 MatSQ Docs - Appendix (Eng)

MatSQ provides a tutorial video for users who are not familiar with the service.

How would you simulate materials used in your research with DFT? DFT can compute electronic structures for only a few to dozens of models because of the limitations of computing performance. Periodic boundary conditions were introduced as a way of overcoming these limitations and simulating a bulk condition similar to the macroscopic system. In periodic boundary conditions, a material is defined as follows: In periodic boundary conditions, a structure is repeated infinitely, so a silicon unit cell with eight atoms, a silicon supercell with 32 atoms, and a silicon bulk are theoretically identical. Moreover, because atoms are repeated by the space-group rules within the unit cell, silicon unit cells can be modeled only with the following information: The computer recognizes a calculation model with a view that the structure shown on Structure Builder is repeated infinitely. If the cell size increases because of increased vacuum, the vacuum is recognized as repetitive, and the calculation is performed in the vacuum space too, so the amount of computation also increases. Roughly speaking, computational cost is proportional to V N (2 < N < 3), as the number of basis functions (plane waves) proportional to the volume of periodic unit cell. If you add a vacuum to model an atom, molecule, or slab structure, it is appropriate to have 10 to 15 Å clearance with the next repetitive model. You can check the repetitive structure by ticking "Ghost" in the right-click menu in the Visualizer Canvas of Structure Builder.

You can obtain the information or structure file required for unit cell modeling at the following link:

The following section gives a brief introduction to Quantum Espresso (QE), one of the DFT codes available on Materials Squire to run materials simulations. To understand in detail how Quantum Espresso works and what it can do, we recommend reading the documentation provided at www.quantum-espresso.org.

Quantum Espresso is an integrated suite of open-source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on the density-functional theory (DFT), plane waves, and pseudopotentials.
• The Quantum Espresso package is an expandable distribution of related packages. Two core packages for DFT electronic structure calculations, PWscf (Plane Wave self-consistent field), and CP (Car-Parrinello Molecular Dynamics) are supplemented by various packages for specialized applications as well as plug-ins. For more information on all packages, refer to the Quantum Espresso official user guide .
• Quantum Espresso provides open-source software packages. This means that everyone can study, expand, and modify the source code, allowing for continuous improvement.
• The theory behind Quantum Espresso’s algorithm for electronic structure calculations and materials modeling is determined by the Kohn-Sham density functional theory (KS-DFT). In other words, the code implements the common iterative self-consistent method to solve the Kohn-Sham equations.
• To perform materials simulations by a computer, we must expand functions like the wave function or the electron density in a basis set. Quantum Espresso uses plane waves as a basis set under the Bloch’s theorem. For the Gamma point, it is a Fourier series expansion of functions. A finite number of expansion coefficients, which is required for computation, can be achieved by an energy cutoff (ecutwfc, ecutrho).
• Pseudopotentials are used to smoothen the Coulomb potential by atomic nucleis, resulting in fewer plane waves, without affecting the result too much. Quantum Espresso allows the use of various pseudopotentials (norm-conserving, ultrasoft, PAW). Choosing the pseudopotential for a given system is a science in itself. Refer to the Quantum Espresso documentation for further information.
Quantum Espresso is written mostly in Fortran-90. The code enables parallel computing.

Based on DFT, Quantum Espresso has numerous applications, ranging from ground-state energy calculations and structural optimization to molecular dynamics as well as the modeling of response and spectroscopic properties. DFT simulations can be done on any crystal structure or supercell, which features some form of periodicity. Furthermore, Quantum Espresso works for insulators, semiconductors, and metals, offering different options for k-point sampling as well as smearing of energy states. To speed up computations, Quantum Espresso can deal with various pseudopotentials and approximate exchange-correlation functionals. For more information, visit the Quantum Espresso website .

