The ABINIT Users Mailing List ( CLOSED )

[yshtogun@cas.usf.edu]

 Dear ABINIT users!
  I have two questions, one about optimization of the unit cell and the 
second about speed up optimization for super cell.
  First, I running optimization of my unit cell, there is my input file:

# bond legth a = 1.428 angstrom
# the potential files - 6c.pspnc LDA (Troullier - Martins)

#Optimization of the lattice parameters
optcell 0
ionmov  3
ntime  100
#dilatmx 1.05 (using default value)
ecutsm  0.5

#Definition of the unit cell
acell 33.0665018318 33.0665018318 4.2840000000 angstrom   # The size of unit 
cell in angstrom

#Definition of the atom types
ntypat 1          # There is only one type of atom
znucl 6           # The keyword "znucl" refers to the atomic number of the
                  # possible type(s) of atom. The pseudopotential(s)
                  # mentioned in the "files" file must correspond
                  # to the type(s) of atom. Here, the only type is Silicon.
#Definition of the atoms
natom 28          # There are 28 atoms
typat 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
                  # They all are of type 1, that is, Carbon.

xangst            # This keyword indicate that the location of the atoms
                  # will follow, one triplet of number for each atom
                  # Triplet giving the cartesian coordinates of all atoms, in 
Angstrom
19.2887927159  16.5332509159  0.0000000000
19.0159083159  17.7288357159  0.7140000000
……………………………………………….
18.2513031159  14.3788816159  2.8560000000
19.0159083159  15.3376661159  2.1420000000
19.2887927159  16.5332509159  2.8560000000

#Definition of the planewave basis set
ecut  32.0         # Maximal kinetic energy cut-off, in Hartree

#Exchange-correlation functional
ixc 1             # LDA Teter Pade parametrization
iscf 2

#Definition of the k-point grid
kptopt 1          # Option for the automatic generation of k points, taking
                  # into account the symmetry
ngkpt 1 1 4       # This is a 1x1x4 grid based on the primitive vectors
nshiftk 1
shiftk  0 0 0.5


#Definition of the SCF procedure
nstep 100         # Maximal number of SCF cycles
toldfe 1.0d-6     # Will stop when, twice in a row, the difference
                    # between two consecutive evaluations of total energy
                    # differ by less than toldfe (in Hartree)
diemac 12.0       # Although this is not mandatory, it is worth to
   ***********************************************************

    after several steps I got next warning, but my calculation still running: 

BROYDEN STEP NUMBER   9  -------------------------------------------------

 findmin : WARNING -
  The 2nd degree equation has no positive root (choice=4).

 findmin : COMMENT -
  There is a problem, since the new total energy is larger
  than the old (choice=4).
  I take a point between the old and new, close to the old .
   line minimization, algorithm   4
                        lambda      etotal            dedv        d2edv2
   old point         :  0.0000E+00 -1.6877357422E+02 -5.9156E-08  4.9407-324
   new point         :  1.0000E+00 -1.6877357389E+02  1.3913E-07  8.6856-317
   predicted point   :  2.5000E-01 -1.6877357421E+02  0.0000E+00  0.0000E+00
 
     What does it mean, maybe I need specified some additional parameter?

    The second question: How can I speed up my calculation for optimization 
of super cell? I want to optimize three unit cells of (7,0) Carbon nanotubes 
– 84 atoms per 3 unit cells. There is my input files without coordinate of 
atoms: 

#Optimization of the lattice parameters
optcell 0
ionmov  3
ntime  200
ecutsm  0.5

#Definition of the unit cell
acell 33.0665018318 33.0665018318 12.8520000000 angstrom    # The size of 
unit cell in angstrom

#Definition of the atom types
ntypat 1          # There is only one type of atom
znucl 6           # The keyword "znucl" refers to the atomic number of the

#Definition of the atoms
natom 84          # There are 84 atoms
typat 84*1
                  # They all are of type 1, that is, Carbon.

xangst            # This keyword indicate that the location of the atoms
                  # will follow, one triplet of number for each atom
                  # Triplet giving the cartesian coordinates of all atoms, in 
Angstrom
19.2887927159  16.5332509159  0.0000000000
19.0159083159  17.7288357159  0.7140000000
……………………………………………….
17.1464166159  19.2197055159  10.7100000000
15.9200852159  19.2197055159  11.4240000000

#Definition of the planewave basis set
ecut  32.0         # Maximal kinetic energy cut-off, in Hartree

#Exchange-correlation functional
ixc 1             # LDA Teter Pade parametrization
iscf 2

#Check whether the cell is primitive, if the symetry finder is used, a 
non-zero velue of chkprim will make the code stop
                  #if a non-primitive cell is used. If chkprim = 0, a warning 
is issued, but the run doesnt stop.
chkprim 0

#Definition of the k-point grid
kptopt 1          # Option for the automatic generation of k points, taking
                  # into account the symmetry
ngkpt 1 1 4       # This is a 1x1x4 grid based on the primitive vectors
nshiftk 1
shiftk  0 0 0.5

#Definition of the SCF procedure
nstep 200         # Maximal number of SCF cycles
toldfe 1.0d-6     # Will stop when, twice in a row, the difference
                  # between two consecutive evaluations of total energy
                  # differ by less than toldfe (in Hartree)
diemac 12.0       # Although this is not mandatory, it is worth to

     In this calculation I have just 2 – k points, so I used two processor 
but it is not enough memory for such calculation, that’s why I used 4 or 6 
processors it is running (also give me message that I waist time because  2 – 
k points),  I using university computer core with next specification: 
I.R.C.E. is a grid system designed to facilitate many forms of computational 
research. 
I.R.C.E. is currently made up of two main parts, the High-Throughput Grid 
which is supported by Condor and over 130 Intel Pentium 4-based computer lab 
machines, the High-Performance Cluster Grid which currently contains 36 
compute nodes and 5 file server nodes in the following configurations: 
•       12 compute nodes, each with 8.0GB of DDR-ECC RAM, two AMD Opteron 248 
Processors at 2.2 Ghz, and inter-connected with a high-bandwidth, low-latency 
Myrinet switching fabric.
 
   Does somebody have suggestion how to speed up such calculation?

   I appreciate all comments and suggestion!
    
   Thank you in advance!
    
   Yaroslav!