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adding templates for running and getting V-scans; adjusting the E-fie…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
| #!/bin/bash | ||
| module load gcc/9.3.0 openmpi/4.0.3 cp2k/7.1-omp | ||
| export OMP_NUM_THREADS=1 | ||
| ulimit -s unlimited | ||
| export ppath=/scratch/project_2003835/programs_KPFM | ||
| export PYTHONPATH=$PYTHONPATH:$ppath/CP2k_mtools3:$ppath/DFT_gridIO3:$ppath/KPFM_FEM3:$ppath/KPFM_sim3 | ||
| KPFM_GLOBAL_SCRIPTS=$ppath/KPFM_sim3/scripts | ||
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| # **************************************************************************************************** # | ||
| # # | ||
| # script for putting all the results from all the KPFM workers to be saved in the global results db # | ||
| # # | ||
| # **************************************************************************************************** # | ||
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| echo "start combining results from different workers" | ||
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| GR='glob_res/afm_copy.db' # adjust the global results name # | ||
| bu=$GR | ||
| bu+='.bak' | ||
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| echo $GR $bu | ||
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| cp $GR $bu | ||
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| # adjust the voltages, where it was calculated # | ||
| vol="0.31 0.2 -0.2 -0.31 -2.0 -1.7 -1.5 -1.3 -1 -0.7 -0.5 -0.3 -0.1 -0.05 -0.01 0.01 0.05 0.1 0.3 0.5 0.7 1 1.3 1.5 1.7 2.0" | ||
| vol+=" 1000.0" | ||
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| for i in {0..0}; # adjust amount of y points # | ||
| do | ||
| for j in {0..0}; # adjust amout of x points # | ||
| do | ||
| for vi in $vol; | ||
| do | ||
| ar=kpfm_res_$i | ||
| ar+=_$j | ||
| ar+=_$vi.db # adjust the input db file name(s) # | ||
| echo $ar | ||
| wr=worker_$i | ||
| wr+=_$j | ||
| wr+=_$vi | ||
| python3 $KPFM_GLOBAL_SCRIPTS/copy_scan_points_and_wfn_files.py -i $ar -o $GR # -w $vi wfn_data # -k ## -k -- if kpts are necessary ## | ||
| done | ||
| done | ||
| done | ||
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| echo "Done, done" | ||
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|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| #!/bin/bash | ||
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| ## to creat input and running files for 2 tip-descents and multiple Voltages ## | ||
| # first try whatever point (in this nomenclature it will be 0 0 )) # | ||
| # to prepare files for the first y line then have - true - in the if # | ||
| grdb=glob_res/kpfm.db | ||
| #global results db file# | ||
| cpdb=false | ||
| # copy database # | ||
| dbf="kpfm_res_" | ||
| if true ; then | ||
| b=0 | ||
| Af=0 | ||
