Questions on surface prediction
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Wennie Xi
Sep 12, 2025, 4:57:56 AM (yesterday) Sep 12
to USPEX
Dear all：
Recently I've been trying to conduct a surface prediction on a system containing 3 elements.The substrate is ZrO2,which is covered by a In2O3 overlayer.However, the structures generated in each iteration only contain In and O. Moreover, the Zr atoms in the POSCAR_SUBSTRATE are somehow being replaced by In.
My question is, how should I set up the INPUT.txt file to keep the ZrO2 substrate fixed while allowing the In2O3 overlayer to evolve on the surface?
Fowllowing are my INPUT.txt , POSCAR_SUBSTRATE and structure example in the 1st generation.
Any suggestions will be appreciated.
INPUT.txt:
PARAMETERS EVOLUTIONARY ALGORITHM
******************************************
******************************************
* TYPE OF RUN AND SYSTEM *
******************************************
******************************************
USPEX : calculationMethod (USPEX, VCNEB, META)
201 : calculationType (dimension: 0-3; molecule: 0/1; varcomp: 0/1)
1 : AutoFrac
% optType
1
% EndOptType
% atomType
In O
% EndAtomType
% numSpecices (maximum number of ad-atoms per 1*1 cell from POSCAR_SUBSTRATE)
2 3
% EndNumSpecices
*******************************************
*******************************************
* Surfaces *
*******************************************
*******************************************
% symmetries (Structure are generated by plane groups)
2-17
% endSymmetries
3.0 : thicknessS (thickness of surface region, 2 A by default )
1.6 : thicknessB (thickness of buffer region in substrate, 3 A by default)
4 : reconstruct (the maximum multiplication: 1*1 1*2 2*1 1*3 3*1 2*2)
% : E_AB (eV/forumula unit)
-2.727 : Mu_A (eV/atom)
-4.927 : Mu_B (eV/atom)
******************************************
* POPULATION *
******************************************
40 : populationSize (how many individuals per generation)
60 : initialPopSize
40 : numGenerations (how many generations shall be calculated)
20 : stopCrit
******************************************
* SURVIVAL OF THE FITTEST AND SELECTION *
******************************************
1 : reoptOld
0.6 : bestFrac
******************************************
******************************************
* VARIATION OPERATORS *
******************************************
******************************************
0.30 : fracGene (fraction of generation produced by heredity)
0.50 : fracRand (fraction of generation produced randomly from space groups)
0.20 : fracAtomsMut (fraction of the generation produced by softmutation)
0.00 : fracTrans (fraction of the generation produced by transmutations)
****************************************
* CONSTRAINTS *
****************************************
% IonDistances
1.0 0.8
0.8 0.8
% EndDistances
*****************************************
* DETAILS OF AB INITIO CALCULATIONS *
*****************************************
% abinitioCode
1 1 1 1
% ENDabinit
% commandExecutable
/share/intel/2024/oneapi/mpi/2021.11/bin/mpirun /share/apps/vasp/6.4.2_cpu_dftd4/bin/vasp_std > vasp.out
% EndExecutable
% KresolStart
0.15 0.12 0.09 0.07
% Kresolend
% vacuumSize
10 12 15 20
% endVacuumSize
10 : numParallelCalcs (how many parallel calculations shall be performed)
1 : whichCluster (0: no-job-script, 1: local submission, 2: remote, To denfine your cluster)
******************************************
******************************************
* TYPE OF RUN AND SYSTEM *
