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.
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.


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.
- 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.
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

The following links might be helpful to learn more about Quantum Espresso:
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 |
---|---|
ngauss | Type of gaussian broadening |
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 calculation. 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. | ||
&ENERGY_GRID | Broadening | Gaussian | Apply the gaussian broadening. |
Lorentzian | Apply the Lorentzian broadening. | ||
Inter-band Broadening (eV) | Determine the broadening parameter | ||
Intra-band Broadening (eV) | Determine the broadening parameter | ||
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 name | Complete name | Short description | References |
---|---|---|---|
pz | sla+pz | Perdew-Zunger LDA | J.P.Perdew and A.Zunger, PRB 23, 5048 (1981) |
bp | b88+p86 | Becke-Perdew grad.corr. | |
pw91 | sla+pw+ggx+ggc | PW91 (aka GGA) | J.P.Perdew and Y. Wang, PRB 46, 6671 (1992) |
blyp | sla+b88+lyp+blyp | BLYP | C.Lee, W.Yang, R.G.Parr, PRB 37, 785 (1988) |
pbe | sla+pw+pbx+pbc | PBE | J.P.Perdew, K.Burke, M.Ernzerhof, PRL 77, 3865 (1996) |
revpbe | sla+pw+rpb+pbc | revPBE (Zhang-Yang) | Zhang and Yang, PRL 80, 890 (1998) |
pw86pbe | sla+pw+pw86+pbc | PW86 exchange + PBE correlation | |
b86bpbe | sla+pw+b86b+pbc | B86b exchange + PBE correlation | |
pbesol | sla+pw+psx+psc | PBEsol | J.P. Perdew et al., PRL 100, 136406 (2008) |
q2d | sla+pw+q2dx+q2dc | PBEQ2D | L. Chiodo et al., PRL 108, 126402 (2012) |
hcth | nox+noc+hcth+hcth | HCTH/120 | Handy et al, JCP 109, 6264 (1998) |
olyp | nox+lyp+optx+blyp | OLYP | Handy et al, JCP 116, 5411 (2002) |
wc | sla+pw+wcx+pbc | Wu-Cohen | Z. Wu and R. E. Cohen, PRB 73, 235116 (2006) |
sogga | sla+pw+sox+pbec | SOGGA | Y. Zhao and D. G. Truhlar, JCP 128, 184109 (2008) |
optbk88 | sla+pw+obk8+p86 | optB88 | |
optb86b | sla+pw+ob86+p86 | optB86 | |
ev93 | sla+pw+evx+nogc | Engel-Vosko | Engel-Vosko, Phys. Rev. B 47, 13164 (1993) |
tpss | sla+pw+tpss+tpss | TPSS Meta-GGA | J.Tao, J.P.Perdew, V.N.Staroverov, G.E. Scuseria, PRL 91, 146401 (2003) |
m06l | nox+noc+m6lx+m6lc | M06L Meta-GGA | Y. Zhao and D. G. Truhlar, JCP 125, 194101 (2006) |
tb09 | sla+pw+tb09+tb09 | TB09 Meta-GGA | F Tran and P Blaha, Phys.Rev.Lett. 102, 226401 (2009) |
pbe0 | pb0x+pw+pb0x+pbc | PBE0 | J.P.Perdew, M. Ernzerhof, K.Burke, JCP 105, 9982 (1996) |
b86bx | pb0x+pw+b86x+pbc | B86bPBE hybrid | |
bhahlyp | pb0x+pw+b88x+blyp | Becke half-and-half LYP | |
hse | sla+pw+hse+pbc | Heyd-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). |
b3lyp | b3lp+b3lp+b3lp+b3lp | B3LYP | P.J. Stephens,F.J. Devlin,C.F. Chabalowski,M.J. Frisch, J.Phys.Chem 98, 11623 (1994) |
