Thank you very much for your cooperation in advance.
ESM.direction x # x|y|z, default=xThe default direction is the x-axis. Related information can be found in the Effective screening medium method.
scf.eigen.lib elpa1 # elpa1|elpa2, default=elpa1The default choice is ELPA1. Our benchmark calculations suggest that ELPA1 and ELPA2 are comparable to each other with respect to the computational speed. Related information can be found in the ELPA| ELPA.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
Thank you very much for your cooperation in advance.
where 128 MPI processes and 2 OpenMP threads on CRAY-XC30 were used for both the versions. It is found that Ver. 3.7 is about three times faster than Ver. 3.6 for the benchmark sets. The elapsed time for each input file can be confirmed from 'runtestL.result_xc30_v3.6' and 'runtestL.result_xc30' stored in 'work/large_example'.
% mpirun -np 128 openmx -runtestL2 -nt 4Then, OpenMX will run with 7 test files, and compare calculated results with the reference results which are stored in 'work/large2_example'. The following is a result of 'runtestL2' performed using 128 MPI processes and 4 OpenMP threads on CRAY-XC30.
1 | large2_example/C1000.dat | Elapsed time(s)= 1731.83 | diff Utot= 0.000000002838 | diff Force= 0.000000007504 |
2 | large2_example/Fe1000.dat | Elapsed time(s)=21731.24 | diff Utot= 0.000000010856 | diff Force= 0.000000000580 |
3 | large2_example/GRA1024.dat | Elapsed time(s)= 2245.67 | diff Utot= 0.000000002291 | diff Force= 0.000000015333 |
4 | large2_example/Ih-Ice1200.dat | Elapsed time(s)= 952.84 | diff Utot= 0.000000000031 | diff Force= 0.000000000213 |
5 | large2_example/Pt500.dat | Elapsed time(s)= 6831.16 | diff Utot= 0.000000002285 | diff Force= 0.000000004010 |
6 | large2_example/R-TiO2-1050.dat | Elapsed time(s)= 2259.97 | diff Utot= 0.000000000106 | diff Force= 0.000000001249 |
7 | large2_example/Si1000.dat | Elapsed time(s)= 1655.25 | diff Utot= 0.000000001615 | diff Force= 0.000000005764 |
The quality of all the calculations is at a level of production run where double valence plus a single polarization functions are allocated to each atom as basis functions. Except for 'Pt500.dat', all the systems include more than 1000 atoms, where the last number of the file name implies the number of atoms for each system, and the elapsed time implies that geometry optimization for systems consisting of 1000 atoms is possible if several hundred processor cores are available. It is noted that the parallel eigenvalue solver introduced in OpenMX Ver. 3.7 is not exactly the same as ELPA1 distributed in here. Since we found that the original ELPA1 tends to encounter a numerical instability on some platforms, we modified ELPA1 to make it stabilized. The original parallel eigenvalue solver used in OpenMX Ver. 3.6 is also available by the following keyword:
scf.eigen.lib elpa1 # elpa1|lapack, default=elpa1One can choose either 'elpa1' or 'lapack' depending on computational environment. The default is 'elpa1'. Due to the introduction of the ELPA based eigenvalue solver, users are requested to specify a FORTRAN compiler.
More information can be found in here and here.
where the diamond structure consisting of 131072 carbon atoms was considered as a benchmark system, and eight OpenMP threads were used for all the cases. The parallel efficiency is about 68 % using 131072 cores by taking the case with 16384 cores as a reference. No additional keyword is introduced for the development. The new development has been already applied to two large-scale systems, resulting in two papers: J. Chem. Phys. 136, 134101 (2012) and Modelling Simul. Mater. Sci. Eng. 21, 045012 (2013).
Related information can be found in the manual.
MD.NEB.Parallel.Number 3In this example, the calculations of every three images are parallelized at once where the MPI processes are classified to three groups and utilized for the parallelization of each image among the three images. In order to complete the calculations of all the images, the grouped calculations are repeated by floor[(the number of images)/(MD.NEB.Parallel.Number)] times. The scheme may be useful for the NEB calculation of a large-scale system. If the keyword is not specified in your input file, the default parallelization scheme is employed. Related information can be found in the manual.
