USPEX 9.3.4 with SIESTA

[Stepan Botman]

Hello.
I've started using USPEX recently and tried to set up calculation with SIESTA.
However I faced some errors during it.
Calculation type was 300 (3 dimensional, non-molecular, non-variable compositions).
So there were some errors in file writeCalcFilesSIESTA.m:
lines 5-7:

numMols = POP_STRUC.POPULATION(Ind_No).numMols;
MtypeLIST = POP_STRUC.POPULATION(Ind_No).MtypeLIST;
typesAList= POP_STRUC.POPULATION(Ind_No).typesAList;

Even though calculation was non-molecular they tried to initialize (as I understand,
they are engaged only in molecular calculations) so I add 'if' construction:

if ORG_STRUC.molecule==1
numMols = POP_STRUC.POPULATION(Ind_No).numMols;
MtypeLIST = POP_STRUC.POPULATION(Ind_No).MtypeLIST;
typesAList= POP_STRUC.POPULATION(Ind_No).typesAList;
end

Then line 44 inside AtomicCoordinatesAndAtomicSpecies block generator:

if ORG_STRUC.atomType(j)==typesAList(i)

typesAlist was not intialized on line 7 after my changes so this also did not work
so I rewrited it for my purposes as follows:

fprintf(fid,'AtomicCoordinatesFormat   Fractional\n');
fprintf(fid,'%%block AtomicCoordinatesAndAtomicSpecies\n');
%%%%%%%%%%%%%%%%%%%%%%%%%%__fixed__%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
numbers=1:sum(ORG_STRUC.atomType);
tmpSpecices=zeros(1,sum(numIons));
tmpSpecices([1 cumsum(numIons(1:end-1))+1]) = 1;
SpecicesNumber=numbers(cumsum(tmpSpecices));
SpecicesTypes=ORG_STRUC.atomType(cumsum(tmpSpecices));
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
for i=1:sum(numIons)
fprintf(fid,'%10.6f %10.6f %10.6f %d %2d\n', COORDINATES(i,:), SpecicesNumber(i), SpecicesTypes(i));
end
fprintf(fid,'%%endblock AtomicCoordinatesAndAtomicSpecies\n');
%%%%%%%%%%%%%%%%%%%%%%%%__Block_added__%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%comment out if scpecificated in input.fdf
fprintf(fid,'%%%block ChemicalSpeciesLabel\n');
for i=1:length(ORG_STRUC.atomType)
fprintf(fid,'%d %2d %s\n', i, ORG_STRUC.atomType(i), megaDoof(ORG_STRUC.atomType(i)));
end
fprintf(fid,'%%endblock ChemicalSpeciesLabel\n');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

I am not sure if this would work in case of molecular calculations.
But, anyway, after all this changes I was able to start my calculations.
Next error occurred during reading output files: "PROBLEM 1" (then "PROBLEM 2" ans so on).
This was caused by misprint on line 89 in file readCalcFilesSIESTA.m instead of

POP_STRUC.POPULATION(Ind_No).Vol(end+1)=det(LATTICE);

should be:

POP_STRUC.POPULATION(Ind_No).Vol(end+1)=det(POP_STRUC.POPULATION(Ind_No).LATTICE);

After that all worked fine.
I hope that provided information will be useful.
Stepan Botman.

[Qiang Zhu]

Dear Stepan,

Thanks for your nice comment. I will have a look. If it is right, I will update it in our code.

Best regards,

Qiang

Stepan Botman.

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--

Qiang Zhu (Ph.D)
ESS 365
Department of Geosciences
Stony Brook University
NY 11794-2100

USPEX download Page: http://uspex.stonybrook.edu/