The Quantum Espresso input script contains all information about the system of interest and defines the calculation process. The information consists of the namelist and input_cards. The following figure shows the general syntax of the input script. The Quantum Espresso code is a collection of input variables, which specify all information in a definitive format. Input variables can be real, integer, or character (string) values and must be entered in the syntax shown below. If an input parameter is not explicitly stated in the input script, it will be assigned with the default value. Refer to the Quantum Espresso pw.x description to see a complete set of input variables used in the PWscf (pw.x) calculations. There are three mandatory namelists in the PWscf package:
• It lists input variables that control the calculation process or determine the number of I/O. Examples include the calculation type, information amount (verbosity), and directory.
• It includes input variables that determine the calculation system such as the number of atoms, Bravais lattice index, cutoff energies, and smearing methods.
• It controls the algorithms used to reach the self-consistent solution of Kohn-Sham equations. Examples include the convergence threshold for self-consistency and mixing beta.
In addition to the above mandatory namelists, some calculations require the following namelists:
• If the nuclei of the system are allowed to move in a calculation, this namelist contains necessary variables to control their motion. Variable atomic positions occur in molecular dynamics or structural relaxation computations.
• Similar to &IONS, this namelist must be included for calculations with variable cell dimensions.
Quantum Espresso reads namelists in a specific order, whereas keywords (variables, keywords, tags) in each namelist can be inserted in an arbitrary order. Unnecessary namelists, such as &CELL in an scf calculation, is ignored.

For some input data, such as atomic coordinates, it is inconvenient to write it in the namelist syntax. To make life easier, Quantum Espresso, therefore, features input_cards that allow you to enter data in a more practical format. There are three mandatory input_cards to be entered:
• Lists the name, mass, and PP of the atomic species included in a calculation model
• Lists the name and coordinates of all atoms in a calculation model
• Refers to the k-point grid and shift information, which are used to determine the number of k-points to be sampled in each lattice direction
CELL_PARAMETERS and OCCUPATIONS input cards do not have a specific order, but the data in each input card must follow a specific format to be read correctly. The following figure displays an example of the input script used in a graphene unit cell model. For more information on the input_card, refer to the PWscf input description . Parameter Value Description
Calculation type scf It performs self-consistent field calculations without affecting the atoms’ position. Namelists &IONS and &CELL are ignored in calculations. An iterative solution process runs to calculate the total energy, forces, and stresses.
relax In a relax calculation, the atoms are allowed to move to find their minimum energy (structural optimization). Includes geometric optimization steps and iterative self-consistent field calculations.
vc-relax It optimizes the structure for the atom position and the cell. The cell shape (angles, lattice constants) may change to find the optimized structure. It also includes geometric optimization steps and iterative self-consistent field calculations.
(vc-)md It calculates molecular dynamics with DFT. (ab-initio MD, AIMD)
restart nscf It performs non-scf calculations. Using this scheme, you make a single step calculation with the superposition of atomic orbitals. In contrast with the scf calculation, unoccupied electron states are also considered. Therefore, an nscf calculation is an economical choice for calculations that require a large k-point sampling.
bands It calculates only the Kohn-Sham states for the given set of k-points.
Max scf steps It determines the maximum number of scf algorithm runs until convergence is reached (scf is fixed to 1 unconditionally).
Information amount low Default
high It adds detailed information about k-points or the character table to a job.stdout file.
Force threshold It is the convergence threshold for the force to an ionic minimization. Any force for all elements must be less than this value (3.8E-4 Ry/Bohr = 0.01 eV/Å ).
Time step It sets the time step for an MD simulation (atomic unit, 1 a.u. = 4.8378*10^-17 s).

