文件列表:

CHANGELOG.md (5242, 2016-06-16)
examples (0, 2016-06-16)
examples\params.h (2025, 2016-06-16)
povray (0, 2016-06-16)
povray\base.pov (3488, 2016-06-16)
povray\garamond.ttf (648744, 2016-06-16)
povray\render.sh (346, 2016-06-16)
povray\temperature.pov (3716, 2016-06-16)
src (0, 2016-06-16)
src\Makefile (454, 2016-06-16)
src\aux.c (1122, 2016-06-16)
src\cg.c (40211, 2016-06-16)
src\cg.h (9840, 2016-06-16)
src\draw.c (5170, 2016-06-16)
src\io.c (8098, 2016-06-16)
src\macrofunctions.c (3498, 2016-06-16)
src\mesofunctions.c (13986, 2016-06-16)
src\microfunctions.c (6476, 2016-06-16)
src\verlet.c (6186, 2016-06-16)

CG-Method ========= *CG-Method* obtains mesoscopic information like density profiles, force interactions, stress tensors, and so on, from a microscopic configuration obtained through a MD simulation. A MD input script for LAMMPS can be obtained in https://github.com/UNEDSoftMatter/Nanopore. *CG-Method* needs blas, lapack and GSL. If you get an error compiling the code, verify that the development version of these libraries are installed. All the parameters are specified in the header file `params.h`. Note that **you should compile whenever the parameters are changed**. A good practice is to do a `make clean`, followed by `make`. An example `params.h` file can be found in `~/examples/` directory. Note that **you should copy the file to ~/src/ before compiling the code**. If you obtain the following error ``` ~/CG-Method/src$ make gcc -c cg.c -o cg.c.o -lm -lblas -llapack -Wall -lgsl -lgslcblas -fopenmp -O2 -std=gnu99 In file included from cg.c:15:0: cg.h:19:20: fatal error: params.h: No existe el fichero o el directorio #include "params.h" ^ compilation terminated. Makefile:13: recipe for target 'cg.c.o' failed make: *** [cg.c.o] Error 1 ``` it is because you did not copy `params.h` into the `src` directory. Note that *CG-Method* is currently limited to 100000 snaphots (see `char basename[7];` in `cg.c`). The file `params.h` should contains the location (see below) of the positions file and the velocities file created by LAMMPS. In LAMMPS, use a custom dump output like this one ``` dump custom positions 100 id type x y z output.positions dump custom positions 100 id type vx vy vz output.velocities ``` Please, see LAMMPS documentation to understand the meaning of these commands. *CG-Method* admits arguments. ### *CG-Method* with arguments If you do not provide any argument, *CG-Method* calls to the function `void PrepareInputFiles(void)` (located in `src/io.c`). This function will create snapshots for the positions and velocities using system calls. Then, it will create a file list called `sim` which will be used to process each snapshot. Essentially, `PrepareInputFiles` will do the following: ``` ~$ if [ ! -d data/positions ]; then mkdir -p data/positions; fi ~$ cd data/positions ~/data/positions$ ln -s ../../PositionsFileStr ./output.positions ~/data/positions$ split -a 4 -d --lines=NParticles+9 output.positions ~/data/positions$ for i in $(ls |grep x); do cat $i | tail -n +10 | sort -n |awk '{print $2,$3,$4,$5}' > $i.pos ; rm $i ; done ~/data/positions$ rm output.positions ~/data/positions$ cd ../../ ~$ if [ -d data/velocities ]; then mkdir -p data/velocities; fi ~$ cd data/velocities ~/data/velocities$ ln -s ../../VelocitiesFileStr ./output.velocities ~/data/velocities$ split -a 4 -d --lines=NParticles+9 output.velocities ~/data/velocities$ for i in $(ls |grep x); do cat $i | tail -n +10 | sort -n |awk '{print $3,$4,$5}' > $i.vel ; rm $i ; done ~/data/velocities$ rm output.velocities ~/data/velocities$ cd ../../ ``` Note that both `PositionsFilesStr` and `VelocitiesFilesStr` are given in `src/params.h`. **You should specify the relative path from where the binary `CG` is located**. Once the snapshots are created, *CG-Method* creates a txt file with the basename of each snapshot: ``` ~$ for i in $(ls data/positions/ | grep .pos); do basename $i .pos; done > sim ``` The program uses the file `sim` to process each snapshot. ### *CG-Method* without arguments If you provide an argument to *CG-Method*, it will omit the creation of snapshots and it will use `argv[1]` as the file list. ## Checklist 1. *CG-Method* needs blas, lapack and GSL. If you get an error compiling the code, verify that these libraries are installed. 2. Note that the position files have 4 columns: the type of atom, and the coordinates x, y and z. The velocitiy files have 3 columns: the velocities in x, y and z. 3. The file `params.h` should be in `~/src` directory. 4. You should compile whenever you change `params.h`. 5. If called without arguments, `params.h` should contain the relative path of positions and velocities.

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