cdftpy 0.1.17

Classical density functional theory code

CDFTPY: Python package for performing classical density functional theory calculations for molecular liquids

Marat Valiev and Gennady Chuev

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Quick Start:

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Single ion solvation calculation with RSDFT flavor of CDFT can be performed as

cdft1d <input_file>

where example input file for Cl- ion is given by

<solute>
# site   sigma        eps(kj/mol)    charge(e)    x   y   z
Cl       4.83         0.05349244     -1.0         0.0 0.0 0.0

<simulation>
tol 1.0E-7
max_iter 200
rmax 100

<analysis>
rdf_peaks

<output>
rdf

The output will contain solvation free energy as well as peak analysis of solvent density around the ion, e.g.

....
-----------------------------
   Self-consistent cycle     
-----------------------------
iter  d_g         Free Energy 
0     4.21e+00   -8.2510119
10    9.02e-01   -195.0800613
20    1.17e-02   -297.0235445
30    2.71e-03   -297.1768922
40    2.87e-06   -296.7840683
41    8.80e-08   -296.7836460

Reached convergence, d_g < 1e-07


Total Free Energy               -296.783646
----------------------------------
Solvent density structure analysis
----------------------------------
O 1st peak position/height: 3.13 4.68  
O 2nd peak position/height: 5.93 1.38  
O 1st min position/height: 4.44 0.54  
  
H 1st peak position/height: 2.16 8.00  
H 2nd peak position/height: 4.93 1.29  
H 1st min position/height: 3.26 0.37 

The same calculation but with RISM methodology can be run as

cdft1d -m rism <input_file>

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General usage:

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cdft1d [OPTIONS] [INPUT_FILE]



Options:

  -m, --method [rism|rsdft]
    Define calculation method, with rsdft as a default

  -s, --solvent <solvent_model>
    Define solvent_model with default as s2. 
    Other avaialble models include hcl, n2, hcl_neutral.
    An additional model restricted to RISM is spce.

  -a, --adjust [charge|sigma|eps] <value>
    Adjust solute charge, sigma, or eps parameters

  -d, --dashboard [filename]      
    Generate dashboard for analysis. 
    The dashboard will be saved under the [filename] if provided, 
    otherwise it will be open in browser window

  -r --range [charge|sigma|eps] <values>
    Run calculation over the range of solute "charge","sigma",or "eps" 
    parameter values. Values could specified as comma
    delimited array ( e.g. 0,0.5,...)
    or in triplets notation [start:]stop:nsteps

  --help                     
     Show help message

  --version                  
     Display version

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References:

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G.N. Chuev, M. V. Fedotova and M. Valiev, Renormalized site density functional theory, J. Stat. Mech. (2021) 033205, https://doi.org/10.1088/1742-5468/abdeb3

G.N. Chuev, M. V. Fedotova and M. Valiev, Chemical bond effects in classical site density functional theory of inhomogeneous molecular liquids. J. Chem Phys. 2020 Jan 31;152(4):041101, https://doi.org/10.1063/1.5139619

M. Valiev and G.N. Chuev, Site density models of inhomogeneous classical molecular liquids, J. Stat. Mech. (2018) 093201, https://doi.org/10.1088/1742-5468/aad6bf