about input file of espresso

[bhabya sahoo]

i am a new user of of uspex
i want some good quaantum espresso input files
for which i will be able to understand the input and output files

[USPEX]

Hello,

sadly no one in the USPEX developer team uses Quantum Espresso
routinely. Though I think some of our users do. My advise would be to
go to Quantum Espresso forums/website and learn how to do calculations
with the program. When we developed the interface between QE and
USPEX, we used an example of 4-step calculation for carbon. For that
you would need 4 input files name qEspresso_options_1,
qEspresso_options_2, qEspresso_options_3 and qEspresso_options_4 (for
USPEX to recognize them they should always be named like that). I will
post them below, but remember (!) that USPEX will add the coordinates
of atoms, the unit cell parameters and k-points to them. These input
files are therefore not complete. But at least you will see, how they
look like.

So, here is the file qEspresso_options_1:
&CONTROL
calculation = "relax",
restart_mode = "from_scratch",
prefix = "pp",
pseudo_dir = "./",
outdir = "./",
wf_collect = false
nstep = 35
disk_io = 'none'
/
&SYSTEM
ibrav = 0
nat = 8
ntyp = 1
ecutwfc = 40.D0
nosym = .true.
occupations='smearing'
degauss=0.02
smearing='marzari-vanderbilt'
/
&ELECTRONS
conv_thr = 5.D-04,
mixing_beta=0.5,
electron_maxstep = 250
/
&IONS
ion_dynamics='bfgs'
trust_radius_max = 0.2
/
ATOMIC_SPECIES
C 12. C.pbe-van_bm.upf



here is the file qEspresso_options_2:

&CONTROL
calculation = "relax",
restart_mode = "from_scratch",
prefix = "pp",
pseudo_dir = "./",
outdir = "./",
wf_collect = false
nstep = 55
disk_io = 'none'
/
&SYSTEM
ibrav = 0
nat = 8
ntyp = 1
ecutwfc = 40.D0
nosym = .true.
occupations='smearing'
degauss=0.02
smearing='marzari-vanderbilt'
/
&ELECTRONS
conv_thr = 1.D-06,
mixing_beta=0.5,
electron_maxstep = 250
/
&IONS
ion_dynamics='bfgs'
trust_radius_max = 0.2
/
ATOMIC_SPECIES
C 12. C.pbe-van_bm.upf


here is the file qEspresso_options_3:

&CONTROL
calculation = "vc-relax",
restart_mode = "from_scratch",
prefix = "pp",
pseudo_dir = "./",
outdir = "./",
wf_collect = false
nstep = 65
/
&SYSTEM
ibrav = 0
nat = 8
ntyp = 1
ecutwfc = 40.D0
nosym = .true.
occupations='smearing'
degauss=0.02
smearing='marzari-vanderbilt'
/
&ELECTRONS
conv_thr = 1.D-06,
mixing_beta=0.5,
electron_maxstep = 250
/
&IONS
ion_dynamics='bfgs'
/
&CELL
cell_dynamics='bfgs'
press = 0.01
cell_factor=3.0
/
ATOMIC_SPECIES
C 12. C.pbe-van_bm.upf


here is the files qEspresso_options_4:

&CONTROL
calculation = "vc-relax",
restart_mode = "from_scratch",
prefix = "pp",
pseudo_dir = "./",
outdir = "./",
wf_collect = .false.
nstep = 35
/
&SYSTEM
ibrav = 0
nat = 8
ntyp = 1
ecutwfc = 40.D0
nosym = .true.
occupations='smearing'
degauss=0.02
smearing='marzari-vanderbilt'
/
&ELECTRONS
conv_thr = 1.D-08,
mixing_beta=0.5,
electron_maxstep = 250
/
&IONS
ion_dynamics='bfgs'
/
&CELL
cell_dynamics='bfgs'
press = 0.01
cell_factor=1.5
/
ATOMIC_SPECIES
C 12. C.pbe-van_bm.upf


Sincerely,
USPEX group

[Amin]

Dear USPEX!

