Classical density functional theory code
Project description
CDFTPY: Python package for performing classical density functional theory calculations for molecular liquids
Marat Valiev and Gennady Chuev
Quick Start:
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>
General usage:
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
References:
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
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