Octopus 钠链脚本

Octopus Na 脚本

for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
do
rm -rf $i
mkdir $i
cd $i/
cat <<EOF > inp
CalculationMode = gs
UnitsOutput = eV_angstrom
FromScratch = yes
Radius = 8*angstrom
Spacing = 0.5*angstrom
%Coordinates
  "Na" |           0 |          0 |           0 | no
%
TDDeltaStrength = 0.05/angstrom
%TDPolarization
 1 | 0 | 0
 0 | 1 | 0
 0 | 0 | 1
%
TDPolarizationDirection = 1
TDPropagator = aetrs
TDTimeStep = 0.005/eV
TDMaxSteps = 10000
AbsorbingBoundaries = not_absorbing
EOF
        for ((j=1;j<i;j++))
            do
            p=$(echo "scale=4;$j*3.72"|bc)
            sed -i "9a \  \"Na\" |       \\$p |          0 |           0 | no" ./inp
            done
cat <<EOF >run.oct.sh
#PBS -N log
#PBS -l nodes=1:ppn=12
#PBS -l walltime=10:00:00:00
#PBS -q batch
#PBS -V
#PBS -S /bin/bash 
### Set intel environment###
source /opt/intel/composer_xe_2015/bin/compilervars.sh intel64
source /opt/intel/mkl/bin/intel64/mklvars_intel64.sh
source /opt/intel/impi/5.0.2.044/bin64/mpivars.sh
cd \$PBS_O_WORKDIR
#EXEC=/opt/software/octopus/octopus-7.1/bin/oct-propagation_spectrum
EXEC=/opt/software/octopus/octopus-7.1/bin/octopus
#EXEC=/opt/software/octopus/octopus-4.1/bin/octopus_mpi
NP=\`cat \$PBS_NODEFILE | wc -l\`
NN=\`cat \$PBS_NODEFILE | sort | uniq | tee /tmp/nodes.\$$ | wc -l\`
cat \$PBS_NODEFILE > /tmp/nodefile.\$$
mpirun -genv I_MPI_DEVICE rdssm -machinefile /tmp/nodefile.\$$ -n \$NP \$EXEC >& oct.out
rm -rf /tmp/nodefile.\$$
rm -rf /tmp/nodes.\$$
EOF
qsub run.oct.sh
cd ..
done

用来计算电荷密度的

PROGRAM Density
    real*8                    :: tmpx(1:3), &
                                 gsrho,     &
                                 frho(1:16)           ! (1:Nw)
    integer                   :: i, Nw, NP
    real                      :: a=0.529177d0
    real                      :: c=27.2d0*(0.529177d0**3)                              
!------------------------start
    open(41,file='NP_fre')
    read(41,*) NP                                                                      
    read(41,*) Nw                                                                      
    close(41)
    frho(:) = 0.d0
    open(42, file='gsrho', form='unformatted')
    open(43, file='frho', form='unformatted')
    open(40, file='dens.dat')
    do i =1, NP , 1
        read(42) tmpx(1:3),gsrho
        read(43) frho(1:Nw)
        tmpx(:) = tmpx(:)*a
        gsrho = gsrho/a**3
        frho(1:Nw) = frho(1:Nw)/c
        write (40, "(E20.8\)")  tmpx(1:3), gsrho, frho(1:Nw)
        write (40,*)
    enddo
    close(42)
    close(43)
    close(40)
end

用来处理电荷密度震荡的

#include <iostream>
#include <cstdio>
#include <cstring>
#include <cmath>
#include <fstream>
using namespace std;
/*******************************    main     **************************/
int main(void) {
        double  x, y, z, gsrho;
        long    i, j, nP, nW;
        double  *frho;
        ifstream   rhof, frequ;
        ofstream   densf;
        rhof.open("dens.dat",ios::in);
        frequ.open("NP_fre",ios::in);
        frequ  >> nP >> nW ;
        frequ.close();
        frho = new double [nW];
        densf.open("z_0.dat",ios::out);
        for (i=0; i<nP; i++){
                rhof >> x >> y >> z >> gsrho;
                for (j=0; j<nW ; j++ ) rhof >> frho[j];
                if (abs(z)<0.01) {
                        densf << x << "\t" << y << "\t" << gsrho ;
                        for (j=0; j<nW ; j++ ) densf << "\t" << frho[j];
                        densf << endl;
                }
        }
        rhof.close();
        densf.close();
        delete[] frho;
        return   0;
}