b3lypv1r | b3lp+b3lpv1r+b3lp+b3lp | B3LYP-VWN1-RPA | |
x3lyp | x3lp+x3lp+x3lp+x3lp | X3LYP | X. Xu, W.A Goddard III, PNAS 101, 2673 (2004) |
vwn-rpa | sla+vwn-rpa | VWN LDA using vwn1-rpa parametriz | |
gaupbe | sla+pw+gaup+pbc | Gau-PBE (also "gaup") | |
vdw-df | sla+pw+rpb +vdw1 | vdW-DF1 | M. Dion et al., PRL 92, 246401 (2004); T. Thonhauser et al., PRL 115, 136402 (2015) |
vdw-df2 | sla+pw+rw86+vdw2 | vdW-DF2 | Lee et al., Phys. Rev. B 82, 081101 (2010) |
vdw-df-c09 | sla+pw+c09x+vdw1 | vdW-DF-C09 | |
vdw-df2-c09 | sla+pw+c09x+vdw2 | vdW-DF2-C09 | |
vdw-df-obk8 | sla+pw+obk8+vdw1 | vdW-DF-obk8 (optB88-vdW) | Klimes et al, J. Phys. Cond. Matter, 22, 022201 (2010) |
vdw-df-ob86 | sla+pw+ob86+vdw1 | vdW-DF-ob86 (optB86b-vdW) | Klimes et al, Phys. Rev. B, 83, 195131 (2011) |
vdw-df2-b86r | sla+pw+b86r+vdw2 | vdW-DF2-B86R (rev-vdw-df2) | |
vdw-df-cx | sla+pw+cx13+vdW1 | vdW-DF-cx | K. Berland and P. Hyldgaard, PRB 89, 035412 (2014) |
vdw-df-cx0 | sla+pw+cx13+vdW1+HF/4 | vdW-DF-cx-0 | K. Berland, Y. Jiao, J.-H. Lee, T. Rangel, J. B. Neaton and P. Hyldgaard, J. Chem. Phys. 146, 234106 (2017) |
vdw-df2-0 | sla+pw+rw86+vdw2+HF/4 | vdW-DF2-0 | |
vdw-df2-br0 | sla+pw+b86r+vdW2+HF/4 | vdW-DF2-b86r-0 | |
vdw-df-c090 | sla+pw+c09x+vdw1+HF/4 | vdW-DF-C09-0 | |
vdw-df-x | sla+pw+????+vdwx | vdW-DF-x, reserved Thonhauser, not implemented | |
vdw-df-y | sla+pw+????+vdwy | vdW-DF-y, reserved Thonhauser, not implemented | |
vdw-df-z | sla+pw+????+vdwz | vdW-DF-z, reserved Thonhauser, not implemented | |
rvv10 | sla+pw+rw86+pbc+vv10 | rVV10 | R. 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 |
This is a brief introduction to GAMESS, the first-principle calculation code available in Material Square. For more information on how GAMESS works and possible applications, refer the official manual at https://www.msg.chem.iastate.edu/gamess/
GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Excited states can be computed by CI, EOM, or TD-DFT procedures. Nuclear gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies, with IR or Raman intensities. Solvent effects may be modeled by the discrete Effective Fragment potentials, or continuum models such as the Polarizable Continuum Model. Numerous relativistic computations are available, including infinite order two component scalar relativity corrections, with various spin-orbit coupling options.
A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, together with effective core potentials or model core potentials, so that essentially the entire periodic table can be considered.
Most computations can be performed using direct techniques, or in parallel on appropriate hardware.
This group specifies the type of wavefunction, the type of calculation, use of core potentials, spherical harmonics, coordinate choices, and similar fundamental job options.