Parameter Value Description
occupations smearing It performs Gaussian smearing of occupation numbers on the assumption that an electron would occupy up to a point slightly above the balance band (suitable for metals).
fixed It calculates without smearing on the assumption that the structure is an insulator.
tetrahedra The tetrahedron method (P.E. Bloechl, PRB 49, 16223 (1994)) is used, which is suitable for DOS calculations. It must use a Monkhorst’s pack (automatic) k-point.
Ecut(wfc) It is the kinetic energy cutoffs for wave functions.
Ecut(rho) It is the kinetic energy cutoffs for charge densities and potentials. The default value is "ecutrho = 4*ecutwfc". Norm-conserving potentials and ultrasoft pseudopotentials require a higher ecut (rho) (about 8 to 12 times ecutwfc).
Gaussian broadeing It is the value required for Gaussian spreading in the Brillouin zone (broadening similar to '0.002 Ry = 27E-3eV = approx.300 K').
Number of electron spin 1 (all up) It calculates without considering the spin.
2 (up, down) It calculates taking into account the spin polarization. The amount of calculation doubles the case of "nspin=1."
4 (Noncolinear) It is used in noncollinear cases.
Van der Walls correction It is used to compensate data for models that are significantly affected by the Van der Waals force, such as a layered structure.
grimme-d2 (DFT-D) It corrects by the semi-empirical Grimme’s DFT-D2 method (S. Grimme, J. Comp. Chem. 27, 1787 (2006), V. Barone et al., J. Comp. Chem. 30, 934 (2009)).
grimme-d3 (DFT-D3) It corrects by the semi-empirical Grimme’s DFT-D3 method (S. Grimme et al., J. Chem. Phys 132, 154104 (2010)).
tkatchenko-scheffler It corrects the Tkatchenko-Scheffler dispersion with the C6 coefficient induced by the first principles (A. Tkatchenko and M. Scheffler, PRL 102, 073005 (2009)).
XDM It performs corrections with the exchange-hole dipole-moment model (A. D. Becke et al., J. Chem. Phys. 127, 154108 (2007), A. Otero de la Roza et al., J. Chem. Phys. 136, 174109 (2012)).
Hubbard_U the U parameter for the element of interest.

Parameter Value Description
Max iteration step Within an scf step, it sets the maximum step value for iteration, which continues until the convergence is completed. It is recommended to increase this value for structures with poor convergence.
Mixing beta The rate at which the final electron density is mixed with the initial electron density under the scf algorithm. It is recommended to decrease this value for structures with poor convergence.
Convergence threshold The value that sets the convergence threshold, which is the limit of the energy difference before and after an scf step.
Mixing mode plain The Broyden charge density mixing method
TF It adds a simple Thomas-Fermi screening (applicable to highly consistent systems).
local-TF It screens TF depending on the local density (applicable to highly consistent systems).
Starting wavefunction atomic It starts wave function calculations from the superposition of atomic orbitals. Calculations are performed normally in most cases, but some fail occasionally.
atomic+random In addition to the superposition of atomic orbitals, it considers random wave functions.
random It starts a calculation with random wave functions. It has a slower but safer start of scf.

Parameter Value Description
Ion dynamics It specifies the algorithm in Structural Relaxation to consider atomic movement.
relax bfgs It uses the BFGS quasi-newton algorithm for structural relaxation; cell_dynamics must be "bfgs" too. (Default).
damp It uses damped (quick-min Verlet) dynamics for structural relaxation.
vc-relax bfgs It uses BFGS quasi-newton algorithm; cell_dynamics must be "bfgs" too.
damp It uses damped (Beeman) dynamics for structural relaxation
md verlet It uses the Verlet algorithm to integrate Newton’s equation (Default).
langevin The ion dynamics is the overdamped Langevin.
langevin-smc The overdamped Langevin with Smart Monte Carlo (R.J. Rossky, JCP, 69, 4628 (1978)).
vc-md beeman It uses Beeman’s algorithm to integrate Newton’s equations (Default).
upscale It reduces conv_thr by conv_thr/upscale during structural optimization to increase accuracy when the relaxation approaches convergence (available in the bfgs option only).
Ion temperature (vc-)md not_controlled It does not control ionic temperatures (Default).
rescaling It controls ionic temperatures via velocity rescaling (first method).
md rescale-v It controls ionic temperatures via velocity rescaling (second method).
rescale-T It controls ionic temperatures via velocity rescaling (third method).
reduce-T It reduces ionic temperatures for every nraise step by the ΔT value.
berendsen It controls ionic temperatures with "soft" velocity rescaling.
andersen It controls ionic temperatures with the Andersen thermostat method.
initial It initializes ion temperatures to the starting temperature and leaves uncontrolled further on.
Starting temperature (K) The starting temperature in MD simulations.
ΔT Ion temperature = "rescale-T": At each step, the instantaneous temperature is multiplied by ΔT.
Ion temperature = "reduce-T": In every "nraise" step, the instantaneous temperature is reduced by ΔT.
nraise It rescales the instantaneous temperature (https://www.quantum-espresso.org/Doc/INPUT_PW.html#idm938).