#pragma optimization_level 1Then, the optimization level is always set to 1 for those routines without depending on the optimization level user defines. The other purposes of the patch can be found at README.txt.
vps.type MBKThe MBK pseudopotential is a norm-conserving version of the Vanderbilt's ultrasoft pseudopotential (Phys. Rev. B 41, 7892 (1990)). The feature allows us to take multiple states with the same angular momentum quantum number into account for construction of a separable pseudopotential. Thus, it is guranteed that the MBK scheme is more accurate than the other norm-conserving schemes when semi-core states are included in the construction of pseudopotential.
% mpirun -np 32 openmx DIA512-1.dat -nt 4 > dia512-1.std &where '-nt' means the number of threads in each process managed by MPI. If '-nt' is not specified, then the number of threads is set 1, which corresponds to the pure MPI parallelization. For the installation, please see the manual.
AtomSpecies 6.2 total.electron 6.2 valence.electron 4.2 <ocupied.electrons 1 2.0 2 2.0 2.2 ocupied.electrons>The above example is for a virtual atom on the way of carbon and nitrogen atoms. Also, it is noted that basis functions for the pseudopotential of the virtual atom must be generated for the virtual atom with the same fractional nuclear charge, since the atomic charge density stored in *.pao is used to make the neutral atom potential. As an illustration, the DOS of CN calculated using the method is shown in Fig. The input file is DIA8-VA.dat which can be found in the directory, work. In the calculation, one of eight carbon atoms in the unit cell was replaced by a virtual atom with an effective nuclear charge of 4.2, which corresponds to a stoichiometric compound of CN.
For the serial running
% ./openmx -runtestLFor the MPI parallel running
% mpirun -np 4 openmx -runtestLFor the OpenMP/MPI parallel running
% mpirun -np 4 openmx -runtestL -nt 1Then, OpenMX will run with 20 test files, and compare calculated results with the reference results which are stored in 'work/large_example'. The comparison (absolute difference in the total energy and force) is stored in a file 'runtestL.result' in the directory 'work'. Since the automatic running test requires considerable memory size, you may encounter a segmentation fault on computational environment with small memory. Also it is noted that the total elapsed time is more than 1 day even using 40 cores.
AtomSpecies 6.2 total.electron 6.2 valence.electron 4.2 <ocupied.electrons 1 2.0 2 2.0 2.2 ocupied.electrons>The above example is for a virtual atom on the way of carbon and nitrogen atoms. By just controling the above keywords, you can easily generate pseudopotentials and basis functions for virtual atoms. When you use those in OpenMX as input data, no specification by keywords is required. Please make sure that only OpenMX Ver. 3.4 or later accepts the pseudopotentials and the basis functions for the virtual atoms. Also, it is noted that basis functions for the pseudopotential of the virtual atom must be generated for the virtual atom with the same fractional nuclear charge, since the atomic charge density stored in *.pao is used to make the neutral atom potential in OpenMX.
MD.Type EF # Opt|DIIS|BFGS|RF|EF MD.Opt.DIIS.History 3 # default=3 MD.Opt.StartDIIS 5 # default=5 MD.Opt.EveryDIIS 200 # default=200 MD.maxIter 100 # default=1 MD.Opt.criterion 1.0e-4 # default=0.0003 (Hartree/bohr)Since the usages of these keywords are same as in the previous version 3.2, you can find the details in the manual of the previous version 3.2. The initial step in the optimization is automatically tuned by monitoring the maximum force in the initial structure, while it was specified by the keyword "MD.Initial.MaxStep" in the previous version 3.2 (the keyword "MD.Initial.MaxStep" is not available in OpenMX3.3). As shown in the figure which shows the number of geometry steps to achieve the maximum force of below 0.0001 hartree/bohr in molecules and bulks, in most cases the EF method seems to be the most robust and efficient scheme, while the RF method also shows a good performance.
typedef float Type_DS_VNA; /* type of DS_VNA */ #define MPI_Type_DS_VNA MPI_FLOAT /* type of DS_VNA */ typedef float Type_Orbs_Grid; /* type of Orbs_Grid */ #define MPI_Type_Orbs_Grid MPI_FLOAT /* type of Orbs_Grid */By changing 'float' and 'MPI_FLOAT' into 'double' and 'MPI_DOUBLE', it is possible to allocate them in double-precision floating point if you like it.