Parameter | Value | Description | |
---|---|---|---|
SCF Type | RHF (Default) | Restricted Hartree Fock calculation | |
UHF | Unrestricted Hartree Fock calculation | ||
ROHF | Restricted open shell Hartree-Fock. | ||
MCSCF | Multiconfigurational SCF wavefunction | ||
MPLEVL | Chooses Møller-Plesset perturbation theory level, after the SCF. See $MP2, or $MRMP for MCSCF. | ||
0 (Default) | Skip the MP computation | ||
2 | Perform second order energy correction. | ||
RUN Type | ENERGY (Default) | Molecular energy without structure optimization | |
HESSIAN | Molecular energy plus gradient plus second derivatives, including harmonic vibrational analysis. See the $FORCE and $CPHF input groups. | ||
OPTIMIZE | Optimize the molecular geometry using analytic energy gradients. See $STATPT. | ||
SADPOINT | Locate saddle point (transition state). See $STATPT. | ||
RAMAN | computes Raman intensities, see $RAMAN. | ||
DFT Type | NONE (Default) | ab initio computation (Hartree-Fock Method) | |
BLYP | perform density functional theory run, using the functional specified. Please refer to the following link to look at the 'DFTTYP' tag description. https://www.msg.chem.iastate.edu/gamess/GAMESS_Manual/docs-input.txt | ||
B3LYP | |||
PBE | |||
PBE0 | |||
PW91 | |||
REVPBE | |||
TDDFT | NONE (Default) | no excited states | |
EXCITE | generate time-dependent DFT excitation energies, using the DFTTYP= functional, for RHF or UHF references. Analytic nuclear gradients are available for RHF. See $TDDFT. | ||
Charge | Total charge of the molecular system | ||
0 (Default) | Neutral | ||
+1, -1, -2, ... | monovalent cation, monovalent anion, divalent anion, ... | ||
Multiplicity | Multiplicity of the electronic state | ||
1 (Default) | Singlet | ||
2, 3, … | doublet, triplet, and so on. | ||
ISPHER | Spherical Harmonics option | ||
-1 (Default) | Use Cartesian basis functions to construct symmetry-adapted linear combination (SALC) of basis functions. The SALC space is the linear variation space used. | ||
0 | Use spherical harmonic functions to create SALC functions, which are then expressed in terms of Cartesian functions. The contaminants are not dropped, hence this option has EXACTLY the same variational space as ISPHER=-1. The only benefit to obtain from this is a population analysis in terms of pure s,p,d,f,g functions. | ||
1 | Same as ISPHER=0, but the function space is truncated to eliminate all contaminant Cartesian functions [3S(D), 3P(F), 4S(G), and 3D(G)] before constructing the SALC functions. The computation corresponds to the use of a spherical harmonic basis. | ||
PP | NONE (Default) | All electron calculation | |
SBKJC | Stevens/Basch/Krauss/Jasien/Cundari valence basis set, for Li-Rn. This choice implies an unscaled -31G basis for H-He. | ||
HW | Hay/Wadt valence basis. This is a -21 split, available Na-Xe, except for the transition metals. This implies a 3-21G basis for H-Ne. | ||
MCP | Select PP=MCP in $CONTRL to automatically use the model core potential matching your basis choice below. References for these bases, and other information about MCPs can be found in the REFS.DOC chapter. Another family covering almost all elements is available in $DATA only. | ||
READ | Read ECP potentials in the $ECP input. |
This group allows certain standard basis sets to be easily requested. Basis sets are specified by several keywords: GBASIS, NDFUNC, BASNAM, etc.
Parameter | Class | Value | Keywords | Description | Available Elements |
---|---|---|---|---|---|
BASIS | Semiempirical | AM1 | GBASIS=AM1 | selects AM1 model Hamiltonian | C, H, O, N |
PM3 | GBASIS=PM3 | selects PM3 model Hamiltonian | H, C-F, Al-Cl, Br, I | ||
Gaussian functions | STO-3G | GBASIS=STO NGAUSS=3 | Pople's STO-NG minimal basis set. | H-Xe | |
3-21G (Default) | GBASIS=N21 NGAUSS=3 | Pople's N-21G split valence basis set + 3 gaussian functions. | H-Xe | ||
6-31G* | GBASIS=N31 NGAUSS=6 NDFUNC=1 | Pople's N-31G split valence basis set + 6 gaussian functions and heavy atom polarization functions. | H-Kr | ||
6-311G** | GBASIS=N311 NGAUSS=6 NDFUNC=1 NPFUNC=1 | Pople's "triple split" N-311G basis set + 6 gaussian functions, heavy atom polarization functions, and p type polarization functions for light atom (H-He). | H-Ne | ||
6-311G**+ | GBASIS=N311 NGAUSS=6 NDFUNC=1 NPFUNC=1 DIFFSP=.TRUE. | Pople's "triple split" N-311G basis set + 6 gaussian functions, p type polarization functions for light atom (H-He), and polarizaiton function, diffuse function for heavy atoms. | H-Ne | ||
