potfiles:main
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potential_files [2013/03/05 09:13] – daniel | potfiles:main [2018/09/23 09:31] – daniel | ||
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====== Potential files ====== | ====== Potential files ====== | ||
---- | ---- | ||
- | The interactions | + | The interactions supported by //potfit// are defined in terms of tabulated functions, given by analytic parameters |
- | given by analytic parameters. Typical functions are central pair potentials, which depend on the distance | + | |
- | of two atoms and the two atom types involved. | + | Each potential file consists of a header and a body, just like the configurations. While the header format |
- | which are equidistant in the distance, which is the fundamental difference to | + | |
- | [[http://imd.itap.physik.uni-stuttgart.de/|IMD]], where those functions are tabulated with steps equidistant | + | For potentials implemented in //potfit// the number |
- | in the square | + | |
- | and the host electron density at the position | + | |
- | equidistant in the electron density. For analytic | + | |
- | have to be given. | + | |
==== Potential File Header | ==== Potential File Header | ||
- | The header is comparable | + | The header |
- | which format the current | + | |
- | The number of data columns depends on the potential | + | |
- | < | + | < |
- | ## this is just a comment line | + | #F < |
- | #F 3 n | + | #T <interaction name> |
- | #T <TYPE> | + | #C <element 0> <element 1> ... |
- | #C Mg Zn | + | #I 0 1 ... n entries |
- | #I 0 1 .... n entries | + | #G 2 3 ... n entries |
- | #G 2 3 .... n entries | + | #E |
- | ## this is another comment line | + | |
- | #E this is the very last header line | + | |
</ | </ | ||
- | Header lines start with the hash character | + | Header lines have to start with the number sign ''#'' |
- | specifier 0, 3 or 4 (to distinguish from IMD potential files, format types 1 or 2) and the number n of | + | |
- | data columns of the functions are read from the rest of the line. The very last header line must have | + | |
- | a character '' | + | |
- | '' | + | |
- | two ''#'' | + | |
- | The line starting with ''# | + | The second character can be any of the following specifiers. Lines with unknown specifiers will be treated like comments, but it is recommended that such lines start with two '' |
- | if you are dealing | + | |
- | The line ''# | + | Not all specifiers all mandatory, some of them are optional. |
- | matching run. Each digit corresponds to one function table, so there should be n digits in total. A | + | |
- | value of '' | + | |
- | keeps it fixed. This is useful for example if a third component is to be added to a binary system | + | |
- | and only the additional potentials | + | |
- | The line '' | + | == #F == |
- | or as an additional degree of freedom. Each digit corresponds to one function table, so there should be | + | |
- | n digits in total. The information is bit-coded, '' | + | |
- | '' | + | |
- | This does not apply to analytic potentials. | + | |
- | The line ''# | + | The mandatory format specifier |
- | read for potentials, it is only given in the output to facilitate | + | It requires two arguments, the format itself and the number |
- | addition there will also be a comment on how the potentials | + | Valid formats |
- | a header for an EAM-potential could look like the following: | + | * [[potfiles: |
+ | * [[potfiles:format3|Format 3]] - tabulated potentials with fixed spacing | ||
+ | * [[potfiles: | ||
+ | * [[potfiles: | ||
- | < | + | The value for the number of potential functions needs to be the correct value for the selected potential type. |
- | #F 0 12 | + | If the number of atom types in the parameter file is 2 and the potential is '' |
- | #C Al Pd Mn | + | |
- | ## Al-Al Al-Pd Al-Mn Pd-Pd Pd-Mn Mn-Mn Al Pd Mn Al Pd Mn | + | |
- | #I 0 0 0 0 0 0 0 0 0 0 0 0 | + | |
- | #E | + | |
- | </code> | + | |
- | The order of the different potential functions for a specific potential can be found on the | + | == #T == |
- | corresponding potential page. | + | |
- | ==== Format 0 ==== | + | The optional interaction type specifier ''# |
- | The potential format | + | Even though this line is optional, a mismatch in the string and the compiled //potfit// binary will lead to a runtime error. A //potfit// binary compiled for '' |