| #Vf="2.0 1.7 1.5 1.3 1.0 0.7 0.5 0.3 -0.3 -0.5 -0.7 -1.0 -1.3 -1.5 -1.7 -2.0" | ||
| Vf="1000.0 2.0 1.7 1.5 1.3 1 0.7 0.5 0.31 0.3 0.2 0.1 0.05 0.01 -0.01 -0.05 -0.1 -0.2 -0.3 -0.31 -0.5 -0.7 -1 -1.3 -1.5 -1.7 -2.0" | ||
| for Vi in $Vf; do | ||
| echo $b $Af $Vi | ||
| y="`echo $b`"; | ||
| x="`echo $Af`"; | ||
| V="`echo $Vi`" | ||
| #sed "s/BBB/$y/g" pdtt_V.template > pdtt.tmp ; | ||
| #sed "s/AAA/$x/g" pdtt.tmp > pdtt_$b.$Af.tmp ; | ||
| #sed "s/CCC/$V/g" pdtt_$b.$Af.tmp > pdtt_$b.$Af.$Vi.py; | ||
| #rm pdtt.tmp pdtt_$b.$Af.tmp | ||
| sed "s/BBB/$y/g" pdtt_V_run.template > pdtt_run.tmp ; | ||
| sed "s/AAA/$x/g" pdtt_run.tmp > rw_$b.$Af.tmp ; | ||
| sed "s/CCC/$V/g" rw_$b.$Af.tmp > rw_$b.$Af.$Vi.slrm; | ||
| rm pdtt_run.tmp rw_$b.$Af.tmp | ||
| if $cpdb; then | ||
| tdbf=$dbf | ||
| tdbf+=$b | ||
| tdbf+=_$Af | ||
| tdbf+=_$Vi | ||
| tdbf+=.db | ||
| echo $tdbf | ||
| cp $grdb $tdbf | ||
| fi | ||
| done | ||
| fi | ||
| if false ; then | ||
| b=0 | ||
| Af=1 | ||
| Vf="2.0 1.7 1.5 1.3 1.0 0.7 0.5 0.3 -0.3 -0.5 -0.7 -1.0 -1.3 -1.5 -1.7 -2.0" | ||
| #Vf="2.0 1.7 1.5 1.3 0.7 0.5 0.3 -0.3 -0.5 -0.7 -1.3 -1.5 -1.7 -2.0" | ||
| for Vi in $Vf; do | ||
| echo $b $Af $Vi | ||
| y="`echo $b`"; | ||
| x="`echo $Af`"; | ||
| V="`echo $Vi`" | ||
| sed "s/BBB/$y/g" pdtt_V.template > pdtt.tmp ; | ||
| sed "s/AAA/$x/g" pdtt.tmp > pdtt_$b.$Af.tmp ; | ||
| sed "s/CCC/$V/g" pdtt_$b.$Af.tmp > pdtt_$b.$Af.$Vi.py; | ||
| rm pdtt.tmp pdtt_$b.$Af.tmp | ||
| sed "s/BBB/$y/g" pdtt_V_run.template > pdtt_run.tmp ; | ||
| sed "s/AAA/$x/g" pdtt_run.tmp > rw_$b.$Af.tmp ; | ||
| sed "s/CCC/$V/g" rw_$b.$Af.tmp > rw_$b.$Af.$Vi.slrm; | ||
| rm pdtt_run.tmp rw_$b.$Af.tmp | ||
| if $cpdb; then | ||
| tdbf=$dbf | ||
| tdbf+=$b | ||
| tdbf+=_$Af | ||
| tdbf+=_$Vi | ||
| tdbf+=.db | ||
| echo $tdbf | ||
| cp $grdb $tdbf | ||
| fi | ||
| done | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| #!/bin/bash | ||
| # check modules.txt for updating following lines: # module purge | ||
| #module load gcc/9.3.0 openmpi/4.0.3 cp2k/7.1-omp | ||
| export OMP_NUM_THREADS=1 | ||
| ulimit -s unlimited | ||
| export ppath=./programs_KPFM # | ||
| export PYTHONPATH=$PYTHONPATH:$ppath/CP2k_mtools3:$ppath/DFT_gridIO3:$ppath/KPFM_FEM3:$ppath/KPFM_sim3 #:$ppath/pycp2k | ||
| export PYTHONPATH=$PYTHONPATH:/u/88/krejcio1/unix/WORK/lib_cp2k_copy/ | ||
| KPFM_GLOBAL_SCRIPTS=$ppath/KPFM_sim3/scripts | ||
| ORIG_DIR=`pwd` | ||
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| ## after adjust the modules above and PYTHONPATH, this script will allow to get Mulliken charges from the descent tip scan (style metallic) with different voltage ## | ||
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| if true ; then | ||
| y=0.0 ## adjust /x/ and /y/ as well as voltages /Vf/ <- for chanrges those which are lower than -100 and larges than +100 makes sense ## | ||
| x=0.0 ## look at wiki for more details ## | ||
