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.