Parameter Value Description
Cell dynamics It specifies the type of algorithms for variable cell relaxations to control the cell size.
bfgs The BFGS quasi-newton algorithm; ion_dynamics must be "bfgs" too.
none no dynamics
sd It is the steepest descent (not implemented).
damp-pr It is the damped (Beeman) dynamics of the Parrinello-Rahman extended lagrangian.
damp-w It is the damped (Beeman) dynamics of the new Wentzcovitch extended lagrangian.
Cell factor It is the maximum strain ratio of the cell size.
Press threshold It is the convergence threshold of the pressure applied to cells (Kbar).

Parameter Value Description
Sampling automatic It is an option to sample k-points in the Monkhorst-Pack method. It also distributes the k-point grid evenly to the supercell.
GAMMA It is similar to automatic 1x1x1 in that only one k-point is sampled, but there is a difference: the k-point is recognized as real rather than a complex number. It has the benefit of fast calculation.
crystal(_b) It designates the k-point as the relative coordinates to the reciprocal lattice vector. If the last column of data is {crystal}, it represents the weight for each k-point. If the last column of data is {crystal_b}, it represents the k-point number to be sampled by the next crystal coordination.
# k-points It is the number of k-points in the direction of the three lattice vectors, respectively.
shift It shifts the k-point grid with respect to the origin. Depending on the symmetry of the supercell, shifting the k-points could lead to better results.
crystal(_b) Path You can use a high-symmetric point to set the path for k-point sampling. You have to enter the weight.
weight crystal: the weight for each k-point to have
crystal_b: the number of k-points to be sampled until the next k-point

Option Description
degauss Decide how much Gaussian Broadening will be done. You should note that the unit is Ry, not eV!
DeltaE Energy grid step (eV)
Emin Minimum of energy (eV) for DOS plot
Emax Maximum of energy (eV) for DOS plot

Option Description
spin_component Detemine the kind of spin when plotting the Band structure. In this time, the 'Spin-down' option can be selected when you performed the spin-polarized calculation.
lsym The bands will be classified according to the irreducible representation with considering the symmetry of k-points, if it set as '.TRUE.'.

Section Option Description
&INPUTPP Data to plot Detemine the data to obtain from the pp.x calculaiton. For further information, please refer to the link.
https://www.quantum-espresso.org/Doc/INPUT_PP.html#idm24
Planar/Macroscopic Average The number of points Set the density of datapoint of the result graph.
The size of the window Determine the number of the slab.

Section Option Value Description
&INPUTPP calculation eps Compute the complex macroscopic dielectric function, at the RPA (Random phase approximation) level, neglecting local field effects. eps is computed both on the real or imaginary axis.
jdos Compute the optical joint density of states.
Frequency Range (eV) Determine the Frequency range
Frequency Mesh Set the number of datapoints
Optional Rigid Shift Give shift when calculating the transition energy.

This is the entire list of functions available in Quantum Espresso. Put 'Short name' in the DFT Functional input field.