******************************************
******************************************
USPEX : calculationMethod (USPEX, VCNEB, META)
201 : calculationType (dimension: 0-3; molecule: 0/1; varcomp: 0/1)
1 : AutoFrac
% optType
1
% EndOptType
% atomType
In O
% EndAtomType
% numSpecices (maximum number of ad-atoms per 1*1 cell from POSCAR_SUBSTRATE)
2 3
% EndNumSpecices
*******************************************
*******************************************
* Surfaces *
*******************************************
*******************************************
% symmetries (Structure are generated by plane groups)
2-17
% endSymmetries
3.0 : thicknessS (thickness of surface region, 2 A by default )
1.6 : thicknessB (thickness of buffer region in substrate, 3 A by default)
4 : reconstruct (the maximum multiplication: 1*1 1*2 2*1 1*3 3*1 2*2)
% : E_AB (eV/forumula unit)
-2.727 : Mu_A (eV/atom)
-4.927 : Mu_B (eV/atom)
******************************************
* POPULATION *
******************************************
40 : populationSize (how many individuals per generation)
60 : initialPopSize
40 : numGenerations (how many generations shall be calculated)
20 : stopCrit
******************************************
* SURVIVAL OF THE FITTEST AND SELECTION *
******************************************
1 : reoptOld
0.6 : bestFrac
******************************************
******************************************
* VARIATION OPERATORS *
******************************************
******************************************
0.30 : fracGene (fraction of generation produced by heredity)
0.50 : fracRand (fraction of generation produced randomly from space groups)
0.20 : fracAtomsMut (fraction of the generation produced by softmutation)
0.00 : fracTrans (fraction of the generation produced by transmutations)
****************************************
* CONSTRAINTS *
****************************************
% IonDistances
1.0 0.8
0.8 0.8
% EndDistances
*****************************************
* DETAILS OF AB INITIO CALCULATIONS *
*****************************************
% abinitioCode
1 1 1 1
% ENDabinit
% commandExecutable
/share/intel/2024/oneapi/mpi/2021.11/bin/mpirun /share/apps/vasp/6.4.2_cpu_dftd4/bin/vasp_std > vasp.out
% EndExecutable
% KresolStart
0.15 0.12 0.09 0.07
% Kresolend
% vacuumSize
10 12 15 20
% endVacuumSize
10 : numParallelCalcs (how many parallel calculations shall be performed)
1 : whichCluster (0: no-job-script, 1: local submission, 2: remote, To denfine your cluster)
POSCAR_SUBSTRATE:
POSCAR_SUBSTRATE
1.000000
6.345 0.000 0.000
0.000 3.600 0.000
0.000 0.000 5.254
4 8
Direct
0.05447 0.09518 0.18931
0.37638 0.09518 0.75359
0.55447 0.59518 0.18931
0.87638 0.59518 0.75359
0.84984 0.59518 0.35960
0.17175 0.59518 0.92387
0.18889 0.59518 0.07746
0.51080 0.59518 0.64174
0.42006 0.09518 0.30117
0.74197 0.09518 0.86544
0.75911 0.09518 0.01903
0.08102 0.09518 0.58330
1.000000
6.345 0.000 0.000
0.000 3.600 0.000
0.000 0.000 5.254
4 8
Direct
0.05447 0.09518 0.18931
0.37638 0.09518 0.75359
0.55447 0.59518 0.18931
0.87638 0.59518 0.75359
0.84984 0.59518 0.35960
0.17175 0.59518 0.92387
0.18889 0.59518 0.07746
0.51080 0.59518 0.64174
0.42006 0.09518 0.30117
0.74197 0.09518 0.86544
0.75911 0.09518 0.01903
0.08102 0.09518 0.58330
Structure example in 1st generation:
EA0 25.380 3.600 17.254 90.000 90.000 90.000 Sym.group: no SG
1.0000
25.380000 0.000000 0.000000
0.000000 3.600000 0.000000
0.000000 0.000000 17.254000
