xdatbus.fun_mtd
Functions
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Calculate the 1D free energy profile from a HILLSPOT file. |
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Calculate the 2D free energy profile from a HILLSPOT file. |
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Calculate the 2D free energy profile from a HILLSPOT file. |
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Convert HILLSPOT file to HILLS file |
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Initialize a trajectory writer instance for filename. |
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Convert a VASP XDATCAR file to an XTC trajectory file. |
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Reweight a metadynamics simulation to the unbiased ensemble using histogram reweighting. |
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project 3d free energy surface to 1d |
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Module Contents
- xdatbus.fun_mtd.fes_1d(hillspot_path, hills_count, cv_range, resolution=100)
Calculate the 1D free energy profile from a HILLSPOT file.
- hillspot_pathstr
The path of the HILLSPOT file
- hills_countint
The number of hills to be read
- cv_rangelist
The range of the collective variable
- resolutionint (optional)
The resolution of the free energy profile
- xdatbus.fun_mtd.fes_2d(hillspot_path, hills_count, cv_1_range, cv_2_range, resolution=100)
Calculate the 2D free energy profile from a HILLSPOT file.
- hillspot_pathstr
The path of the HILLSPOT file
- hills_countint
The number of hills to be read
- cv_1_rangelist
The range of the first collective variable
- cv_2_rangelist
The range of the second collective variable
- resolutionint (optional)
The resolution of the free energy profile
- xdatbus.fun_mtd.fes_3d(hillspot_path, hills_count, cv_1_range, cv_2_range, cv_3_range, resolution=100)
Calculate the 2D free energy profile from a HILLSPOT file.
- hillspot_pathstr
The path of the HILLSPOT file
- hills_countint
The number of hills to be read
- cv_1_rangelist
The range of the first collective variable
- cv_2_rangelist
The range of the second collective variable
- cv_3_rangelist
The range of the third collective variable
- resolutionint (optional)
The resolution of the free energy profile
- xdatbus.fun_mtd.hillspot2hills(hillspot_dir, hills_dir, cv, height_conversion=1, sigma_conversion=1, del_inter=False)
- Convert HILLSPOT file to HILLS file
- hillspot_dirstr
Path to HILLSPOT file
- hills_dirstr
Path to the directory where the HILLS file will be created
- cvstr or list
Name of the collective variable(s)
- height_conversionfloat(optional)
Conversion factor to convert the unit of the height from eV to kJ/mol
- sigma_conversionfloat(optional)
Conversion factor to convert the unit of the sigma based on the lattice in Angstrom
- del_interbool(optional)
Delete the intermediate files created by this function.
- xdatbus.fun_mtd.report_loader(aimd_path, load_pre_report=True, load_last_report=False, delete_intermediate_folders=True)
Initialize a trajectory writer instance for filename.
- aimd_pathstr
Output filename of the trajectory; the extension determines the format.
- load_pre_reportbool (optional)
If
True, the trajectory will contain the previous frames (before the current run)- load_last_reportbool (optional)
If
True, the trajectory will contain the last frame- delete_intermediate_foldersbool (optional)
If
True, the intermediate folders will be deleted
- xdatbus.fun_mtd.xdc2xtc(xdc_path)
Convert a VASP XDATCAR file to an XTC trajectory file.
Parameters
- xdc_pathstr
Path to the XDATCAR file
- xdatbus.fun_mtd.reweight(fes, cv, nv, kb, t, grid_min, grid_max, grid_num)
Reweight a metadynamics simulation to the unbiased ensemble using histogram reweighting.
In many cases you might decide which variable should be analyzed after having performed a metadynamics simulation. For example, you might want to calculate the free energy as a function of CVs other than those biased during the metadynamics simulation. At variance with standard MD simulations, you cannot simply calculate histograms of other variables directly from your metadynamics trajectory, because the presence of the metadynamics bias potential has altered the statistical weight of each frame. To remove the effect of this bias and thus be able to calculate properties of the system in the unbiased ensemble, you must reweight (unbias) your simulation.
- fesnp.ndarray
The free energy surface calculated from the metadynamics simulation.
- cvnp.ndarray
The collective variable used in the metadynamics simulation.
- nvnp.ndarray
The new collective variable for which the potential of mean force will be calculated.
- kbfloat
The Boltzmann constant.
- tfloat
The temperature of the simulation.
- grid_minfloat
The minimum value of the collective variable.
- grid_maxfloat
The maximum value of the collective variable.
- grid_numint
The number of bins in the histogram.
Returns
- np.ndarray
The unbiased free energy surface.
- xdatbus.fun_mtd.pmf_321(fes3d, axis1, axis2)
project 3d free energy surface to 1d
Parameters
- fes3dnp.ndarray
The 3d free energy surface.
- axis1int
The axis to be projected.
- axis2int
The axis to be projected.
Returns
- np.ndarray
The 2d free energy surface.
- xdatbus.fun_mtd.neb_2d(fes, minima_1, minima_2, n_images, n_steps, spring_constant)
- xdatbus.fun_mtd.local_minima(data, size=3)