gromacs.util.densityProfile

About

Fortran code for Density Profile program with Gromacs 4.x and 5.x

Requirement

• installed xdr library supported by Frans van Hoesel.
  • See GibHub Page to get detail.
  • For convenience, you can get the v1.2 'libxdrf_v1.2.tgz', in xdr folder. Then 'make' and you can see 'libxdrf.a'.
• installed xdr file conversion supported by Gromacs
  • See Gromacs Website if you want to get a recent version.
  • For convenience, you can get the v1.1.4 library, 'xdrfile-1.1.4.tar.gz', in xdr folder. Then install, for example:

$ ./configure --prefix=/home/(username)/xdr1.1.4
$ make install

After installing, add the following line to .bashrc file in your home directory.

export LD_LIBRARY_PATH=/home/(username)/xdr1.1.4/lib

• Compiled with xtc normal or xtc wrapper version written by James Wes Barnett
  • In details, see Blog of James Wes Barnett broken currently. Instaed visit GitHub Page.
  • For convenience, the files are uploaded in xtc folder.
  • As for xtc normal version, How to compile is like:

$ ifort -c xtc-interface.f90 -lxdrfile -L/home/hjung/xdr1.1.4/lib

To check, the command './a.out' with 'traj.xtc' file will print out Time, Step, Precision, No.Atoms for test. Then compile wrapper version of read_xtc_file after compiling:

ifort xtc-interface.o readxtc.f90 -lxdrfile -L/home/hjung/xdr1.1.4/lib

As for xtc wrapper version, compile like:

$ ifort -c xtc-interface-wrap.f90 -L/home/hjung/xdr1.1.4/lib -lxdrfile

Test mode:

$ ifort xtc-interface-wrap.o readxtc-wrap.f90 -lxdrfile -L/home/hjung/xdr1.1.4/lib

To test, do './a.out' and/or compare with previous result './a.out'.

• Change of original code of wrapper version I did is that I modify module name xtc to xtc_mod in source files because intel fortran compiler prints errors that 'defined type, xtc is the same as module xtc.'. I think it comes from dulicate module names of two versions. *In my case, I choose wrapper version for xtc conversion. Either is fine.

Install

It needs DensProf.f90, xtc-interface-wrap.o, and xtc_mod.mod (the last two file comes from compiling xtc code) to compile. 'xtc_mod.mod' file should be located in the same folder with DensProf.f90.

$ ifort -O2 DensProf.f90 xtc-interface-wrap.o -L/home/hjung/xdr1.1.4/lib -lxdrfile -o D-Prof.x 

Usage for help

$ ./D-Prof.x