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[求助]
LAMMPS 的坐標(biāo)文件怎么構(gòu)建呢?不可能一個(gè)一個(gè)原子的輸入吧?
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以前用過(guò)VASP,是在MS中建立好超胞,然后用castep模塊導(dǎo)出坐標(biāo)文件。 現(xiàn)在想用LAMMPS。不知道有沒(méi)有類似的方法可以生成坐標(biāo)文件啊。 |
和畢設(shè)有關(guān)的 |

木蟲(chóng) (正式寫(xiě)手)

木蟲(chóng) (正式寫(xiě)手)
木蟲(chóng) (正式寫(xiě)手)
新蟲(chóng) (著名寫(xiě)手)
木蟲(chóng) (正式寫(xiě)手)
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If you know how to construct a LAMMPS data file for a single molecule, then you can use the "moltemplate" program to build complex periodic structures with it. http://www.moltemplate.org In addition to "moltemplate" there are several other modeling programs: http://sites.google.com/site/akohlmey/software/topotools http://sourceforge.net/projects/moleculardynami/ Here are some pictures of simulations we have run in LAMMPS built with moltemplate: http://lammps.sandia.gov/images/ ... ayer32x37_t=0ps.jpg http://lammps.sandia.gov/images/ ... _rainbow_t=80ps.jpg http://www.moltemplate.org/image ... ane+watMW_t=0ps.jpg http://www.moltemplate.org/image ... tein_t=0ps_side.jpg http://www.moltemplate.org/image ... otein_t=0ps_top.jpg If you want to use "moltemplate" you must first build a file which describes the molecule (or molecules) you want to use to build your liquid crystal. (This file can be in either lammps "DATA" format, or "LT" format.) Moltemplate can not do this automatically, but you can build the molecule by hand if it is not complicated. This is what I usually do for my simple molecules. Otherwise you can use VMD/topotools or "Molecular Dynamics Studio" to create a DATA file for a single molecule (see links above). Then you can import it into moltemplate. Currently, you must manually specify ALL of the parameters for the force-field you want to use. (There is no way to infer the force-field parameters automatically from atom-type.) This is the difficult part of setting up the simulation. However you have complete freedom to use any force-field you want. |
金蟲(chóng) (小有名氣)

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