Output File Formats in MD++: Difference between revisions
(New page: <P ALIGN="CENTER"> <FONT SIZE="+3" color="darkred"><STRONG> Output File Formats in MD++</STRONG></font></P> <DIV> <P ALIGN="CENTER"><STRONG> </STRONG></P> </DIV> This tutorial describes...) |
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==Configuration (.cn) File== |
==Configuration (.cn) File== |
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The saved cn files have the following format. |
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The first line is the number of atoms (NP). |
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Then there are NP lines of data, each corresponding to an atom (more explanation below). |
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Then there is a 3x3 matrix (H) whose column vectors are the three repeat vector of the supercell. |
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The next line contains the number of species and the name of the species. (The species name can be set by variable "element0", "element1", etc in the input file. If they are not set, the default value is "Mo". This is just to provide some information for the user --- it is not used by the code.) |
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The last line contains two numbers: zeta and zetav. These are variables used in the Nose-Hoover thermostat. We save them to enhance reproducibility of results when restarting an MD simulation from a saved file. These values are zero if the file is saved after quasi-static simulations. |
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When writeall = 0 and writevelocity = 0, the saved cn files have the following format. |
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sx_i, sy_i, sz_i |
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they are the scaled coordinates of atom i. |
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When writeall = 0 and writevelocity = 1, the saved cn files have the following format. |
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==Property (.out) File== |
==Property (.out) File== |
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Revision as of 04:20, 17 August 2009
Output File Formats in MD++
This tutorial describes the formats of MD++ output files. The most frequently used file in MD++ is the .cn file describing atomic positions (and other attributes). Also used a lot is the property (.out) file produced by Molecular Dynamics simulations. MD++ can also read and write VASP (POSCAR) and LAMMPS files.
Configuration (.cn) File
The saved cn files have the following format.
The first line is the number of atoms (NP). Then there are NP lines of data, each corresponding to an atom (more explanation below). Then there is a 3x3 matrix (H) whose column vectors are the three repeat vector of the supercell. The next line contains the number of species and the name of the species. (The species name can be set by variable "element0", "element1", etc in the input file. If they are not set, the default value is "Mo". This is just to provide some information for the user --- it is not used by the code.) The last line contains two numbers: zeta and zetav. These are variables used in the Nose-Hoover thermostat. We save them to enhance reproducibility of results when restarting an MD simulation from a saved file. These values are zero if the file is saved after quasi-static simulations.
When writeall = 0 and writevelocity = 0, the saved cn files have the following format.
sx_i, sy_i, sz_i
they are the scaled coordinates of atom i.
When writeall = 0 and writevelocity = 1, the saved cn files have the following format.