Computational Spectroscopy

Introduction

This code is a computational spectroscopic toolkit for calculating spectroscopic observables from molecular dynamics simulations.

Thus far, the currently implemented spectroscopies are as follows:

One Dimensional Infrared Spectroscopy
- Dipole Spectral Density
- Frequency Distribution
Two Dimentional Infrared Spectroscopy
One Dimensional Raman Spectroscopy
One Dimensional Sum-Frequency Generation Spectroscopy
Frequency Frequency Time Correlation Function

This code works through the vibrational frequency mapping approach developed by Corcelli, Skinner, and others, and uses this approach to calculate spectroscopic observables from classical molecular dynamics simulations.

For a detailed description of the theory underlying this approach, please see the following publication:

[ Insert Publication Here ]

Limitations

For currently identified limitations, please see the issue tracker.

Requirements

1) GCC Fortran Compiler. I have tested the following codes with GGC 10.8 2) FFTW3 Library 3) HDF5 Library

Additionally, for installation, it uses a CMAKE build process, so you will need a version of cmake installed during this process.

Installation

This package can be installed with cmake. The general approach for such a build is the following:

mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=../bin/
make
make install

Usage

Input File Format

#noh
1710 
# ntimes, timestep, ncorr, nskip
2500 4.0d0 250 250
#wfreq
4.0
# flag_hist, nhist
.false. 100
#w1min w1max w2min w2max
3000.0 3800.0 3000.0 3800.0
#zmin, zmax, zhist
-35 35 50
#zcenter
  34.78215
# NTw
5
#Tw(1), Tw(2)...Tw(NTw)
0.0 200.0 400.0 600.0 800.0

Here, the meaning of the input arguments are described:

noh: number of ohs (typically 2x number of waters)
ntimes: number of times to calculate
timestep: timestep of configurations in calculation
ncorr: correlation length (in steps)
nskip: steps to skip between origins
wfreq: resolution of frequencies
flag_hist: Should it do histogramming? (deprecated)
nhist: number of histogram bins
w1_min, w1max : frequency range for spectrum
w3_min, w3_max : frequency range for 2d spectrum (second axis)
zmin, zmax: min and max z distance for 2d spectral density
zhist: number of z dimension histogram bins
zcenter: center of box (for sfg)
Ntw: number of waiting times
Tw(1)...: waiting times in fs (list)

Empirical Map Files

The empirical map files for the paper associated with TIP3P maps are located in the examples directory. Two map files are included.

spce_map.in is a map generated for SPC/E water.

tip3p_map.in is a map generated for TIP3P water.

Command Line Arguments

Command line arguments for the present software act effectively to override the inputs recieved from the input files for specific use cases (for instance, if you mostly want the spectra you calculate to use set parameters, but for the FFCF want longer TCFs).

The CLI argument options that are available are the following:

-h, help
    -> Displays a useful help message.
-ncorr [value]
    -> overrides ncorr value from input file
-nskip [value]
    -> overrides nskip value from input file
-in [filename]
    -> Reads filename as input file 
       rather than spectra.in
-map [filename]
    -> Reads filename as empirical map file
       rather than empirical_map.in
-tag [tagname]
    -> This CLI labels output files with tagname
       so sfg_tcf.dat would become 
       new_sfg_tcf.dat with the command -tag new_
-avfreq [freq]
    -> Used for the FFCF calculation to     
       override the average frequency in
       in scenarios where many trajectories
       are being used in parallel.
-zmin [value] (Not Yet Used)
    -> Set the minimum z position for molecules 
       to be included in the calculation. Based 
       on the Oxygen atom
-zmax [value] (Not Yet Used)
    -> Set the maximum z position for molecules 
       to be included in the calculation. Based 
       on the Oxygen atom

piskuliche / Spectroscopy

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