Can you please provide me with the INPUT_EA.txt file, associated with
this previous QE input files?

I am in the process of installing and interfacing USPEX with QE, and
need this file to do my first calculation and check if everything is
in accordance!

Many thanks!
Amin

On Oct 19, 8:53 pm, USPEX <us...@googlegroups.com> wrote:
> Hello,
>
> sadly no one in the USPEX developer team usesQuantumEspresso
> routinely. Though I think some of our users do. My advise would be to

> go toQuantumEspressoforums/website and learn how to do calculations

> > i want some good quaantumespressoinput files

[USPEX]

Hello,

here are the parameters, related to QuantumEspresso files (everything
else is related to algorithm and your particular system size, etc).

abinitioCode
10 10 10 10
ENDabinit

%Resolution for KPOINTS - one number per step or just one number in
total)
% KresolStart
0.16 0.14 0.12 0.10
% Kresolend

And the line number 10 in the parameter commandExecutable was :
mpirun -np 4 pw.x < qe.in > output

Of course, commandExecutable parameter depends on how you launch your
own version of QE.

Sincerely,
USPEX group

[Amin]

Dear USPEX,

Can I ask you to post the complete version of INPUT_EA.txt, associated
with your qEspresso_options_# files?
This algorithm and the code is all new to me and not everything is
clear for me at this time to complete the INPUT_EA.txt
I appreciate your help.
Thanks

[Andriy Lyakhov]

PARAMETERS EVOLUTIONARY ALGORITHM
% In this file the parameters of the evolutionary algorithm can be
set. Please keep the
% format as it is - only change the values!!!

******************************************
******************************************
* TYPE OF RUN AND SYSTEM *
******************************************
******************************************
1 : calculationType (1 = bulk, 2 = clusters, 4 = varcomp bulk, 11
= molecular crystals)
0 : chargeNeutrality
% vacuumSize (only used in cluster)
20 20 20 10 10
% endVacuumSize
2 : numberparents (only used in cluster)
% optimisation criteria
enthalpy : optType (optimise by: enthalpy, volume, hardness,
struc_order, aver_dist)

% numIons
8
% EndNumIons
% Above are numbers of ions of each type
%%%%%%%%%%%%%%%%%%%%
% Here come the atomic numbers of the atoms involved
% atomType
6
% EndAtomType
%%%%%%%%%%%%%%%%%%%%

% if we want hardness to be calculated, define the next few parameters
(valence, number of valence electrons, etc) , otherwise just put 1
% valencies
4
% endValencies

% valenceElectr
4
% endValenceElectr

% bonds with nu higher than this value are always included into
hardness formula, even if connectivity isn't increased. Need either
matrix (like minDist) or a single value
%%%%%%%%%%%%%%%%
% goodBonds
0.15
% EndGoodBonds
%%%%%%%%%%%%%%%%

0 : checkConnectivity % 1 = default; 0 - used only for big
system, switches off hardness calculation and connectivity related
criteria in softmutation

******************************************
******************************************
* POPULATION *
******************************************
******************************************
10 : populationSize (how many individuals per generation)
10 : initialPopSize (how many individuals in the first generation -
if =0 then equal to the size specified above)
3 : numGenerations (how many generations shall be calculated)
40 : stopCrit (stop when maximum AVERAGE difference between a
fitness and the best fitness of is below this value in eV)

******************************************
******************************************
% FIRST VAR. COMP. GENERATION *
******************************************
******************************************
300 : firstGeneMax (how many different compositions for first
generation - if =0 then equal to initial population size)
3 : minAt (minimum amount of atoms/cell for first generation)
30 : maxAt (maximum amount of atoms/cell for first generation)

******************************************
******************************************
* SURVIVAL OF THE FITTEST AND SELECTION *
******************************************
******************************************
5 : keepBestHM (how many structures should survive and compete in
the next generation)
2 : dynamicalBestHM (1: number of surviving structures varies
during calculations with previous parameter as upper bound; 2:
clusterisation, so that number of surviving structures is always equal
to KeepBestHM)
0 : reoptOld (should the old structures be reoptimized? 1:yes,
0:no)
1.0 : bestFrac (What fraction of current generation shall be used to
produce the next generation)

