8.1.2. 3D Streamplot¶
8.1.2. Multicore 3D streamplot Python library for MDAnalysis —
MDAnalysis.visualization.streamlines_3D
¶
Authors: Tyler Reddy and Matthieu Chavent Year: 2014 Copyright: GNU Public License v3 Citation: [Chavent2014]
MDAnalysis.visualization.streamlines_3D.
generate_streamlines_3d
(coordinate_file_path, trajectory_file_path, grid_spacing, MDA_selection, start_frame, end_frame, xmin, xmax, ymin, ymax, zmin, zmax, maximum_delta_magnitude=2.0, num_cores='maximum')[source]¶Produce the x, y and z components of a 3D streamplot data set.
Parameters:
- **coordinate_file_path** – str Absolute path to the coordinate file
- **trajectory_file_path** – str Absolute path to the trajectory file. It will normally be desirable to filter the trajectory with a tool such as GROMACS g_filter (see [Chavent2014])
- **grid_spacing** – float The spacing between grid lines (angstroms)
- **MDA_selection** – str MDAnalysis selection string
- **start_frame** – int First frame number to parse
- **end_frame** – int Last frame number to parse
- **xmin** – float Minimum coordinate boundary for x-axis (angstroms)
- **xmax** – float Maximum coordinate boundary for x-axis (angstroms)
- **ymin** – float Minimum coordinate boundary for y-axis (angstroms)
- **ymax** – float Maximum coordinate boundary for y-axis (angstroms)
- **zmin** – float Minimum coordinate boundary for z-axis (angstroms)
- **zmax** – float Maximum coordinate boundary for z-axis (angstroms)
- **maximum_delta_magnitude** – float Absolute value of the largest displacement (in dx,dy, or dz) tolerated for the centroid of a group of particles (angstroms; default: 2.0). Values above this displacement will not count in the streamplot ( treated as excessively large displacements crossing the periodic boundary)
- **num_cores** – int, optional The number of cores to use. (Default ‘maximum’ uses all available cores)
Returns:
- array of floats
An array object containing the displacements in the x direction
- dy_array : array of floats
An array object containing the displacements in the y direction
- dz_array : array of floats
An array object containing the displacements in the z direction
Return type: dx_array
Examples: import np as np import MDAnalysis import MDAnalysis.visualization.streamlines_3D import mayavi, mayavi.mlab #assign coordinate system limits and grid spacing: x_lower,x_upper = -8.73, 1225.96 y_lower,y_upper = -12.58, 1224.34 z_lower,z_upper = -300, 300 grid_spacing_value = 20 x1, y1, z1 = MDAnalysis.visualization.streamlines_3D.generate_streamlines_3d('testing.gro', 'testing_filtered.xtc',xmin=x_lower,xmax=x_upper,ymin=y_lower,ymax=y_upper,zmin=z_lower,zmax=z_upper, grid_spacing = grid_spacing_value, MDA_selection = 'name PO4',start_frame=2,end_frame=3,num_cores='maximum') x,y,z = np.mgrid[x_lower:x_upper:x1.shape[0]*1j,y_lower:y_upper:y1.shape[1]*1j,z_lower:z_upper:z1.shape[ 2]*1j] #plot with mayavi: fig = mayavi.mlab.figure(bgcolor=(1.0,1.0,1.0),size=(800,800),fgcolor=(0, 0, 0)) for z_value in np.arange(z_lower,z_upper,grid_spacing_value): st = mayavi.mlab.flow(x,y,z,x1,y1,z1,line_width=1,seedtype='plane',integration_direction='both') st.streamline_type = 'tube' st.tube_filter.radius = 2 st.seed.widget.origin = np.array([ x_lower, y_upper, z_value]) st.seed.widget.point1 = np.array([ x_upper, y_upper, z_value]) st.seed.widget.point2 = np.array([ x_lower, y_lower, z_value]) st.seed.widget.resolution = int(x1.shape[0]) st.seed.widget.enabled = False mayavi.mlab.axes(extent = [0,1200,0,1200,-300,300]) fig.scene.z_plus_view() mayavi.mlab.savefig('test_streamplot_3D.png') #more compelling examples can be produced for vesicles and other spherical systems![]()