cdftpy 1.0.0

Classical density functional theory code

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

Marat Valiev and Gennady Chuev

• Introduction
• Running from command line
  • First steps
  • Calculation options
• References

Introduction

Classical Density Functional Theory (CDFT) is a rigrous theoretical framework that builds statistical mechanics model of molecular liquid system in terms of its average density. The cdftpy python package provides implementation of two CDFT methods - the Renormalized Site Density Functional Theory (RSDFT) and Reference Interaction Site Model (RISM). At this stage of development, the code allows to investigate the problem of ion solvation providing free energy of solvation and solvent density profiles around the ion.

Running from command line

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First steps

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Running CDFT calculaton from the command line requires an input file. Simple example of what it may look like for Cl- solvation calculation is given below:

<solute>
#name   sigma(A)        eps(kj/mol)    charge(e)  
  Cl       4.83         0.05349244     -1.0      

Once the input file has been prepared, CDFT calculation can be run using cdft1d executable script as shown below

cdft1d <input_file>

In this simple case, RSDFT calculation will be performed using s2 water model. 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 

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

where example input file for Cl- ion is given by

<solute>
#name   sigma(A)        eps(kj/mol)    charge(e)  
  Cl       4.83         0.05349244     -1.0      
<simulation>
  solvent s2
  method rsdft
  tol 1.0E-7
  max_iter 200
  output_rate 10
  rcoul 1.25
  rmax 100

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     1.13e+00   -258.8752239
10    4.14e+01   -4839.5648029
20    9.29e-02   -292.7447959
30    1.53e-03   -301.9588939
40    7.17e-05   -301.5734464
50    2.65e-07   -301.5653213
53    9.82e-08   -301.5653695

Reached convergence, d_g < 1e-07


Total Free Energy               -301.565369 kj/mol
----------------------------------
Solvent density structure analysis
----------------------------------
O 1st peak position/height: 3.12 4.785  
O 2nd peak position/height: 5.91 1.384  
O 1st min position/height: 4.43 0.543  
  
H 1st peak position/height: 2.15 8.291  
H 2nd peak position/height: 4.92 1.301  
H 1st min position/height: 3.24 0.359  

The same calculation but with RISM methodology can be run as

cdft1d -m rism INPUT_FILE

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Calculation options

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There are number options that may be used with cdft1d. The complete list of those can be displayed by running

cdft1d --help

The choice of the calculation method, as mentioned earlier, is affected through -m option, which will default to RSDFT calculation.

The choice of solvent is controlled by -s option, with default being the s2 model. For example, the use of hcl solvent can accomplished by

cdft1d -s hcl INPUT_FILE

To examine calculation results in greater detail, we can use -d option. Used by itself

cdft1d -d INPUT_FILE

it will open interactive dashboard in the dafault browser, where one can interactively examine solvent density profiles, solute-solvent potential of mean force, and solvent electrostatic potentials. Alternatively, the dashboard can be saved to html file (e.g. analysis.html)

cdft1d -d analysis.html INPUT_FILE

which can be opened at a later point. The content of dashboard will depend on the type of the calculation. For example, for single ion solvation calculation it will look like this and for multiple parameter calculation as this

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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