config:main
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configurations [2013/03/01 08:03] – daniel | config:main [2018/09/22 13:35] (current) – daniel | ||
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+ | ~~NOTOC~~ | ||
====== Configurations ====== | ====== Configurations ====== | ||
---- | ---- | ||
- | The reference | + | |
- | [[http://cms.mpi.univie.ac.at/vasp/|VASP]] output. | + | The atomic |
+ | |||
+ | There is a [[utilities: | ||
+ | [[https://www.vasp.at/|VASP]] output. | ||
==== Configuration Files ==== | ==== Configuration Files ==== | ||
- | A //potfit// configuration file is an ASCII file, consisting of a [[# | + | A //potfit// configuration file is a plain text file, consisting of a [[# |
===== Header | ===== Header | ||
- | The header consists of at least six lines starting with the hash symbol | + | The header consists of at least six lines starting with the number sign # and has the following format: |
- | < | + | < |
#N natoms useforce | #N natoms useforce | ||
#C type_0 type_1 type_2 ... | #C type_0 type_1 type_2 ... | ||
Line 25: | Line 29: | ||
#W weight | #W weight | ||
#E coh_eng | #E coh_eng | ||
- | #S stress_xx stress_yy stress_zz | + | #S stress_xx stress_yy stress_zz stress_xy |
# | # | ||
</ | </ | ||
- | The lines starting with #N, #X, #Y, #Z, #E and #F are mandatory, while the lines starting with #C, #W, #B and #S are optional. All other lines are ignored. #N must head the first line specifying the number of atoms in the configuration and an integer flag to control whether to use or to ignore force and stress information in this configuration. #F signifies the last header line. All parameters except the //type_i// are numbers and have the following meaning: | + | The lines starting with '' |
- | ;natoms | + | **natoms**\\ |
- | >number of atoms in configuration | + | < |
- | ;useforce | + | |
- | >if 0, forces from this configuration are ignored | + | |
- | ;boxi.j | + | |
- | > | + | |
- | ;weight | + | |
- | >all contributions to the error sum from this configuration will be multiplied with this weight | + | |
- | ;coh_eng | + | |
- | > | + | |
- | ; | + | |
- | > | + | |
- | Lines beginning with #B describe the [[Box|of Contributing Particles]] and are optional. | + | **useforce**\\ |
+ | < | ||
- | The #C line contains information about the chemical elements and the corresponding atom types contained in this configuration. The elements are assigned to the corresponding atom types and have to be consistent throughout the configuration file. | + | **boxi.j**\\ |
+ | < | ||
+ | |||
+ | **weight**\\ | ||
+ | < | ||
+ | |||
+ | **coh_eng**\\ | ||
+ | < | ||
+ | |||
+ | **stress_ij**\\ | ||
+ | < | ||
+ | |||
+ | Lines beginning with ''# | ||
+ | |||
+ | The '' | ||
**Please note:** | **Please note:** | ||
- | In all directions the sample should have a size of at least the potential cutoff distance. This distance is measured perpendicular to the corresponding face. If this is not the case, additional periodic copies of the sample | + | In all directions the sample should have a size of at least the potential cutoff distance. This distance is measured perpendicular to the corresponding face. If this is not the case, additional periodic copies of the configuration |
=== Deprecated header format | === Deprecated header format | ||
Line 69: | Line 78: | ||
===== Body ===== | ===== Body ===== | ||
- | Following the header, there is one line for each atom. The format of each line, described also in the header, is as follows: | + | Following the header, there is one line for each atom. The format of each line looks like this: |
< | < | ||
These items stand for: | These items stand for: | ||
- | ;type | + | |
- | >type of the atom; must be in the range [[0,|.., ntypes-1]] | + | **type**\\ |
- | ;x, y, z | + | < |
- | > | + | |
- | ;f_x, f_y, f_z | + | **x, y, z**\\ |
- | >net force components on the atom | + | < |
+ | |||
+ | **f_x, f_y, f_z**\\ | ||
+ | < | ||
Please note that the forces **cannot** be omitted, even when they are ignored. | Please note that the forces **cannot** be omitted, even when they are ignored. | ||
Line 87: | Line 99: | ||
//potfit// uses **periodic boundary conditions**. If a particle coordinate is not within the simulation box, it is mapped back into the simulation box. | //potfit// uses **periodic boundary conditions**. If a particle coordinate is not within the simulation box, it is mapped back into the simulation box. | ||
- | === Multiple Configurations | + | ===== Multiple Configurations |
Multiple configuration files can just be concatenated. //potfit// continues reading from a reference file until it reaches the end of file. Should this not coincide with the end of a single configuration, | Multiple configuration files can just be concatenated. //potfit// continues reading from a reference file until it reaches the end of file. Should this not coincide with the end of a single configuration, | ||
config/main.1362121395.txt.gz · Last modified: 2013/03/01 08:03 (external edit)