mdkits

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mdkits provides a variety of tools. Installation script: bash pip install mdkits --upgrade

General Option Parameter Types

1. CELL TYPE: Specifies lattice cell parameters, e.g., 10,10,10, 10,10,10,90,90,90, etc.
2. FRAME RANGE: Specifies the frame range, e.g., 1, 1:10:2, etc.
3. --group and --surface: Select analysis objects using selection language.
4. --update_water, --distance, and --angle: Enable dynamic update of water molecule positions during trajectory analysis.

Trajectory File Processing Scripts

md is the trajectory file processing tool, which includes several processing utilities.

Density Distribution

density is used to analyze the density distribution of a specific element along the z-axis in a system. For example, to analyze the density distribution of the O element along the z-axis: bash mdkits md density [FILENAME] --group="name H" --cell [FILENAME] This will output a file named density_name_H.dat, where the first column is the z-axis coordinate and the second column is the density distribution in units of mol/L. To output the density distribution in units of $g/cm^3$, you can specify the --atomic_mass option, for example: bash mdkits md density [FILENAME] --group="name H" --cell [FILENAME] --atomic_mass=1.00784 This will output the density distribution in units of $g/cm^3$. You can specify surface atoms to normalize the density distribution to the surface, for example: bash mdkits md density [FILENAME] --group="name O" --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru" This will normalize the density distribution to the surface and analyze the density distribution of water molecules using the positions of O atoms as the reference for water molecules. For systems with $OH^-$ ions, you can use the --update_water option to update the positions of water molecules in each frame, without needing to specify an element explicitly, for example: bash mdkits md density [FILENAME] --update_water --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru" The output file will be named density_water.dat.

Hydrogen Bonds

hb is used to analyze hydrogen bonds in a system, for example, to analyze the distribution of hydrogen bonds along the z-axis: bash mdkits md hb [FILENAME] --cell 10,10,40 --surface "prop z < 10" --update_water Or to analyze hydrogen bonds of a single water molecule: bash mdkits md hb [FILENAME] --cell 10,10,40 --index 15

Angle

angle is used to analyze the abundance distribution of the angle between the bisector vector of a water molecule's OH bond and the surface normal. For example, to analyze the angle abundance distribution of water molecules within 5 Å of the surface: bash mdkits md angle [FILENAME] --cell 10,10,40 --surface "name Pt" --water_height 5

Dipole Distribution

diople is used to analyze the dipole ($\cos \phi \rho{H2 O}$) distribution in a system. For example, to analyze the $\cos \phi \rho{H2 O}$ distribution in the system: bash mdkits md diople [FILENAME] --cell 10,10,40 --surface "name Pt"

Radial Distribution Function (RDF)

rdf is used to analyze the radial distribution function between two groups. For example, to analyze the radial distribution function between O and H elements in the system: bash mdkits md rdf [FILENAME] --group "name O" "name H" --cell 10,10,40 --range 0.1 5

Mean Squared Displacement (MSD)

msd is used to analyze the mean squared displacement of certain atoms in a system. For example, to analyze the MSD of Li atoms along the z-axis: bash mdkits md msd [FILENAME] z "name Li"

Monitor

monitor is used to monitor changes in atom height, bond length, and bond angle in a system. For example, to monitor the height of the atom with index 0: bash mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 0 This will output the height from the surface as a function of each frame. To monitor the bond length between atoms 0 and 1: bash mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 0 -i 1 This will output the heights from the surface for atoms 0 and 1, and the bond length between 0 and 1 as a function of each frame. To monitor the bond angle of 1-0-2: bash mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 1 -i 0 -i 2 This will output the heights from the surface for atoms 1, 0, and 2, the bond lengths between 1-0 and 0-2, and the bond angle 1-0-2 as a function of each frame. Note that atoms at the vertex of an angle should be placed in the middle.

Position Normalization

wrap is used to normalize the atomic positions in a trajectory file. For example, to normalize the atomic positions in [FILENAME] within the unit cell and output it as wrapped.xyz. By default, it reads ABC and ALPHA_BETA_GAMMA information from the cp2k output file input_inp as lattice cell parameters: bash mdkits md wrap [FILENAME] Or specify the cp2k input file: bash mdkits md wrap [FILENAME] --cp2k_input_file setting.inp Or specify the lattice cell parameters: bash mdkits md wrap [FILENAME] --cell 10,10,10 The default [FILENAME] is *-pos-1.xyz.

Vibrational Density of States (VDOS)

vac is used to analyze the velocity autocorrelation function of a trajectory and compute the Fourier transform of the velocity autocorrelation function, which is the vibrational density of states (VDOS). For example, to analyze the VDOS of the system: bash mdkits md vac h2o-vel-1.xyz The default [FILENAME] is *-vel-1.xyz.

DFT Property Analysis Scripts

dft is the DFT property analysis tool, which includes several analysis utilities.

PDOS

pdos is used to analyze the PDOS of a system. To analyze the d-orbital DOS of [FILENAME]: bash mdkits dft pdos [FILENAME] -t d

CUBE Files

cube is used to process files in cube format, averaging them along the z-axis: bash mdkits dft cube [FILENAME] The processed data will be output to cube.out. You can also calculate the average value within a specific region: bash mdkits dft cube [FILENAME] -b 1 2 This will print the average value to the screen and also record it in the comment line of cube.out.