- | except for the ''# | + | |
- | Every analytic potential has to be specified as follows: | + | == #C == |
- | < | + | The optional line ''# |
- | type identifier | + | order of chemical elements in the configuration file. In output files //potfit// will write a comment on how the potentials are ordered. For the ternary system AlPdMn this looks like this: |
- | cutoff value | + | |
- | # rmin 1.0 | + | < |
- | p_1 value min max | + | #C Al Pd Mn |
- | p_2 value min max | + | ## Al-Al Al-Pd Al-Mn Pd-Pd Pd-Mn Mn-Mn Al Pd Mn Al Pd Mn |
- | ... | + | |
</ | </ | ||
- | The type keyword has to be followed by the [[analytic_functions|unique identifier]] for | + | == #I == |
- | your potential. You can also enable the smooth cutoff option by adding a '' | + | |
- | the '' | + | |
- | every potential and can thus be different for different potentials. The next line starting with # is | + | |
- | a comment which is written by //potfit//. It indicates the minimum neighbor distance for this interaction. | + | |
- | Following these lines, the values for the analytic parameters have to be specified. Each line starts | + | |
- | with an identifier for that parameter followed by the starting value, the minimum and maximum value for | + | |
- | that parameter. The order of these parameters is fixed, for the implemented analytic functions the order | + | |
- | can be found [[analytic_functions|here]]. | + | |
- | A sample format | + | The optional line ''# |
- | {{format_0.pot.txt|here}}. | + | matching run. Each argument corresponds to one function, so there need to be as much digits as there are potential functions. |
+ | and only the additional potentials are to be allowed to change. If this line is omitted all potential functions will be optimized. | ||
- | ==== Format 3 ==== | + | == #G == |
- | In a potential file in format 3, each data column has its own range and spacing. Sampling points are | + | The optional line ''# |
- | equidistant in the atomic distance r or (when using EAM-type interactions) electron density n. If we | + | or as an additional degree of freedom. Each argument corresponds to one potential function, so there should be |
- | have n data columns, the file starts with n lines of the form | + | n arguments in total. The information is bit-coded, '' |
+ | '' | ||
+ | This does not apply to analytic potentials. | ||
- | < | + | == #E == |
- | specifying the start, end, and the number | + | The last line of the header must have the ''# |
- | argument x is either | + | |
- | by n blocks with the function values, one for each atom type pair or atom type. The spacing of function | + | |
- | values is computed from the begin, | + | |
- | can be different for the different data columns. | + | |
- | If the ''# | + | ---- |
- | gradient of the function at the lower and upper boundaries. A value of 10^30 or higher triggers the | + | |
- | usage of natural splines (curvature 0 at boundaries). You should not make the gradient variable at | + | |
- | boundaries where natural splines are specified. This will lead to undesired results. | + | |
- | A sample format 3 potential | + | The order of the different |
- | {{format_3g.pot.txt|with}} or {{format_3.pot.txt|without}} the ''# | + | corresponding |
- | + | ||
- | ==== Format 4 ==== | + | |
- | + | ||
- | As with potential files in format 3 each data column has its own spacing. But with potential format | + | |
- | 4 the requirement that the sampling points | + | |
- | points are possible, but the sampling points have to be given in order. | + | |
- | + | ||
- | Preceding the data columns is a header with one line per column, containing the number of sampling | + | |
- | points in the corresponding | + | |
- | the columns has the form | + | |
- | + | ||
- | < | + | |
- | r_0 | + | |
- | r_1 | + | |
- | ... | + | |
- | r_steps f(r_steps) | + | |
- | </ | + | |
- | Please note that $r_0 < r_1 < \ldots < r_{steps}$ is required. The order of the columns is the same | ||
- | as with format 3. | ||
- | A sample format 4 potential file for a binary system (EAM potential) is available | ||
- | {{format_4g.pot.txt|here}} (with the ''# | ||
potfiles/main.txt · Last modified: 2018/09/24 17:29 by daniel