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【求助】DL_POLY的config文件如何生成?? 已有9人参与
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我想模拟聚合物在金属团簇表面的吸附,想请教大家这样的体系的config文件如何生成? 另外我把手册已经看了一遍,但是希望运行一下.有么有人根据手册的算例给写一个模拟过程,给传一个谢谢!! |
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您好,又来麻烦了.. 因为HISTORY的坐标不能直接用来统计分析(从前面的几个截图可以看出来,有的分子是断开的). 所以需要一定的转换吧,下面这段程序是在官方论坛上面有人这样写的,虽然讲的很清楚,可是我不明白他的算法是什么意思? 大家能给解释一下吗?谢谢!! here is a way to generate image flags (or unwrapped coordinates) from the HISTORY file which contains the wrapped coordinates: Assumptions: 1. All the atoms listed in the first configuration listed in the HISTORY file are assumed to be inside the box 2. The time between successive configurations in the HISTORY file is small enough for the atoms to not cross the simulation box boundaries more than once 3. Simulation box is cuboid, should be easily modifiable for other geometries Procedure: 1. Initialize the image flags ix, iy and iz in the x, y and z directions to 0, i.e. Code:ix = 0; iy = 0; iz = 0; where i = index of atoms going from 1 to nAtoms 2. Read the coordinates of all the atoms in the first configuration (config_old) and label them x_old, y_old and z_old 3. Read the coordinates of all the atoms from the next configuration (config_new) and label them x_new, y_new and z_new 4. The image flags for the configuration denoted as 'config_new' are then given as follows Code: ix = ix+int(2*(x_old-x_new)/L_x); iy = iy+int(2*(y_old-y_new)/L_y); iz = iz+int(2*(z_old-z_new)/L_z); where, int(k) = the integer part of the floating point number k L_x = Simulation box length in the x direction L_y = Simulation box length in the y direction L_z = Simulation box length in the z direction Note 1. If the box were cubic, L_x = L_y = L_z = L 2. Do not reset the image flags to zero, just keep on incrementing them 5. The unwrapped coordinated for the configuration denoted as 'config_new' are then given as Code: x_uw = x_new+L_x*ix y_uw = y_new+L_y*iy z_uw = z_new+L_z*iz 6. You can then use the unwrapped coordinates to fine the diffusion, etc. |
78楼2010-04-08 15:17:20
老虎大王
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2楼2010-01-24 16:53:03
3楼2010-01-24 20:21:22
老虎大王
木虫 (著名写手)
- 模拟EPI: 17
- 应助: 26 (小学生)
- 贵宾: 0.17
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- 专业: 金属结构材料
4楼2010-01-25 09:45:24