Auxiliary basis set | cc-pVDZ | GBASIS=CCD | cc-pVDZ basis | H-Ar | |
cc-pVTZ | GBASIS=CCT | cc-pVTZ basis | H-Ar | ||
aug-cc-pVDZ | GBASIS=ACCD | aug-cc-pVDZ basis | H-Ar | ||
Effective Core Potential (ECP) | SBKJC | GBASIS=SBKJC | Stevens/Basch/Krauss/Jasien/Cundari valence basis set, for Li-Rn. This choice implies an unscaled -31G basis for H-He. | H-Rn | |
Custom | def2-svp | GBASIS=d2svp EXTFIL=.TRUE. | Custom basis set for heavy metal elements | H-Rn, La-Lu | |
def2-tzvp | GBASIS=d2tzvp EXTFIL=.TRUE. | Custom basis set for heavy metal elements | H-Rn, La-Lu | ||
LANL2DZ | GBASIS=lanl2dz EXTFIL=.TRUE. | Custom basis set for heavy metal elements | H-Bi, La, U-Pu | ||
CUSTOM | GBASIS={User Define} EXTFIL=.TRUE. | Please refer to the following link to look at the 'GBASIS' tag description. https://www.msg.chem.iastate.edu/gamess/GAMESS_Manual/docs-input.txt You can download your custom basis set from Basis Set Exchange. https://www.basissetexchange.org/ | User Define |
This group controls the selection of initial molecular orbitals.
Parameter | Value | Description |
---|---|---|
Initial Orbital | Write type of initial orbital guess. | |
Huckel (Default) | Carry out an extended Huckel calculation using a Huzinaga MINI basis set, and project this onto the current basis. This is implemented for atoms up to Rn, and will work for any all electron or core potential basis set. (default for most runs) | |
HCORE | Diagonalize the one electron Hamiltonian to obtain the initial guess orbitals. This method is applicable to any basis set, but does not work as well as the HUCKEL guess. | |
MOREAD | Read in formatted vectors punched by an earlier run. This requires a $VEC deck, and you MUST pay attention to NORB below. | |
RDMINI | Read in a $VEC deck from a converged SCF calculation using GBASIS=MINI, to project the MINI orbitals onto the current basis. The option improves upon the Huckel guess because it involves SCF orbitals, which are typically easily obtained in the small MINI basis. This option doesn't work if the current basis uses core potentials. potentials. The $VEC from the MINI run must contain all virtual orbitals. | |
MOSAVED | (default for restarts) The initial orbitals are read from the DICTNRY file of the earlier run. | |
SKIP | Bypass initial orbital selection. The initial orbitals and density matrix are assumed to be in the DICTNRY file. Mostly used for RUNTYP=HESSIAN when the hessian is being read in from the input. |
This group controls solvent effect computations using the Polarizable Continuum Model.
The default calculation, chosen by selecting only the SOLVNT keyword, is to compute the electrostatic free energy. Appropriate numerical constants are provided for a wide range of solvents.
Additional keywords (ICOMP, ICAV, IDISP, or IREP/IDP) allow for more sophisticated computations, namely cavitation, repulsion, and dispersion free energies. The methodology for these is general, but numerical constants are provided only for water.
Parameter | Value | Description | |
---|---|---|---|
Solvent effect | NONE (Default) | ||
WATER | Water (H2O) | ||
CH3OH | Methanol (CH3OH) | ||
C2H5OH | Ethanol (C2H5OH) | ||
CLFORM | Chloroform (CHCl3) | ||
CTCL | Carbon Tetrachloride (CCl4) | ||
METHYCL | Methylene Chloride (CH2Cl2) | ||
12DCLET | 1,2-Dichloroethane (CH2ClCH2Cl) | ||
BENZENE | Benzene (C6H6) | ||
TOLUENE | Toluene (C6H5CH3) | ||
CYClOHEXANE | Cyclohexane (C6H12) | ||
CUSTOM | ACETONE | Acetone (CH3COCH3) | |
ANILINE | Aniline (C6H5NH2) | ||
CLBENZ | Chlorobenzene (C6H5Cl) | ||
DMSO | Dimethylsulfoxide (DMSO) | ||
NEPTANE | N-Heptane (C7H16) | ||
NITMET | Nitromethane (CH3NO2) | ||
THF | Tetrahydrofuran (THF) |
This group controls the computation of the hessian matrix (the energy second derivative tensor, also known as the force constant matrix), and an optional harmonic vibrational analysis. This can be a very time consuming calculation. However, given the force constant matrix, the vibrational analysis for an isotopically substituted molecule is very cheap. Related input is HESS= in $STATPT, and the $MASS, $HESS, $GRAD, $DIPDR, $VIB inputs. Calculation of the hessian automatically yields the dipole derivative tensor, giving IR frequencies. Raman intensities are obtained by following with RUNTYP=RAMAN.