Short nameComplete nameShort descriptionReferences
pzsla+pzPerdew-Zunger LDAJ.P.Perdew and A.Zunger, PRB 23, 5048 (1981)
pw91sla+pw+ggx+ggcPW91 (aka GGA)J.P.Perdew and Y. Wang, PRB 46, 6671 (1992)
blypsla+b88+lyp+blypBLYPC.Lee, W.Yang, R.G.Parr, PRB 37, 785 (1988)
pbesla+pw+pbx+pbcPBEJ.P.Perdew, K.Burke, M.Ernzerhof, PRL 77, 3865 (1996)
revpbesla+pw+rpb+pbcrevPBE (Zhang-Yang)Zhang and Yang, PRL 80, 890 (1998)
pw86pbesla+pw+pw86+pbcPW86 exchange + PBE correlation
b86bpbesla+pw+b86b+pbcB86b exchange + PBE correlation
pbesolsla+pw+psx+pscPBEsolJ.P. Perdew et al., PRL 100, 136406 (2008)
q2dsla+pw+q2dx+q2dcPBEQ2DL. Chiodo et al., PRL 108, 126402 (2012)
hcthnox+noc+hcth+hcthHCTH/120Handy et al, JCP 109, 6264 (1998)
olypnox+lyp+optx+blypOLYPHandy et al, JCP 116, 5411 (2002)
wcsla+pw+wcx+pbcWu-CohenZ. Wu and R. E. Cohen, PRB 73, 235116 (2006)
soggasla+pw+sox+pbecSOGGAY. Zhao and D. G. Truhlar, JCP 128, 184109 (2008)
optbk88sla+pw+obk8+p86 optB88
optb86bsla+pw+ob86+p86 optB86
ev93sla+pw+evx+nogcEngel-VoskoEngel-Vosko, Phys. Rev. B 47, 13164 (1993)
tpsssla+pw+tpss+tpssTPSS Meta-GGAJ.Tao, J.P.Perdew, V.N.Staroverov, G.E. Scuseria, PRL 91, 146401 (2003)
m06lnox+noc+m6lx+m6lcM06L Meta-GGAY. Zhao and D. G. Truhlar, JCP 125, 194101 (2006)
tb09sla+pw+tb09+tb09TB09 Meta-GGAF Tran and P Blaha, Phys.Rev.Lett. 102, 226401 (2009)
pbe0pb0x+pw+pb0x+pbcPBE0J.P.Perdew, M. Ernzerhof, K.Burke, JCP 105, 9982 (1996)
b86bxpb0x+pw+b86x+pbcB86bPBE hybrid
bhahlyppb0x+pw+b88x+blypBecke half-and-half LYP
hsesla+pw+hse+pbcHeyd-Scuseria-Ernzerhof (HSE 06, see note below)Heyd, Scuseria, Ernzerhof, J. Chem. Phys. 118, 8207 (2003); Heyd, Scuseria, Ernzerhof, J. Chem. Phys. 124, 219906 (2006).
b3lypb3lp+b3lp+b3lp+b3lpB3LYPP.J. Stephens,F.J. Devlin,C.F. Chabalowski,M.J. Frisch, J.Phys.Chem 98, 11623 (1994)
b3lypv1rb3lp+b3lpv1r+b3lp+b3lpB3LYP-VWN1-RPA
x3lypx3lp+x3lp+x3lp+x3lpX3LYPX. Xu, W.A Goddard III, PNAS 101, 2673 (2004)
vwn-rpasla+vwn-rpaVWN LDA using vwn1-rpa parametriz
gaupbesla+pw+gaup+pbcGau-PBE (also "gaup")
vdw-dfsla+pw+rpb +vdw1 vdW-DF1M. Dion et al., PRL 92, 246401 (2004); T. Thonhauser et al., PRL 115, 136402 (2015)
vdw-df2sla+pw+rw86+vdw2 vdW-DF2Lee et al., Phys. Rev. B 82, 081101 (2010)
vdw-df-c09sla+pw+c09x+vdw1 vdW-DF-C09
vdw-df2-c09sla+pw+c09x+vdw2 vdW-DF2-C09
vdw-df-obk8sla+pw+obk8+vdw1 vdW-DF-obk8 (optB88-vdW)Klimes et al, J. Phys. Cond. Matter, 22, 022201 (2010)
vdw-df-ob86sla+pw+ob86+vdw1 vdW-DF-ob86 (optB86b-vdW)Klimes et al, Phys. Rev. B, 83, 195131 (2011)
vdw-df2-b86rsla+pw+b86r+vdw2 vdW-DF2-B86R (rev-vdw-df2)
vdw-df-cxsla+pw+cx13+vdW1 vdW-DF-cxK. Berland and P. Hyldgaard, PRB 89, 035412 (2014)
vdw-df-cx0sla+pw+cx13+vdW1+HF/4 vdW-DF-cx-0K. Berland, Y. Jiao, J.-H. Lee, T. Rangel, J. B. Neaton and P. Hyldgaard, J. Chem. Phys. 146, 234106 (2017)
vdw-df2-0sla+pw+rw86+vdw2+HF/4 vdW-DF2-0
vdw-df2-br0sla+pw+b86r+vdW2+HF/4 vdW-DF2-b86r-0
vdw-df-c090sla+pw+c09x+vdw1+HF/4 vdW-DF-C09-0
vdw-df-xsla+pw+????+vdwx vdW-DF-x, reserved Thonhauser, not implemented
vdw-df-ysla+pw+????+vdwy vdW-DF-y, reserved Thonhauser, not implemented
vdw-df-zsla+pw+????+vdwz vdW-DF-z, reserved Thonhauser, not implemented
rvv10sla+pw+rw86+pbc+vv10rVV10R. Sabatini et al. Phys. Rev. B 87, 041108(R) (2013)