23 43
Selective dynamics
Direct
0.013617 0.095180 0.057647 F F F
0.263618 0.095180 0.057647 F F F
0.513617 0.095180 0.057647 F F F
0.763617 0.095180 0.057647 F F F
0.094095 0.095180 0.229475 F F F
0.344095 0.095180 0.229475 F F F
0.594095 0.095180 0.229475 F F F
0.844095 0.095180 0.229475 F F F
0.138618 0.595180 0.057647 F F F
0.388618 0.595180 0.057647 F F F
0.638618 0.595180 0.057647 F F F
0.888618 0.595180 0.057647 F F F
0.219095 0.595180 0.229475 F F F
0.469095 0.595180 0.229475 F F F
0.719095 0.595180 0.229475 F F F
0.969095 0.595180 0.229475 F F F
0.781420 0.807280 0.362467 T T T
0.222650 0.914870 0.304509 T T T
0.211070 0.348490 0.304509 T T T
0.745640 0.339920 0.304509 T T T
0.743830 0.712350 0.304509 T T T
0.886610 0.002620 0.304509 T T T
0.927750 0.488750 0.304509 T T T
0.212460 0.595180 0.109501 F F F
0.462460 0.595180 0.109501 F F F
0.712460 0.595180 0.109501 F F F
0.962460 0.595180 0.109501 F F F
0.042938 0.595180 0.281327 F F F
0.292938 0.595180 0.281327 F F F
0.542937 0.595180 0.281327 F F F
0.792938 0.595180 0.281327 F F F
0.047223 0.595180 0.023587 F F F
0.297223 0.595180 0.023587 F F F
0.547222 0.595180 0.023587 F F F
0.797222 0.595180 0.023587 F F F
0.127700 0.595180 0.195416 F F F
0.377700 0.595180 0.195416 F F F
0.627700 0.595180 0.195416 F F F
0.877700 0.595180 0.195416 F F F
0.105015 0.095180 0.091709 F F F
0.355015 0.095180 0.091709 F F F
0.605015 0.095180 0.091709 F F F
0.855015 0.095180 0.091709 F F F
0.185493 0.095180 0.263534 F F F
0.435492 0.095180 0.263534 F F F
0.685493 0.095180 0.263534 F F F
0.935493 0.095180 0.263534 F F F
0.189777 0.095180 0.005795 F F F
0.439777 0.095180 0.005795 F F F
0.689777 0.095180 0.005795 F F F
0.939777 0.095180 0.005795 F F F
0.020255 0.095180 0.177620 F F F
0.270255 0.095180 0.177620 F F F
0.520255 0.095180 0.177620 F F F
0.770255 0.095180 0.177620 F F F
0.835460 0.689040 0.362467 T T T
0.709800 0.588850 0.304509 T T T
0.404640 0.417890 0.304509 T T T
0.207080 0.096180 0.362467 T T T
0.447470 0.065120 0.337254 T T T
0.447470 0.065120 0.387679 T T T
0.981220 0.003200 0.362467 T T T
0.671740 0.967840 0.329513 T T T
0.671740 0.967840 0.395420 T T T
0.587390 0.266970 0.304509 T T T
0.856320 0.905750 0.304509 T T T
1.0000
25.380000 0.000000 0.000000
0.000000 3.600000 0.000000
0.000000 0.000000 17.254000
23 43
Selective dynamics
Direct
0.013617 0.095180 0.057647 F F F
0.263618 0.095180 0.057647 F F F
0.513617 0.095180 0.057647 F F F
0.763617 0.095180 0.057647 F F F
0.094095 0.095180 0.229475 F F F
0.344095 0.095180 0.229475 F F F
0.594095 0.095180 0.229475 F F F
0.844095 0.095180 0.229475 F F F
0.138618 0.595180 0.057647 F F F
0.388618 0.595180 0.057647 F F F
0.638618 0.595180 0.057647 F F F
0.888618 0.595180 0.057647 F F F
0.219095 0.595180 0.229475 F F F
0.469095 0.595180 0.229475 F F F
0.719095 0.595180 0.229475 F F F
0.969095 0.595180 0.229475 F F F
0.781420 0.807280 0.362467 T T T
0.222650 0.914870 0.304509 T T T
0.211070 0.348490 0.304509 T T T
0.745640 0.339920 0.304509 T T T
0.743830 0.712350 0.304509 T T T
0.886610 0.002620 0.304509 T T T
0.927750 0.488750 0.304509 T T T
0.212460 0.595180 0.109501 F F F
0.462460 0.595180 0.109501 F F F
0.712460 0.595180 0.109501 F F F
0.962460 0.595180 0.109501 F F F
0.042938 0.595180 0.281327 F F F
0.292938 0.595180 0.281327 F F F
0.542937 0.595180 0.281327 F F F
0.792938 0.595180 0.281327 F F F
0.047223 0.595180 0.023587 F F F
0.297223 0.595180 0.023587 F F F
0.547222 0.595180 0.023587 F F F
0.797222 0.595180 0.023587 F F F
