Re: Problem with Seeds-file

[Qiang Zhu]

I think you took gatheredPOSCARS_order as seeds. You can use POSCARS instead of POSCARS_order.

Otherwise, USPEX does not understand the format with four column in atomic coordinates.

EA2     2.578  2.579  2.566 70.68 109.33 70.46 Sym.group:    1
1.0000
    0.861048    -1.219551    -2.102093
    2.578932     0.004202    -0.004183
    0.854268    -1.211262     2.094490
   S   H
   1    3 
Direct
    0.000381     0.993706     0.998689     3.598713
    0.499200     0.495729     0.990420     2.551023
    0.993023     0.489675     0.500610     2.467645
    0.502972     0.999391     0.498213     2.525205

On Wed, Jul 22, 2015 at 10:03 AM, <chh...@gmx.at> wrote:

Hello all,
I've done a calculation with USPEX and got a few favourable structures for the composition I'm looking at. I would like to refine these structures by doing a second, more precise USPEX run where the start population should be the structures previously found (I've put a corresponding POSCARS file in the Seeds folder). Unfortunately, however, USPEX can only read the first structure of the POSCARS-file and I get the warning:

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
seed number 1 has been successfully added
===== USPEX WARNING @ 14:43:22 22-Jul-2015 =====
Seeds : Meet a problem when reading Seeds-2, so we stop the rest seeds reading...
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

If I exchange the structures in the POSCARS-files, i.e. put the second structure in the first place, I get the same message. This, at least for me, means that the single structures in the POSCARS file are correct. Did anyone of you encounter a similar issue or knows how to circumvent it?


I would greatly appreciate any help or input from you guys
with best wishes,
Christoph







Matlab version: R2014b (8.4.0.150421) 64-bit
USPEX version: Version 9.4.2

INPUT.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
PARAMETERS EVOLUTIONARY ALGORITHM
******************************************
*      TYPE OF RUN AND SYSTEM            *
******************************************
USPEX : calculationMethod (USPEX, VCNEB, META)
300   : calculationType (dimension: 0-3; molecule: 0/1; varcomp: 0/1)
1     : optType (1=enthalpy, 2=volume, 3=hardness, 4=struc_order,...)
1     : AutoFrac

% atomType
S H
% EndAtomType


% numSpecies
1 3
% EndNumSpecies

******************************************
*               POPULATION               *
******************************************
20    : populationSize (how many individuals per generation)
0     : initialPopSize
25    : numGenerations (how many generations shall be calculated)
4     : stopCrit
0     : reoptOld
0.6   : bestFrac

******************************************
*          VARIATION OPERATORS           *
******************************************
0.50  : fracGene (fraction of generation produced by heredity)
0.20  : fracRand (fraction of generation produced randomly from space groups)
0.20  : fracAtomsMut (fraction of the generation produced by softmutation)
0.10  : fracLatMut (fraction of the generation produced by softmutation)

****************************************
*             CONSTRAINTS              *
****************************************
% IonDistances
 1.0 0.6
 0.6 0.5
% EndDistances

*****************************************
*   DETAILS OF AB INITIO CALCULATIONS   *
*****************************************
% abinitioCode (which code from CommandExecutable shall be used for calculation?)
1 1
% ENDabinit

% KresolStart
0.05 0.03
% Kresolend

% commandExecutable
mpirun -np 8 vasp >& out6
mpirun -np 8 vasp >& out7
% EndExecutable


0    : whichCluster (0: no-job-script, 1: local submission, 2: remote submission)
1     : numParallelCalcs
200   : ExternalPressure
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<




POSCARS (for simplicity, I've only included two now)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
EA1     2.572  2.573  2.589 109.62 70.42 70.66 Sym.group:  229
1.0000
    2.569935    -0.033956     0.097628
    0.885701     2.415588    -0.025313
    0.770149    -1.185491     2.169007
   S   H
   1    3
Direct
    0.600615     0.444191     0.755217     3.706617
    0.102306     0.943864     0.757124     2.653441
    0.600977     0.943894     0.251939     2.660203
    0.099389     0.447606     0.255515     2.665925
EA2     2.578  2.579  2.566 70.68 109.33 70.46 Sym.group:    1
1.0000
    0.861048    -1.219551    -2.102093
    2.578932     0.004202    -0.004183
    0.854268    -1.211262     2.094490
   S   H
   1    3
Direct
    0.000381     0.993706     0.998689     3.598713
    0.499200     0.495729     0.990420     2.551023
    0.993023     0.489675     0.500610     2.467645
    0.502972     0.999391     0.498213     2.525205
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

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Qiang Zhu (Research Assistant Professor)
ESS 365
Department of Geosciences
Stony Brook University
NY 11794-2100

http://uspex.stonybrook.edu/qzhu.html

[chh...@gmx.at]

Thanks a lot, that solved the problem!
Thank you very much for the quick answer.