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［求助］DPD模块运行的输入文件格式
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谁用DPD，能不能提供一个输入文件的样板， 在Windows下有图形界面，应该也可以把参数保存成一个输入文件吧， 我的在Linux下运行没有图形界面，只有手写输入文件了， 但是不知道输入文件是什么样格式的，参数是怎么表示在文件中的， 谁能不能贴一下？万分感谢！！！ [ Last edited by freshgirl on 2009-6-21 at 21:05 ] |
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zxzj05(金币+2,VIP+0):3Q！ 3-17 18:26
zxzj05(金币+2,VIP+0):3Q！ 3-17 18:26
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运行RunDPD.sh 需要提供两个输入文件basename.Dpd_con和basename.Dpd_par 但这两个文件里面怎么写参数呢？ 我先随便写个东西在里面。 然后运行 RunDPD.sh basename 生成的输出文件basename.Dpd_out中内容如下： *-----------------------------------------------------------------* Materials Studio DPD version 4.4 DISSIPATIVE PARTICLE DYNAMICS SIMULATION *-----------------------------------------------------------------* --------------------------------------------------------------- Checked out license feature: MS_mesocite --------------------------------------------------------------- comment: Box density is calculated as nan *-----------------------------------------------------------------* Simulation Parameters --------------------- parameter: sizeX, sizeY, sizeZ = 0.00 0.00 0.00 parameter: Total no. of beads = 0 parameter: No. of molecule types = 1 parameter: Density = nan parameter: Temperature (kT) = 1.0000 parameter: Dpd timestep = 0.050 parameter: Rcut for Fd and Fr forces = 1.000 parameter: Universal spring constant = 4.000000 parameter: Shearing (along x) : off parameter: Walls : off Bead Properties --------------- Bead Name Radius Bead Mass Wall Repulsion 1 W 1.0000 1.0000 50.0000 Matrix of Sigma parameters: 1 1 0.0000 Matrix of Gamma (Dissipation) parameters: 1 1 0.0000 Matrix of repulsion parameters: 1 1 25.0000 Matrix of chi-parameters (at rho = 3.0): 1 1 0.0000 *-----------------------------------------------------------------* Runtime Parameters ------------------ *-----------------------------------------------------------------* parameter: Run length 10000 steps parameter: Property sampling interval 1 steps parameter: Overwrite restart file every 10000 steps parameter: Write bead density distribution every 10000 steps parameter: Write molecule coordinate files every 10000 steps parameter: Random number seed 1234 那么这些应该是缺省时的参数，那么怎么在.Dpd_con和.Dpd_par文件中控制这些参数呢？？ |
2楼2009-03-17 15:59:50
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qasd(金币+2,VIP+0):xiexie 3-18 20:17
qasd(金币+2,VIP+0):xiexie 3-18 20:17
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没人帮我提供，我只有自己再下载个MS4.4 for Windows,然后在Windows上安装好。 运行DPD模块，所有缺省值都不改，直接点run旁边的file保存文件，结果我只找到.Dpd_par文件，就是那个Diblock文本，打开可以看到开头是 * * Input file for DPD: * 但找不到.Dpd_con文件。 后来终于在HELP里面找到了两个文件的说明。如下 DPD file formats - DPD_con The .Dpd_con file is a control file which contains a keyword indicating which type of DPD run to perform. The file has the following format: simulation start To begin a new DPD run, or: simulation restart To restart a previous DPD run. Note. A .Dpd_con file must be present on the server in order to begin a DPD calculation. If you run a DPD job from the Materials Studio interface, the .Dpd_con file is created and transferred automatically to the server at the beginning of the run. 嘿嘿，简单，直接两行解决。 .Dpd_par 的说明如下： DPD file formats - DPD_par The .Dpd_par file is the main input file for a DPD calculation. It contains all the system information, simulation parameters and output options required to control a DPD simulation. The file consists of several comment lines (beginning with *) and keyword sections defining quantities of molecules, bead names, molecule properties, interaction parameters, system parameters and simulation_control settings. The .Dpd_par file is created when you launch a DPD job, or when you click on the Save Files button on the DPD Job Files dialog. Under certain circumstances you may wish to edit the parameter file manually before launching a simulation. Any text editor can be used to do this. Example Below is a sample DPD input file for a diblock system using the Materials Studio default values. * * Input file for DPD: * quantities beads 2 molecules 1 bead name A bead name B interaction repulsion A A 25.0000 dissipation A A 4.5000 wallrepulsion A 50.0000 interaction repulsion B A 40.0000 dissipation B A 4.5000 interaction repulsion A B 40.0000 dissipation A B 4.5000 interaction repulsion B B 25.0000 dissipation B B 4.5000 wallrepulsion B 50.0000 molecule name Diblock architecture A 4 B 4 system name DPD comment Dpd calculation from MatStudio *date: 23-01-2002 11:31:36 temperature 1.0000 grid 10 10 10 1.0000 composition Diblock 1.0000 spring_constant 4.0000 density 3.0000 shear off 0.2000 walls off rngseed 2120660 simulation_control time_steps 1000 time_interval 0.0500 status_frame 1 restart_frame 1000 density_frame 20 sample_spacing 1 xyz_frame_multiple 1 running_averages_reset off The first 3 lines are comments. These are followed by a section which describes the quantities and types of beads, their interactions with other beads and with the walls and the associated dissipations. The next section indicates how the beads are linked to form molecules. The various simulation parameters (cell dimensions, temperature, shear, density, and so forth) come next. Finally, the run lengths and averaging frequencies are specified. 在linux下把前三行应该要用＃注释掉吧。 ok,可以运行了。 输出文件有 DPD.log Diblock.cor Diblock.Dpd_diff Diblock.Dpd_out Diblock.Dpd_rst Diblock.prs Diblock.rho Diblock.tmp 当然要将.Dpd_par手动修改成自己需要的情况还要研究研究。 [ Last edited by xuanxuan03 on 2009-3-18 at 14:47 ] |
3楼2009-03-18 14:42:34
4楼2010-03-08 17:09:36