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.
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.
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.
- CG-Method needs blas, lapack and GSL. If you get an error compiling the code, verify that these libraries are installed.
- 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.
- The file
params.hshould be in~/srcdirectory. - You should compile whenever you change
params.h. - If called without arguments,
params.hshould contain the relative path of positions and velocities.