******************************************
******************************************
* VARIATION OPERATORS *
******************************************
******************************************
0.30 : fracGene (what fraction of generated individuals shall be
produced by heredity)
0.40 : fracRand (what fraction of generated individuals shall be
produced randomly from space groups specified by user)
10 : howManySliceIterations (how many slices to produce from each
parent to choose the most ordered, only matters if fingerprints are
used)
1.0 : percSliceShift (what fraction of the structures produced by
heredity shall be shifted in all dimensions)

0.0 : fracPerm (what fraction of the generated individuals shall be
produced by permutations)
5 : howManySwaps (max of the uniform, between 1 and max,
distribution of the number of swaps per MUTANT).
%%%%%%%%%%%%%%%%%%%
% The following are the swaps you want to allow. One line corresponds
to a set
% of interchangeable atoms. Refers to the ordering of the atoms. Put 0
or
% leave empty if you want to allow all kinds of interchange
% specificSwaps (write here the swaps you want to allow)

% EndSpecific
%%%%%%%%%%%%%%%%%%%

0.0 : fracTrans (what fraction of the generated individuals shall be
produced by transmutations)
0.2 : howManyTrans (max fraction of the uniform, between 0 and max,
distribution of the transmutation fraction per MUTANT; i.e. 0.3 means
that 0-30% of atoms are transumutated).
%%%%%%%%%%%%%%%%%%%
% The following are the transmutations you want to allow. One line
corresponds to a set
% of interchangeable atom identities. Refers to the ordering of the
atoms. Put 0 or
% leave empty if you want to allow all kinds of interchange

% specificTrans (write here the transmutations you want to allow)
1 2
% EndTransSpecific
%%%%%%%%%%%%%%%%%%%


0.0 : fracRotMut (only for molecules)
0.5 : sigmaRot (sigma of the gaussian distibution of rotation
angles)
3 : howManyRots (how many molecules are rotationally mutated)

0.2 : fracAtomsMut (what fraction of the generated individuals shall
be produced by atom position mutations)
% the following parameter describes the maximal fraction of the
uniform, between 0 and max, distribution of the mutation fraction per
MUTANT;
% if the number is bigger than one, then ALL atom positions are
mutated according to atom order and the parameter describes the
standard deviation
% for the maximally mutated atom positions
4.0 : mutationDegree
% softMutOnly (what generations are produced by softmutation only,
format : 1-3 5 7-9 15 etc)
12 22 32 42 52 62 72 82 92 102 112 122 132 142 152 162 172 182 192 200
% EndSoftOnly
100 : softMutTill (starting from this generation we use coormutation
as atom mutation and softmutate only one (the best) structure)

% percentage of structures produced by lattice mutation = 1.0-
(fracGene+fracPerm+fracRotMut+fracAtomsMut etc)
% so don't need to specify explicitly
0.50 : mutationRate (standard deviation of the epsilons in the strain
matrix)
1.00 : DisplaceInLatmutation

****************************************
****************************************
* CONSTRAINTS *
****************************************
****************************************

2.5 : minVectorLength ( minimal length of any lattice vector)
1 : optimDistances

%%%%%%%%%%%%%%%%
% IonDistances
0.6
% EndDistances
%%%%%%%%%%%%%%%%
% MolCenters
0
% EndMol
%%%%%%%%%%%%%%%%

% Above is the inter-atomic distance matrix of the different ion
types. IMPORTANT: If only 1 value present, this is taken as DISTANCE,
NOT radius!!!
%%%%%%%%%%%%%%%%%

*****************************************
*****************************************
* CELL *
*****************************************
*****************************************
% The following is what you know about the lattice. If you know the
lattice vectors,
% type them in as 3x3 matrix. If not, type the estimated volume.
% For variable composition - type the estimated atomic volume for each
atom type.
% Latticevalues (this word MUST stay here, type values below)
15
% Endvalues (this word MUST stay here)

