Module: symfunc
| Description | Usage |
|---|---|
| tools for calculating symmetry functions that measure the degree of order in the coordination sphere around atoms | |
| Authors: Gareth Tribello |   |
Details
The actions in this module can be used to calculate symmetry functions that measure the degree of order in the coordination sphere around the atoms and molecules that make up your system. The methods within this class are typically used to investigate nucleation of solids from the liquid phase.
Notice that each symmetry function you calculate can be allocated to a particular position in space; namely, the position of the central atom whose coordination sphere has been used in the calculation of the symmetry function. This fact has been used in the papers cited below to:
- calculate average values for the symmetry function in particular parts of the simulation cell by using this module together with the volumes module.
- calculate average values for the symmetry function in the largest cluster by using this module together with the clusters module.
- calculate phase field models that provide a smooth representation of the average value of the CV as a function of position by using this module together with the gridtools module.
- calculate the gradient of the phase field representation of the CV as a function of position by using the module together with the gridtools module.
- calculate the position of the interface between the solid and liquid parts of the simulation cell by using this module together with the together with the gridtools and contour modules.
Notice that from version 2.10 onwards many of the symmetry functions in this class (particularly the Steinhardt Parameters) have been implemented as shortcuts. The implementations that PLUMED provides from these methods are thus very flexible and allow you to calculate the many subtle variationts of this technique for determining the degree of order in the system that have been used in the literature.
You will get a colossal speedup by specifying the D_MAX keyword in all switching functions that act on distances. D_MAX tells PLUMED that the switching function is strictly zero if the distance is greater than this value. As a result PLUMED knows that it does not need to calculate these zero terms in what are essentially sums with a very large number of terms. In fact when D_MAX is set PLUMED uses linked lists when calculating these coordination numbers, which is what gives you such a dramatic increase in performance.
Actions
The following actions are part of this module
| Name | Description | Tags |
|---|---|---|
| ATOMIC_SMAC | Calculate the atomic smac CV | MCOLVAR |
| COORDINATIONNUMBER | Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of | MCOLVAR |
| COORDINATION_MOMENTS | Calculate moments of the distribution of distances in the first coordination sphere | MCOLVAR |
| COORDINATION_SHELL_AVERAGE | Calculate an arbitrary function of all the bond vectors in the first coordination sphere of an atom and take an average | MCOLVAR |
| COORDINATION_SHELL_FUNCTION | Calculate an arbitrary function of all the bond vectors in the first coordination sphere of an atom | MCOLVAR |
| CYLINDRICAL_HARMONIC | Calculate the cylindrical harmonic function | MCOLVAR |
| FCCUBIC | Measure how similar the environment around atoms is to that found in a FCC structure. | MCOLVAR |
| FCCUBIC_FUNC | Measure how similar the environment around atoms is to that found in a FCC structure. | MCOLVAR |
| GSYMFUNC_THREEBODY | Calculate functions of the coordinates of the coordinates of all pairs of bonds in the first coordination sphere of an atom | COLVAR |
| HEXACTIC_PARAMETER | Calculate the hexatic order parameter | MCOLVAR |
| LOCAL_AVERAGE | Calculate averages over spherical regions centered on atoms | MCOLVARF |
| LOCAL_CRYSTALINITY | Calculate the local crystalinity symmetry function | MCOLVAR |
| LOCAL_Q1 | Calculate the local degree of order around an atoms by taking the average dot product between the q_1 vector on the central atom and the q_3 vector on the atoms in the first coordination sphere. | MCOLVARF |
| LOCAL_Q3 | Calculate the local degree of order around an atoms by taking the average dot product between the q_3 vector on the central atom and the q_3 vector on the atoms in the first coordination sphere. | MCOLVARF |
| LOCAL_Q4 | Calculate the local degree of order around an atoms by taking the average dot product between the q_4 vector on the central atom and the q_4 vector on the atoms in the first coordination sphere. | MCOLVARF |
| LOCAL_Q6 | Calculate the local degree of order around an atoms by taking the average dot product between the q_6 vector on the central atom and the q_6 vector on the atoms in the first coordination sphere. | MCOLVARF |
| Q1 | Calculate 1st order Steinhardt parameters | MCOLVAR |
| Q3 | Calculate 3rd order Steinhardt parameters. | MCOLVAR |
| Q4 | Calculate fourth order Steinhardt parameters. | MCOLVAR |
| Q6 | Calculate sixth order Steinhardt parameters. | MCOLVAR |
| SIMPLECUBIC | Calculate whether or not the coordination spheres of atoms are arranged as they would be in a simple cubic structure. | MCOLVAR |
| SMAC | Calculate the SMAC order parameter for a set of molecules | MCOLVAR |
| SPHERICAL_HARMONIC | Calculate the values of all the spherical harmonic funtions for a particular value of l. | MCOLVAR |
| TETRAHEDRAL | Calculate the degree to which the environment about ions has a tetrahedral order. | MCOLVAR |
| TETRA_ANGULAR | Calculate the angular tetra CV | MCOLVAR |
| TETRA_RADIAL | Calculate the radial tetra CV | MCOLVAR |
References
More information about this module is available in the following articles:
- B. Cheng, G. A. Tribello, M. Ceriotti, Solid-liquid interfacial free energy out of equilibrium. Physical Review B. 92 (2015)
- B. Cheng, G. A. Tribello, M. Ceriotti, The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical Physics. 147 (2017)
- B. Cheng, M. Ceriotti, G. A. Tribello, Classical nucleation theory predicts the shape of the nucleus in homogeneous solidification. The Journal of Chemical Physics. 152 (2020)
- E. Baldi, M. Ceriotti, G. A. Tribello, Extracting the interfacial free energy and anisotropy from a smooth fluctuating dividing surface. Journal of Physics: Condensed Matter. 29, 445001 (2017)
- G. A. Tribello, F. Giberti, G. C. Sosso, M. Salvalaglio, M. Parrinello, Analyzing and Driving Cluster Formation in Atomistic Simulations. Journal of Chemical Theory and Computation. 13, 1317–1327 (2017)
- F. Giberti, G. A. Tribello, M. Parrinello, Transient Polymorphism in NaCl. Journal of Chemical Theory and Computation. 9, 2526–2530 (2013)