This is a brief introduction to LAMMPS, the molecular dynamics code available in Material Square. For more information on how LAMMPS works and possible applications, refer the official manual at lammps.sandia.gov..

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation code, developed at the Sandia National Laboratory, it designed to be calculated effectively with parallel computing. Base on Newton's equation of motion, LAMMPS can calculate a system consists of several hundred to several billion atoms using forcefield for fast speed. It can calculate not only the stability at the given temperature which is a basic property in the materials study, but also mechanical, thermal and chemical properties of material. Recently, the effectivity of parallel computing using the Graphics Processing Unit (GPU) was increased, and machine learning can be used for the expanding interatomic potential.

Parameter Value Description
Reactive Forcefield ID The identification value of each reactive forcefield
Type The type of reactive forcefield
Elements Elements for the reactive forcefield to consider
Author The author of the reactive forcefield
DOI The paper on the corresponding reactive forcefield
Ensemble NVT An NVT ensemble is also known as the canonical ensemble. It assumes a calculation model as an isolated system, which has a fixed temperature, volume, and the number of atoms.
NVE An NVE ensemble is also known as the microcanonical ensemble. This assumes a calculation model as an isolated system, which cannot exchange energy or particles with its environment because the energy of the system is fixed.
After Relax Before starting an MD simulation, a structural relaxation is performed at room temperature (200 K – 300 K) first for structural stabilization. It can reduce the probability that the calculation would fail because of structural instability.
Dump It saves the trajectory in a file for every step selected. For calculations with long simulation times, you can reduce the overall file size.
Temperature Begin (K) The temperature at the start of a simulation
Final (K) The target temperature during simulation
Damping (Step) Resets the temperature for each damping step
Time (ps) Specifies the total simulation time (1 ns = 1000 ps)
Initial Velocity (Å/fs) The initial speed of the atom group selected
Force (Kcal/mole-Å) The force per fs applied to the selected atom group
Move (Linear, Å/fs) The distance traveled per fs for the selected atom group

First-principles calculations were performed using Quantum ESPRESSO package implemented in Materials Square.
----
 Quantum ESPRESSO. https://www.quantum-espresso.org/
 Virtual Lab. Inc., (2017, January 01). Materials Square. https://www.materialssquare.com/

The list shows the publications which applied the calculation results obtained by the calculation package implemented in Materials Square.

• ACS Appl. Mater. Interfaces 2019, 11, 36, 32815–32825, Safa Haghighat-Shishavan, et al., "Exceptionally Reversible Li-/Na-Ion Storage and litrastable Solid-Electrolyte Interphase in Layered GeP5 Anode"
• Appl. Surf. Sci., 526, 146756 (2020), Alaleh Esfandiari et al., "Defect-rich Ni3Sn4 quantum dots anchored on graphene sheets exhibiting unexpected reversible conversion reactions with exceptional lithium and sodium storage performance"
• arXiv:2101.08462, Amretashis Sengupta, "Lithium adsorption properties of monolayer B5Se"
• Sci. Rep., 11, 9320 (2021), JH Lee et al., "Nonlinear optical property measurements of rhenium diselenide used for litrafast fiber laser mode-locking at 1.9 μm"

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