Modeling

build is the modeling tool, which includes several modeling utilities.

Building Bulk Models

bulk is used to build bulk models. For example, to build an fcc bulk model of Pt: bash mdkits build bulk Pt fcc To build as a conventional cell model: bash mdkits build bulk Pt fcc --cubic To build a Caesium chloride structure model: bash mdkits build bulk CsCl cesiumchloride -a 4.123 To build a fluorite structure model: bash mdkits build bulk BaF2 fluorite -a 6.196

Building Surface Models

surface is used to build common surface models. Usage: bash mdkits build surface [ELEMENT] [SURFACE_TYPE] [SIZE] For example, to build an fcc111 surface model of Pt: bash mdkits build surface Pt fcc111 2 2 3 --vacuum 15 To build a graphene surface: bash mdkits build surface C2 graphene 3 3 1 --vacuum 15

Building Surface Models from Existing Structures

cut is used to build surface models from existing structures (the structure must be in a conventional cell). For example, to build an fcc331 surface model from Pt_fcc.cif: bash mdkits build cut Pt_fcc.cif --face 3 3 1 --size 3 3 5 --vacuum 15

Adding Adsorbates to Surface Structures

adsorbate is used to add adsorbates to surface structures. For example, to add an H atom to surface.cif: bash mdkits build adsorbate surface.cif H --select "index 0" --height 1 Or to add an H atom with a coverage of 5 to Pt_fcc111_335.cif: bash mdkits build adsorbate Pt_fcc111_335.cif H --select "prop z > 16" --height 2 --cover 5

Building Solution Phase Models

solution is used to build solution phase models. When using for the first time, you should install juliaup: bash mdkits build solution --install_julia Then install Packmol: bash mdkits build solution --install_packmol After successful installation, you can use the solution functionality. For example, to build a water box with 32 water molecules: bash mdkits build solution --water_number 32 --cell 9.86,9.86,9.86 Or to build a solution containing ions: bash mdkits build solution li.xyz k.xyz --water_number 64 --tolerance 2.5 -n 25 -n 45 --cell 15,15,15 Here, the number of -n arguments must match the number of specified solvent molecule types, used to specify the number of solvents to add, respectively. Alternatively, build a solution phase model from packmol input files: bash mdkits build solution input.pm input2.pm --infile

Building Interface Models

interface is used to build interface models. For example, to build an interface model without vacuum: bash mdkits build interface --slab Pt_fcc100_555.cif --sol water_160.cif Or to build an interface with a gas phase model: bash mdkits build interface --slab Pt_fcc100_555.cif --sol water_160.cif --cap ne --vacuum 20

Building Supercell Models

supercell is used to build supercell models: bash mdkits build supercell Li3PO4.cif 2 2 2

Others

Trajectory Extraction

extract is used to extract specific frames from a trajectory file. For example, to extract frames from the 1000th to the 2000th frame from frames.xyz and output them to 1000-2000.xyz. The parameters for the -r option are consistent with Python's slicing syntax: bash mdkits extract frames.xyz -r 1000:2000 -o 1000-2000.xyz Or to extract the last frame from the default trajectory file *-pos-1.xyz generated by cp2k and output it as frames_-1.xyz (which is the default behavior of extract): bash mdkits extract Or to output a structure every 50 frames into the ./coord directory, while adjusting the output format to cp2k's @INCLUDE coord.xyz format: bash mdkits extract -cr ::50 To extract the positions of specific elements, for example, to extract the positions of O and H elements: bash mdkits extract --select "name O or name H"

Structure File Conversion

convert is used to convert structure files from one format to another. For example, to convert structure.xyz to out.cif (default filename is out). For files that do not store periodic boundary conditions, you can use the --cell option to specify PBC: bash mdkits convert -c structure.xyz --cell 10,10,10 To convert structure.cif to POSCAR: bash mdkits convert -v structure.cif To convert structure.cif to structure_xyz.xyz: bash mdkits convert -c structure.cif -o structure_xyz

Data Processing

data is used for data processing, such as: 1. --nor: Normalizes the data. 2. --gaus: Applies Gaussian filtering to the data. 3. --fold: Folds and averages stacked data. 4. --err: Calculates error bars for the data. And so on.

Plotting Tool

plot is used for plotting data. plot requires reading a YAML format configuration file for plotting. The YAML file format is as follows: ```yaml

plot mode 1

figure1: data: legend1: ./data1.dat legend2: ./data2.dat x: 0: x-axis y: 1: y-axis x_range: - 5 - 15

plot mode 2

figure2: data: y-xais: ./data.dat x: 0: x-axis y: 1: legend1 2: legend2 3: legend3 4: legend4 5: legend5 yrange: - 0.5 - 6 legendfontsize: 12

plot mode error

12dpeerror: data: legend: ./error.dat x: 0: x-axis y: 1: y-axis fold: dp legendfontsize: 12 `` The above illustrates three plotting modes supported byplot:mode 1,mode 2, andmode error.mode 1is used for comparing the same column data from multiple data files,mode 2is used for comparing different column data from the same data file, andmode error` is used for plotting mean squared error plots.

plot can process multiple YAML files simultaneously. Each YAML file can contain multiple plotting configurations. Plotting configurations for mode 1 and mode 2 can be automatically recognized, but the error mode requires explicit specification, for example: bash mdkits plot *.yaml and: bash mdkits plot *.yaml --error