Siesta

generation of pseudopotentiel

Asked by Maria

Dear Nick P.,

I have some questions of the generation of the pseudopotentiel with atoms code and I hope that you answer me.

1- In the input file, there is a number after the tm2 expression which can be 0, 1, 2, 3, 4. In the exemple below is 4. Can you explain for me the role of this number (logder R) and how to specify it ?

pe Sodium NLCC rcore=1.50
tm2 4.0
n=Na c=ca
0.0 0.0 0.0 0.0 0.0 0.0
3 3
3 0 1.00 0.00
3 1 0.00 0.00
3 2 0.00 0.00
2.95 2.95 2.95 2.95 0 1.50

2- when I would like to plot the pseudo.gps, this message appears : " subs.gplot ", line9: undefined variable: ARG1
What is the problem and how I can resolve it?

3- when I would like to run a test pseudopotentiel generation which contain many configurations ?
this message appears:
STOP XC ERROR: invalid functional label
What is the problem and how I can resolve it?

Thank you very much in advance.

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ALOKA RANJAN SAHOO
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Alberto Garcia (albertog) said : 		#1

Please make sure that you are using the current version of the ATOM program, as per the link found in the Pseudopotentials section of the Siesta webpage.

As stated in the manual, the number after the 'tm2' (flavor) is the radius at which the logarithmic derivatives are computed, for tests purposes.

Please pay attention to the very rigid input format of the program.

To plot data after the execution of ATOM, you need to type, for example:

gnuplot pseudo.gps

for creating a .ps file, or

gnuplot -persist pseudo.gplot

for a screen plot.

Revision history for this message
Maria (maria11) said : 		#2

Thank you very much for your reply.

1- For the plot of the pseudo, I have done the same steps but the same error appears?
2- For the generation of vdw pseudopotentiels, we choose relativistic or nonrelativistic?

3- For LDA functionnel, we can apply the Grimme correction or not ?

Revision history for this message
Best ALOKA RANJAN SAHOO (alokrs) said : 		#3

I was facing the same problem. Fixed it by replacing the existing subps.gps and subps.gplot in the 'Utils' directory of atom program/Tutorial/Utils/

 copy this into a file name subps.gplot

# Expects to be passed the L value as a quoted parameter ($0)
#
set data style lines
#
set multiplot
set size 0.5,0.5
set origin 0.0,0.0
plot [0:4] 'PSPOTR$0' using 1:2 title "l=$0 Pseudopot r" with lines,\
           0.0 notitle with lines lt 0
##### goes offscale... 'PSPOTR$0' using 1:3 notitle with linespoints

set origin 0.5,0.0
plot [0:20] 'PSPOTQ$0' using 1:2 title "l=$0 Pseudopot q" with lines,\
           0.0 notitle with lines lt 0
#
set origin 0.0,0.5

plot [0:4] 'AEWFNR$0' using 1:2 title "AE wfn l=$0" with lines, \
           'PSWFNR$0' using 1:2 title "PS wfn l=$0" with lines, \
           0.0 notitle with lines lt 0
set origin 0.5,0.5
#
# Logarithmic derivative
#
there_is_logd=`test -f AELOGD$0 && echo 1 || echo 0`
if (there_is_logd == 1) \
plot 'AELOGD$0' us 1:2 ti "AE logder l=$0" ,\
     'PSLOGD$0' us 1:2 ti "PS logder l=$0"
#
set nomultiplot

#pause -1 "Hit return to end"

------------------------------------------------------------------------------------------
and another file subps.gps

# Expects to be passed the L value as a quoted parameter ($0)
#
set data style lines
#
set multiplot
set size 0.5,0.5
set origin 0.0,0.0
plot [0:4] 'PSPOTR$0' using 1:2 title "l=$0 Pseudopot r" with lines,\
           0.0 notitle with lines lt 0
##### goes offscale... 'PSPOTR$0' using 1:3 notitle with linespoints

set origin 0.5,0.0
plot [0:20] 'PSPOTQ$0' using 1:2 title "l=$0 Pseudopot q" with lines,\
           0.0 notitle with lines lt 0
#
set origin 0.0,0.5

plot [0:4] 'AEWFNR$0' using 1:2 title "AE wfn l=$0" with lines, \
           'PSWFNR$0' using 1:2 title "PS wfn l=$0" with lines, \
           0.0 notitle with lines lt 0
set origin 0.5,0.5
#
# Logarithmic derivative
#
there_is_logd=`test -f AELOGD$0 && echo 1 || echo 0`
if (there_is_logd == 1) \
plot 'AELOGD$0' us 1:2 ti "AE logder l=$0" ,\
     'PSLOGD$0' us 1:2 ti "PS logder l=$0"
#
set nomultiplot

#pause -1 "Hit return to end"

-----------------------------------------------------------------------------------------
hope this helps

Revision history for this message
Maria (maria11) said : 		#4

Thank you for your help