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bulk_optimization

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Lattice parameter

In this section, we explain how to optimize the lattice parameter of Si bulk diamond structure. The diamond structure is characterized by two distinct atom per unit cell with relative coordinates (0 ,0 ,0) and (1/4, 1/4, 1/4). The lattice vector is defined in the relative coordinates alat*(1/4, 1/4, 1/4). Detail description of the diamond structure can be found elsewhere. There is an elegant way to rescale atomic coordinates, lattice vector and k-points by only one parameter rescal defined in the section &OPTIONS. Our input atomic coordinates written in Si.bas look like:

 2
14   0.00000   0.00000   0.00000
14   0.25000   0.25000   0.25000

the lattice vector is defined in Si.lvs file:

 0.50000   0.00000   0.50000
 0.00000   0.50000   0.50000
 0.50000   0.50000   0.00000

and we use Oh symmetry group to generate a k-points set (file Si.kpts)

        60
 -2.74889350   -2.74889350   -2.74889350           0.00390625
 -1.96349549   -1.96349549   -3.53429174           0.01171875
 -1.17809725   -1.17809725   -4.31968975           0.01171875
 -0.39269909   -0.39269909   -5.10508823           0.01171875
  0.39269909    0.39269909   -5.89048624           0.01171875
  1.17809725    1.17809725    5.89048608           0.01171875
  1.96349549    1.96349549    5.10508807           0.01171875
 -3.53429190   -3.53429190   -1.96349581           0.01171875
 -2.74889350   -1.17809725   -2.74889350           0.01171875
 -1.96349549   -0.39269909   -3.53429174           0.02343750
 -1.17809725    0.39269909   -4.31968975           0.02343750
 -0.39269909    1.17809725   -5.10508823           0.02343750
  0.39269909    1.96349549   -5.89048624           0.02343750
 -5.10508815   -3.53429190   -0.39269932           0.02343750
 -4.31968991   -2.74889366   -1.17809733           0.02343750
 -2.74889350    0.39269909   -2.74889350           0.01171875
 -1.96349549    1.17809725   -3.53429174           0.02343750
 -1.17809725    1.96349549   -4.31968975           0.02343750
 -0.39269909    2.74889350   -5.10508823           0.02343750
 -5.89048631   -2.74889366    0.39269916           0.02343750
 -5.10508815   -1.96349565   -0.39269932           0.02343750
 -2.74889350    1.96349549   -2.74889350           0.01171875
 -1.96349549    2.74889350   -3.53429174           0.02343750
 -1.17809725    3.53429174   -4.31968975           0.02343750
  5.89048631   -1.96349565    1.17809717           0.02343750
 -5.89048631   -1.17809717    0.39269916           0.02343750
 -2.74889350    3.53429174   -2.74889350           0.01171875
  4.31968991   -1.96349565    2.74889366           0.02343750
  5.10508815   -1.17809717    1.96349565           0.02343750
  3.53429190   -1.17809717    3.53429190           0.01171875
  4.31968991   -0.39269916    2.74889366           0.02343750
  3.53429190    0.39269932    3.53429190           0.01171875
 -1.96349549   -1.96349549   -1.96349549           0.00390625
 -1.17809725   -1.17809725   -2.74889350           0.01171875
 -0.39269909   -0.39269909   -3.53429174           0.01171875
  0.39269909    0.39269909   -4.31968975           0.01171875
  1.17809725    1.17809725   -5.10508823           0.01171875
 -4.31968991   -4.31968991    0.39269916           0.01171875
 -1.96349549   -0.39269909   -1.96349549           0.01171875
 -1.17809725    0.39269909   -2.74889350           0.02343750
 -0.39269909    1.17809725   -3.53429174           0.02343750
  0.39269909    1.96349549   -4.31968975           0.02343750
  1.17809725    2.74889350   -5.10508823           0.02343750
 -1.96349549    1.17809725   -1.96349549           0.01171875
 -1.17809725    1.96349549   -2.74889350           0.02343750
 -0.39269909    2.74889350   -3.53429174           0.02343750
  0.39269909    3.53429174   -4.31968975           0.02343750
 -1.96349549    2.74889350   -1.96349549           0.01171875
 -1.17809725    3.53429174   -2.74889350           0.02343750
 -1.96349549    4.31968975   -1.96349549           0.01171875
 -1.17809725   -1.17809725   -1.17809725           0.00390625
 -0.39269909   -0.39269909   -1.96349549           0.01171875
  0.39269909    0.39269909   -2.74889350           0.01171875
  1.17809725    1.17809725   -3.53429174           0.01171875
 -1.17809725    0.39269909   -1.17809725           0.01171875
 -0.39269909    1.17809725   -1.96349549           0.02343750
  0.39269909    1.96349549   -2.74889350           0.02343750
 -1.17809725    1.96349549   -1.17809725           0.01171875
 -0.39269909   -0.39269909   -0.39269909           0.00390625
  0.39269909    0.39269909   -1.17809725           0.01171875

to make the total energy calculation of several lattice parameters automatic, we use a script:

alat=" 5.0 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 5.9 6.0"
for i in $alat;
do
 echo $i
 mkdir $i
 lattice="`echo $i`";
 sed "s/AAA/$lattice/g"  fireball.sample > fireball.in;
 ./runTG.com > a-$i.out
 grep "etot/atom" a-$i.out | cut -b50-65
 mv CHARGES $i/
 mv a-$i.out $i/
done

the script runs several tasks for defined lattice vectors, it creates a directory for each lattice parameter and it saves there CHARGES and an output file. It also dumps the energy per atom for a given lattice parameter. A file fireball.sample has following syntax:

&OPTION
basisfile = Si.bas
lvsfile = Si.lvs
kptpreference = Si.kpts
nstepf = 1
rescal = AAA
&END

Afterwards, we simply dump the total energy vs. lattice parameter into a file:

 grep ETOT */*.out | cut -b1-3,34- > etot.dat

and we plot using gnuplot

 gnuplot
 gnuplot> set title "Etot vs. alat"
 gnuplot> set xlabel "alat [Ang]"
 gnuplot> set ylabel "Etot [eV]"
 gnuplot> set format y "%8.2f"
 gnuplot> plot 'etot.dat' with linespoints

bulk_optimization.1298031180.txt.gz · Last modified: 2014/02/09 11:23 (external edit)