% splitInto (possible number of subcells, if > 1 or more that one
value - split cell on smaller subcells; use for big number of atoms to
improve initial population)
1
% EndSplitInto

%%%%%%%%%%%%%%%%


*****************************************
*****************************************
* RESTART *
*****************************************
*****************************************
0 : pickUpYN (if pickUpYN~=0 , then a previous calculation will be
continued )
0 : pickUpGen (at which generation shall the previous calculation
be picked up? If = 0 , then a new calculation is started)
0 : pickUpFolder (number of the results folder to be used. If = 0 ,
then the highest existing number is taken)

*****************************************
*****************************************
* DETAILS OF AB INITIO CALCULATIONS *
*****************************************
*****************************************
abinitioCode (which code shall be used for calculation? Up to now:
vasp, siesta, gulp)

10 10 10 10
ENDabinit

% numProcessors (how many processors per calculation)
1 1 1 1
% EndProcessors

%Resolution for KPOINTS - one number per step or just one number in
total)
% KresolStart
0.16 0.14 0.12 0.10
% Kresolend

2:00 : wallTime (max time for each calculation)
1 : numParallelCalcs (how many parallel calculations shall be
performed)

%%%%%%%%%%%%%%%%%
% What follows is the unix command to call vasp - exactly as you would
type it in the terminal, supported: vasp, siesta, gulp, mol_gulp,
mol_siesta, MD, NeuralNetworks, mol_dmacrys, cp2k, QuantumEspresso,
mol_dlpoly, mol. VASP
% commandExecutable
mpirun -np 2 vasp-1.5 > out
siesta
./job3_gulpNP
job2
/nfs/xt3-homes/users/alyakhov/bin/siesta<input.fdf
./meam-lammps_han test.tcl
timelimit -t 400 ./OptimizeNN.x > log
timelimit -t 400 ./dmacrys <mol.res.dmain >output
mpirun -np 4 cp2k.popt cg.inp > cp2k_output

mpirun -np 4 pw.x < qe.in > output

reserved for DL POLY executable
molecular VASP
% EndExecutable
%%%%%%%%%%%%%%%%%%

1 : doSpaceGroup (0 - no space group, 1 - calculate space
groups)

*****************************************
*****************************************
* HARDWARE-RELATED *
*****************************************
*****************************************
0 : remoteRegime (0 - no remote, 1 - from Talc, 2 - remote
using specially prepared file, see manual)
nonParallel : whichCluster (on which cluster are calculations
performed? Up to now: pegasus, hreidar, gonzales, cscs, SIESTAlocal,
xcom, MVS15k, MVS50k, BJremote, Cyberia, Skif, ABAX, CFN, nonParallel)
7 : maxErrors (how many errors is one individual allowed to
produce before he is killed)

******************************************
******************************************
% REMOTE SETTINGS (only if REMOTE>1) *
******************************************
******************************************
% username (user name to login to remote supercomputer)
aroganov
% EndUsername

% RemotePath (user home folder at supercomputer)
/gpfs/home2
% EndremotePath

% PortNumber
2134
% EndportNumber

% localfolder (TALC folder)
artem
% EndLocalfolder

% remoteFolder (remote folder)
Blind_test
% EndRemoteFolder

******************************************
******************************************
% FINGERPRINTS SETTINGS *
******************************************
******************************************
0.03 : sigmaFing
0.08 : deltaFing
8.0 : RmaxFing
0.003 : toleranceFing (if distance is less than tolerance - structures
are identical)
0.030 : toleranceBestHM
1 : ordering_active % switch the use of order in variation
operators (except coormutation) on and off

% how many times to repeat the calculations with the same initial
conditions
% this option allows to make some statistics rerunning USPEX a few
times after calculations are done
% repeatForStatistics
1
% EndRepeatForStatistics
******************************************
******************************************
% MANY PARENTS SETTINGS *
******************************************
******************************************
0 : manyParents
2 : minSlice
8 : maxSlice
0.25 : maxDistHeredity
*************************************************************************
*************************************************************************
* END OF
INPUT *
*************************************************************************
*************************************************************************