Parameter | Value | Description |
---|---|---|
METHOD | chooses the computational method | |
ANALYTIC (Default) | ANALYTIC is a fully analytic calculation. This is implemented for SCFTYP=RHF, UHF, ROHF, GVB (for NPAIR=0 or 1, only), and MCSCF (for CISTEP=ALDET or ORMAS, only). R-DFT and U-DFT are also analytic. | |
SEMINUM | SEMINUM does numerical differentiation of analytically computed first derivatives. This is the default for UHF, MCSCF using other CISTEPs, all solvent models, relativistic corrections, and most MP2 or CI runs. | |
FULLNUM | FULLNUM numerically differentiates the energy twice, which can be used by all other cases. It requires many energies (a check run will tell how many) and so it is mainly useful for systems with only very few symmetry unique atoms. | |
Temperature (K) | 298.15 (Default) | An array of up to ten temperatures at which the thermochemistry should be printed out. The default is a single temperature, 298.15 K. To use absolute zero, input 0.001 degrees. |
This group controls the search for stationary points (ground state).
Parameter | Value | Description |
---|---|---|
Convergence tolerance (Hartree/Bohr) | 0.0001 (Default) | Gradient convergence tolerance (unit: Hartree/Bohr) Convergence of a geometry search requires the largest component of the gradient to be less than OPTTOL, and the root mean square gradient less than 1/3 of OPTTOL. |
Max iteration step | 500 (Default) | The maximum number of steps to take. Restart data is punched if NSTEP is exceeded. The default is 50 steps for a minimum search, but only 20 for a transition state search, which benefit from relatively frequent Hessian re-evaluations. |
Hessian matrix | GUESS (Default) | GUESS chooses an initial guess for the hessian. (default for RUNTYP=OPTIMIZE) |
CALC | Compute the hessian, see $FORCE input. | |
IR frequency | Flag to control automatic hessian evaluation at the end of a successful geometry search. (default=.FALSE.) |
This group generates molecular excitation energies by time-dependent density functional theory computations (or time-dependent Hartree-Fock, also known as the Random Phase Approximation).
Parameter | Value | Description |
---|---|---|
Nstate | 10 (Default) | Number of states to be found (excluding the reference state). The default is 1 more state. |
MULT | 1 (Default) | Multiplicity (1 or 3) of the singly excited states. This keyword applies only when the reference is a closed shell. This parameter is ignored when TDDFT=SPNFLP. |
Please refer to Acknowledgement page to cite the simulation packages implemented in Materials Square.
The list shows the publications which applied the calculation results obtained by the calculation package implemented in Materials Square.
- Bang, J., Moon, I. K., Choi, K., & Oh, J. (2022). Phase-engineering terraced structure of edge-rich α-Mo2C for efficient hydrogen evolution reaction. Materials Today Energy, 100981.
- Ouserigha, C. E., & Benjamin, A. K. Density Functional Theory Study on the Electronic Properties of Mg Doped FePS3.
- Park, B. C., Ko, M. J., Kim, Y. K., Kim, G. W., Kim, M. S., Koo, T. M., ... & Kim, Y. K. (2022). Surface-ligand-induced crystallographic disorder–order transition in oriented attachment for the tuneable assembly of mesocrystals. Nature Communications, 13(1), 1-11.
- Sengupta, A. (2022). First principles design of 2 dimensional Nickel dichalcogenide Janus materials NiXY (X, Y= S, Se, Te). Computational Materials Science, 206, 111278.
- Sengupta, A. (2022). First principles study of Li adsorption properties of a Borophene based hybrid 2D material B5Se. Applied Surface Science Advances, 8, 100218.