| Vf="102.0 101.7 101.5 101.3 101.0 100.7 100.5 100.3 100.1 100.05 100.01 -100.01 -100.05 -100.01 -100.1 -100.3 -100.5 -100.7 -101.0 -101.3 -101.5 -101.7 -102.0" | ||
| Vf+=" -100.31 -100.2 100.2 100.31 1000.0" | ||
| for Vi in $Vf; do | ||
| python3 $KPFM_GLOBAL_SCRIPTS/extract_descend_tip_charges.py -i glob_res/afm.db -p $x $y -V $Vi | ||
| done | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| #!/bin/bash | ||
| # check modules.txt for updating following lines: # module purge | ||
| #module load gcc/9.3.0 openmpi/4.0.3 cp2k/7.1-omp | ||
| export OMP_NUM_THREADS=1 | ||
| ulimit -s unlimited | ||
| export ppath=./programs_KPFM # | ||
| export PYTHONPATH=$PYTHONPATH:$ppath/CP2k_mtools3:$ppath/DFT_gridIO3:$ppath/KPFM_FEM3:$ppath/KPFM_sim3 #:$ppath/pycp2k | ||
| export PYTHONPATH=$PYTHONPATH:/u/88/krejcio1/unix/WORK/lib_cp2k_copy/ | ||
| KPFM_GLOBAL_SCRIPTS=$ppath/KPFM_sim3/scripts | ||
| ORIG_DIR=`pwd` | ||
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| ## after adjust the modules above and PYTHONPATH, this script will allow to get energies and forces (and also atomic forces) for predefined voltages in Vf ## | ||
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| if true ; then | ||
| y=0.0 ## adjust /x/ and /y/ as well as voltages /Vf/ <- for chanrges those which are around 0 should be the most important (other left here for cross-checking) ## | ||
| x=0.0 ## look at wiki for more details ## | ||
| Vf="1000.0" | ||
| Vf+=" -0.31 -0.2 0.2 0.31 -100.31 -100.2 100.2 100.31" | ||
| Vf+=" 0.1 0.05 0.01 -0.01 -0.05 -0.1 100.1 100.05 100.01 -100.01 -100.05 -100.1" | ||
| Vf+=" 102.0 101.7 101.5 101.3 101.0 100.7 100.5 100.3 -100.3 -100.5 -100.7 -101.0 -101.3 -101.5 -101.7 -102.0" | ||
| Vf+=" 2.0 1.7 1.5 1.3 1.0 0.7 0.5 0.3 -0.3 -0.5 -0.7 -1.0 -1.3 -1.5 -1.7 -2.0" | ||
| for Vi in $Vf; do | ||
| echo "x y V:" $x $y $Vi | ||
| python3 $KPFM_GLOBAL_SCRIPTS/extract_descend_tip_data.py -i glob_res/afm.db -p $x $y -V $Vi -n -N # -n -- no atomic forces -N -- no geometry | ||
| done | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| #!/bin/bash | ||
|
|
||
| ## to creat input and running files for 2 tip-descents with different voltages ## | ||
| # first try whatever point (in this nomenclature it will be 0 0 )) # | ||
| # to prepare files for the first y line then have - true - in the if # | ||
| if true ; then | ||
| b=0 | ||
| Af=0 | ||
| Vf="1000.0 2.0 1.7 1.5 1.3 1 0.7 0.5 0.31 0.3 0.2 0.1 0.05 0.01 -0.01 -0.05 -0.1 -0.2 -0.3 -0.31 -0.5 -0.7 -1 -1.3 -1.5 -1.7 -2.0" | ||
| for Vi in $Vf; do | ||
| sbatch rw_$b.$Af.$Vi.slrm ; | ||
| done | ||
| fi | ||
| if false ; then | ||
| b=0 | ||
| Af=1 | ||
| Vf="2.0 1.7 1.5 1.3 1 0.7 0.5 0.3 -0.3 -0.5 -0.7 -1.0 -1.3 -1.5 -1.7 -2.0" | ||
| for Vi in $Vf; do | ||
| echo rw_$b.$Af.$Vi.slrm ; | ||
| sbatch rw_$b.$Af.$Vi.slrm ; | ||
| done | ||
| fifi |