معرفی شرکت ها

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

توضیحات

Classical density functional theory code

ویژگی	مقدار
سیستم عامل	-
نام فایل	cdftpy-1.0.0
نام	cdftpy
نسخه کتابخانه	1.0.0
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Marat Valiev and Gennady Chuev
ایمیل نویسنده	marat.valiev@gmail.com
آدرس صفحه اصلی	-
آدرس اینترنتی	https://pypi.org/project/cdftpy/
مجوز	GPL

<img src="https://user-images.githubusercontent.com/1958085/149244791-869abe06-a26b-4fdd-855a-28f56c79d5f7.png" width="100"> ![Tests](https://github.com/opencdft/cdftpy/actions/workflows/tests.yaml/badge.svg) # CDFTPY: Python package for performing classical density functional theory calculations for molecular liquids  #### Marat Valiev and Gennady Chuev - [Introduction](#introduction) - [Running from command line](#running-from-command-line) - [First steps](#first-steps) - [Calculation options](#calculation-options) - [References](#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 --- ### First steps ___ 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 ___ ### Calculation options ___ 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](https://opencdft.github.io/cl.html)** and for multiple parameter calculation as **[this](https://opencdft.github.io/charging.html)** ___ ## 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

نیازمندی

مقدار	نام
>=1.7.3	scipy
>=1.21.5	numpy
>=8.0.3	click
>=1.14.7	holoviews
>=0.12.6	panel
>=2.5.0	prettytable

نحوه نصب

نصب پکیج whl cdftpy-1.0.0:

pip install cdftpy-1.0.0.whl

نصب پکیج tar.gz cdftpy-1.0.0:

pip install cdftpy-1.0.0.tar.gz