Embedded Files
This is a tutorial for plotting spin density
The input file of the electron spin density is below and need to save as "spin.d3"
ECH3
50
SCALE
1
POT3
50
5
SCALE
1
END
Submission Script in HPC RCC FSU
The submission script is below and need to save as "Prop_Spin.sh":
#!/bin/bash
#SBATCH -J BG_Model_5A_6x6_Tri_Vac_5B_Reach_dBN
#SBATCH -o BG_Model_5A_6x6_Tri_Vac_5B_Reach_dBN-%J.o
#SBATCH -N 1
#SBATCH -n 24
#SBATCH -p mendoza_q
#SBATCH -t 1000:00:00
export JOB=BG_Model_5A_6x6_Tri_Vac_5B_Rich_dBN
export DIR=$SLURM_SUBMIT_DIR
#export scratch=/gpfs/research/mendozagroup/scratch/crystal/${USER}
#export PATH=/gpfs/research/mendozagroup/crystal/2014/v1_0_4d/bin/Linux-ifort_XE_emt64/v1.0.4:$PATH
export PATH=/gpfs/research/mendozagroup/crystal/2017/v1_0_2/ifort14/bin/Linux-ifort14_XE_emt64/v1.0.2:$PATH
export scratch=/gpfs/research/mendozagroup/scratch/crystal/${USER}/crys17
echo "submit directory: "
echo $SLURM_SUBMIT_DIR
module purge
module load intel-openmpi
rm -fr $scratch/$JOB
mkdir -p $scratch/$JOB
# the following line need be modified according to where your input is located
#cp $DIR/${JOB}.d12 $scratch/$JOB/INPUT
cp $DIR/${JOB}.d3 $scratch/$JOB/INPUT
cp $DIR/${JOB}.f9 $scratch/$JOB/fort.9
cd $scratch/$JOB
touch hostfile
rm hostfile
for i in `scontrol show hostnames $SLURM_JOB_NODELIST`
do
echo "$i slots=24" >> hostfile
done
# in the following, -np parameters should be equal to those specified above.
#mpirun -np 16 -machinefile hostfile Pcrystal >& $DIR/${JOB}.out
# mpirun -np 16 -machinefile hostfile Pproperties >& $DIR/${JOB}.BAND.pout
srun -n 24 Pproperties >& $DIR/${JOB}.ECH3.out
#cp fort.9 ${DIR}/${JOB}.f9
#cp fort.9 ${DIR}/
cp POT_CUBE.DAT ${DIR}/${JOB}_POT_CUBE.cube
cp DENS_CUBE.DAT ${DIR}/${JOB}_DENS_CUBE.cube
cp SPIN_CUBE.DAT ${DIR}/${JOB}_SPIN_CUBE.cube
#cp fort.25 ${DIR}/${JOB}.f25
#cp BAND.DAT ${DIR}/${JOB}.BAND.dat
#cp BAND.DAT ${DIR}/${JOB}.ECH3.cube
#cp DOSS.DAT ${DIR}/${JOB}.DOSS.dat
# uncomment the next 5 lines if you want to remove the scratch directory
if [ $? -eq 0 ]
then
cd ${DIR}
rm -rf $scratch/${JOB}
How to visualize the electron spin densities
The script will generate ${JOB}_DENS_CUBE.cube file after successful execution. It can be opened in VESTA and it will show the electron spin densities.
This is a tutorial for plotting charge density
The input file of the electron charge density is below and need to save as "chdensity.d3"
https://tutorials.crystalsolutions.eu/tutorial.html?td=properties&tf=properties_tut
ECHG #keyword
0 #order of the derivatives: if not 0, the charge density gradients are computed
65 #number of point along the B-A segment (see CRYSTAL User's Manual)
COORDINA #cartesian coordinates of points A.B,C defining the window in a plane
-4. -4. 0.0 #cartesian coordinates of point A (Angstrom)
4. -4. 0.0 #cartesian coordinates of point B (Angstrom)
4. 4. 0.0 #cartesian coordinates of point C (Angstrom)
MARGINS #margins are added to the window, in the order AB,CD,AD,BC
1.5 1.5 1.5 1.5 #width of the margins: in the order AB,CD,AD,BC
END
This is a tutorial for plotting electrostatic potential
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