.py
- Format Data from QM.out Files: QMout_print.py
- Diagonalization Helper: diagonalizer.x
- Methodology
- Absorption Spectrum
- Active and inactive states
- Amdahl's Law
- Bootstrapping for Population Fits
- Damping
- Decoherence
- Essential Dynamics Analysis
- Excitation Selection
- Global fits and kinetic models
- Gradient transformation
- Internal coordinates definitions
- Kinetic energy adjustments
- Laser fields
- Laser interactions
- Normal Mode Analysis
- Optimization of Crossing Points
- Phase tracking
- Random initial velocities
- Representations
- Sampling from Wigner Distribution
- Scaling
- Seeding of the RNG
- Selection of gradients and nonadiabatic couplings
- State ordering
- Surface Hopping
- Velocity Verlet
- Wavefunction propagation
- Bibliography
- List of Tables
- List of Figures