0.127700 0.595180 0.195416 F F F
0.377700 0.595180 0.195416 F F F
0.627700 0.595180 0.195416 F F F
0.877700 0.595180 0.195416 F F F
0.105015 0.095180 0.091709 F F F
0.355015 0.095180 0.091709 F F F
0.605015 0.095180 0.091709 F F F
0.855015 0.095180 0.091709 F F F
0.185493 0.095180 0.263534 F F F
0.435492 0.095180 0.263534 F F F
0.685493 0.095180 0.263534 F F F
0.935493 0.095180 0.263534 F F F
0.189777 0.095180 0.005795 F F F
0.439777 0.095180 0.005795 F F F
0.689777 0.095180 0.005795 F F F
0.939777 0.095180 0.005795 F F F
0.020255 0.095180 0.177620 F F F
0.270255 0.095180 0.177620 F F F
0.520255 0.095180 0.177620 F F F
0.770255 0.095180 0.177620 F F F
0.835460 0.689040 0.362467 T T T
0.709800 0.588850 0.304509 T T T
0.404640 0.417890 0.304509 T T T
0.207080 0.096180 0.362467 T T T
0.447470 0.065120 0.337254 T T T
0.447470 0.065120 0.387679 T T T
0.981220 0.003200 0.362467 T T T
0.671740 0.967840 0.329513 T T T
0.671740 0.967840 0.395420 T T T
0.587390 0.266970 0.304509 T T T
0.856320 0.905750 0.304509 T T T
Wennie Xi
4:21 AM (10 hours ago) 4:21 AM
to USPEX
Never mind, my problem has been solved. Here is my solution:
First, define the elements in the POSCAR_SUBSTRATE file correctly. For example, if you want to model an AxBy overlayer on a CmDn substrate, your POSCAR_SUBSTRATE should include the elements of the substrate (C and D) in the standard POSCAR format. The surface elements (A and B) should then be appended afterward, with their atomic counts set to 0.
Next, configure the parameters in INPUT.txt , including atomType,numSpecies, and the IonDistances matrix. It is important to ensure that the order of the elements remains consistent with that in POSCAR_SUBSTRATE.
Below is an example based on my case:
INPUT.txt:
PARAMETERS EVOLUTIONARY ALGORITHM
******************************************
******************************************
* TYPE OF RUN AND SYSTEM *
******************************************
******************************************
USPEX : calculationMethod (USPEX, VCNEB, META)
******************************************
******************************************
* TYPE OF RUN AND SYSTEM *
******************************************
******************************************
USPEX : calculationMethod (USPEX, VCNEB, META)
200 : calculationType (dimension: 0-3; molecule: 0/1; varcomp: 0/1)
1 : AutoFrac
% optType
1
% EndOptType
% atomType
Zr O In
% EndAtomType
% numSpecices (maximum number of ad-atoms per 1*1 cell from POSCAR_SUBSTRATE)
0 3 2
% EndNumSpecices
*******************************************
*******************************************
* Surfaces *
*******************************************
*******************************************
% symmetries (Structure are generated by plane groups)
2-17
% endSymmetries
4.0 : thicknessS (thickness of surface region, 2 A by default )
1.6 : thicknessB (thickness of buffer region in substrate, 3 A by default)
2 : reconstruct (the maximum multiplication: 1*1 1*2 2*1 1*3 3*1 2*2)
0.8 0.8 0.8
0.8 0.8 0.8
% EndDistances
POSCAR_SUBSTRATE:
POSCAR_SUBSTRATE_NEW
1.000000
6.345 0.000 0.000
0.000 3.600 0.000
0.000 0.000 5.254
Zr O In
4 8 0
4 8 0
Direct
0.05447 0.09518 0.18931
0.37638 0.09518 0.75359
0.55447 0.59518 0.18931
0.87638 0.59518 0.75359
0.84984 0.59518 0.35960
0.17175 0.59518 0.92387
0.18889 0.59518 0.07746
0.51080 0.59518 0.64174
0.42006 0.09518 0.30117
0.74197 0.09518 0.86544
0.75911 0.09518 0.01903
0.08102 0.09518 0.58330
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