- Mishra, P. K., Viji, P., Dobhal, R., Sengupta, A., Rini, E. G., & Sen, S. (2022). Defects assisted photosensing and dye degradation of Ni/Ga co-doped ZnO: A theory added experimental investigation. Journal of Alloys and Compounds, 893, 162229.
- Lee, J., Kwon, S. Y., & Lee, J. H. (2022). Harmonically mode-locked Er-doped fiber laser at 1.3 GHz using a V2AlC MAX phase nanoparticle-based saturable absorber. Optics & Laser Technology, 145, 107525.
- Lee, G. W., Choi, Y. J., Kim, Y. H., Park, B. H., Choi, S. G., Nazarian-Samani, M., & Kim, K. B. (2022). Amorphization of germanium selenide driven by chemical interaction with carbon and realization of reversible conversion-alloying reaction for superior K-ion storage. Chemical Engineering Journal, 430, 132995.
- Enkhtuvshin, E., Kim, K. M., Kim, Y. K., Mihn, S., Kim, S. J., Jung, S. Y., ... & Han, H. (2021). Stabilizing oxygen intermediates on redox-flexible active sites in multimetallic Ni–Fe–Al–Co layered double hydroxide anodes for excellent alkaline and seawater electrolysis. Journal of Materials Chemistry A.
- Lee, J., Lee, K., & Lee, J. H. (2021). Nonlinear absorption property investigation into MAX phase Ti 2 AlC at 1.9 μm. Optical Materials Express, 11(10), 3556-3566.
- Lee, J., Kwon, S. Y., & Lee, J. H. (2021). Investigation on the nonlinear optical properties of V 2 C MXene at 1.9 μm. Journal of Materials Chemistry C, 9(42), 15346-15353.
- Lee, S., Kim, W. B., Lee, J. M., Kim, H. J., Choi, J. H., & Jung, H. S. (2021). Oxide Passivation of Halide Perovskite Resistive Memory Device: A Strategy for Overcoming Endurance Problem. ACS Applied Materials & Interfaces, 13(37), 44577-44584.
- Johnson, A., Gbaorun, F., & Ikyo, B. A. (2021). First-Principles Study of (CsMA) NaSbX6 (MA= Methylammonium; X= Cl, Br, I) Organic-Inorganic Hybrid Double Perovskites For Optoelectronic Applications.
- Sengupta, A. (2021). Lithium adsorption properties of monolayer B5Se. arXiv preprint arXiv:2101.08462.
- Sengupta, A. (2021). An ab-initio study of 2 dimensional metal (Cu, Ag)-1T’ReS 2 van der Waals heterostructure. 2021 Devices for Integrated Circuit (DevIC), 221-223.
- Sengupta, A. (2021). First principles design of 2 dimensional Nickel dichalcogenide Janus materials NiXY. arXiv preprint arXiv:2110.08593.
- Kwon, S. Y., Lee, J., & Lee, J. H. (2021). Passive mode-locking by a Ti2AlN saturable absorber in 1.5 μm region. Optik, 168364.
- Choi, Y. J., Lee, G. W., Kim, Y. H., Kim, H. K., & Kim, K. B. (2021). Graphene with Nanoperforation for High-Capacity Potassium-Ion Storage: Decoupling Structural Defect and Doping Effects of N-doped Graphene. Chemical Engineering Journal, 134260.
- Esfandiari, A., Haghighat-Shishavan, S., Nazarian-Samani, M., Nazarian-Samani, M., Ramakrishna, S., Kashani-Bozorg, S. F., & Kim, K. B. (2020). Defect-rich Ni3Sn4 quantum dots anchored on graphene sheets exhibiting unexpected reversible conversion reactions with exceptional lithium and sodium storage performance. Applied Surface Science, 526, 146756.
- Haghighat-Shishavan, S., Nazarian-Samani, M., Nazarian-Samani, M., Roh, H. K., Chung, K. Y., Oh, S. H., ... & Kim, K. B. (2019). Exceptionally reversible Li-/Na-ion storage and ultrastable solid-electrolyte interphase in layered GeP5 anode. ACS applied materials & interfaces, 11(36), 32815-32825.
- Kilic, M. E., Lee, J. H., & Lee, K. R. (2021). Oxygen ion transport in doped ceria: effect of vacancy trapping. Journal of Materials Chemistry A.