Talk:Mod:Hunt Research Group/cpmd

Car-Parrinello Molecular Dynamics (notes by Ling)

1. Classical MD vs CPMD

a. Classical MD: interactions described by fixed, paramitrized potentials.

b. CPMD: interactions calculated directly from the electron structure in every time step. The forces are obtained from the gradients of the total energy (from DFT + PW) at the positions of the nuclei and thus forming a multi-particle potential. Peculiarity: wfn is propagated following a ficticious Newtonian dynamic while performing the MD simulation. Therefore the wfn does not need to be recalculated in every simulation step and the computation effort is reduced significantly.

Steps: - generate a (equilibrated) start configuration - Wfn optimisation for the start configuration - Car-Parrinello Molecular Dynamics - analyze the trajectory

2. Useful Tutorial Links:

http://www.pci.uzh.ch/index_e.php?page=http://www.pci.uzh.ch/gruppe.hutter/e/information.html

CPMD Water Exercise: http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-intro.html

CPMD Tutorial: http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-tutor/index.html

CPMD Tips: http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-linux.html

3. How to install and compile cpmd2cube on iMac:

a. download cpmd2cube from http://www.cpmd.org/cpmd_download_it.html

b. unzip cpmd2cube.tar.gz into folder cpmd2cube

c. in the folder cpmd2cube: type: "./Configure Linux-PC-GFORTRAN > Makefile"

d. type: "make"

e. cpmd2cube.x is ready to use.

4. How to install CPMD on iMac:

a. need gfortran compiler, BLAS/LAPACK libraries.

BLAS

    The Basic Linear Algebra Subroutines (BLAS) are high quality routines for performing basic vector and
    matrix operations. Level 1 BLAS consists of vector-vector operations, Level 2 BLAS consists of matrix-vector matrixvector
    vector operations, and Level 3 BLAS have matrix-matrix operations.  The efficiency, portability, and
    the wide adoption of the BLAS have made them commonplace in the development of high quality linear
    algebra software such as LAPACK and in  other technologies requiring fast vector and matrix calcula-tions. calculations.
    tions.  All the industry standard FORTRAN BLAS entry points and the standard C BLAS entry points are
    exported from the vecLib framework (the latter are  commonly denoted the legacy C BLAS.)  For more
    information refer to <http://www.netlib.org/blas/faq.html

LAPACK

    LAPACK provides routines for solving systems of simultaneous linear equations, least-squares solutions
    of linear systems of equations, eigenvalue problems, and singular value problems.  The associated
    matrix factorizations (LU, Cholesky, QR, SVD, Schur, generalized Schur) are also provided, as are
    related computations such as reordering of the Schur factorizations and estimating condition numbers.
    Dense and banded matrices are handled, but not general sparse matrices. In all areas, similar function-ality functionality
    ality is provided for real and complex matrices, in both single and double precision.  LAPACK in vecLib
    makes full use of the optimized BLAS and fully benefits from their performance.  All the industry stan-dard standard
    dard FORTRAN LAPACK entry points are exported from the vecLib framework.  C programs may make calls to
    the FORTRAN entry points using the prototypes set out in "/System/Library/Frameworks/vecLib.frame-work/Headers/clapack.h". "/System/Library/Frameworks/vecLib.framework/Headers/clapack.h".
    work/Headers/clapack.h".

    For more information refer to <http://www.netlib.org/lapack/index.html.

    BLAS and LAPACK follow fortran calling conventions (even from C). Users must be aware that:

    ALL arguments must be passed by reference.  This includes all scalar arguments such as matrix dimension
    M and N, further note there is a difference in the memory arrangement of a two-dimensional array in
    Fortran and C.

    For more information refer to <http://www.netlib.org/clapack/readme.

b. how to install BLAS on iMac:

- download blas.tgz from http://www.netlib.org/blas/

- change 'g77' to 'gfortran' in the file make.inc

- type 'make'

- rename 'blas_LINUX.a' to 'libblas.a'

c. how to install LAPACK on iMac:

- download lapack.tgz from http://www.netlib.org/lapack/index.html

- cp make.inc.example to make.inc

- type 'make'

- get 'lapack_LINUX.a', which is the library we need.

d. how to install CPMD on iMac:

- download CPMD-3.13.2 form CPMD.org

- in /Users/ling/CPMD/CPMD-3.13.2/,

mkdir cpmd-MacOSX

cd SOURCE

./mkconfig.sh -m -SRC=$PWD -DEST=../cpmd-MacOSX MACOSX-GFORTRAN-INTEL

cd ../cpmd-MacOSX

make

The executable is called cpmd.x.

To run:

(Please refer to CPMD manual 3.13.2 P21, "compile CPMD outside the source directory.)

(...)/CPMD-3.13.2/cpmd-MacOSX/cpmd.x input.file PSEUDODIR > output.file

PSEUDODIR is the directory containing pseudopotential files (it can be set to ./ or omitted if the pseudopotentials are in the same directory as the input file).

For instance:

....../CPMD-3.13.2/cpmd-MacOSX/cpmd.x h2o.in ./ > h2o.out

Pseudopotential libraries are available from the download section on cpmd.org.