<SO.factor 0 1.0 1 0.5 2 2.0 SO.factor>The beginning of the description must be <SO.factor, and the last of the description must be SO.factor>. The number in the first column corresponds to that in the keyword 'pseudo.NandL', and a scaling factor is given for each pseudopotential by the second column, where '1.0' corresponds to the spin-orbit coupling in a real atom. One can control the strength of spin-orbit coupling by changing the scaling factor.
Grid_Origin xxx yyy zzzThe values will be used in the following calculations (ii) and (iii).
scf.fixed.grid xxx yyy zzzwhere 'xxx yyy zzz' is the coordinate of the origin you got in the calculation (i). Then, you will have a cube file for charge (spin) density. Let it 'A.cube'.
scf.fixed.grid xxx yyy zzzwhere 'xxx yyy zzz' is the coordinate of the origin you got in the calculation (i). Then, you will have a cube file for charge (spin) density. Let it 'B.cube'.
% gcc diff_gcube.c -lm -o diff_gcube % gcc add_gcube.c -lm -o add_gcube(v) generate a cube file for differece charge (spin) density
% ./add_gcube A.cube B.cube A_B.cubeThe file 'A_B.cube' is the cube file for the superposition of charge (spin) density of two isolated systems. Then, you can generate a cube file for the difference charge (spin) density induced by the interaction as follows:
% ./diff_gcube AB.cube A_B.cube dAB.cubeThe file 'dAB.cube' is the cube file for the difference charge (spin) density induced by the interaction, where the difference means (AB - A_B).
DATA.PATH ../DFT_DATA2006/ # default=../DFT_DATA/Both the absolute and relative specifications are available.
DosGauss.fileout on # default=off, on|off DosGauss.Num.Mesh 200 # default=200 DosGauss.Width 0.2 # default=0.2 (eV)When you use the scheme, specify 'on' for the keyword 'DosGauss.fileout'. And the keyword 'DosGauss.Num.Mesh' gives the number of partitioning for the energy range specified by the keyword 'Dos.Erange'. The keyword 'DosGauss.Width' gives the width, a, of the Gaussian exp(-(E/a)^2). The keyword 'DosGauss.fileout' and the keyword 'Dos.fileout' are mutually exclusive. Therefore, when you use the scheme the keyword, 'Dos.fileout' must be 'off' as follows:
Dos.fileout off # on|off, default=offAlso, the following two keywords are valid for both the keywords 'Dos.fileout' and 'DosGauss.file'.
Dos.Erange -20.0 20.0 # default=-20 20 Dos.Kgrid 5 5 5 # default=Kgrid1 Kgrid2 Kgrid3It should be noted that the keyword 'DosGauss.fileout' generates only the Gaussian broadening DOS, which means that the DOS by the tetrahedron method cannot be calculated by the keyword 'DosGauss.fileout'.
scf.NC.Zeeman.Spin on # on|off, default=off scf.NC.Mag.Field.Spin 1.0e+3 # default=0.0(Tesla)When you include the Zeeman term for spin magnetic moment, switch on the keyword 'scf.NC.Zeeman.Spin'. The magnitude of the uniform magnetic field can be specified by the keyword 'scf.NC.Mag.Field.Spin' in units of Tesla. Moreover, we extend the scheme as a constraint scheme in which the direction of the magnetic field can be different from each atomic site atom by atom. Then, the direction of magnetic field for spin magnetic moment can be controlled, for example, by the keyword 'Atoms.SpeciesAndCoordinates':
<Atoms.SpeciesAndCoordinates 1 Sc 0.000 0.000 0.000 6.6 4.4 10.0 50.0 160.0 20.0 1 on 2 Sc 2.000 0.000 0.000 6.6 4.4 80.0 50.0 160.0 20.0 1 on Atoms.SpeciesAndCoordinates>The 8th and 9th columns give the Euler angles, theta and phi, in order to specify the magnetic field for spin magnetic moment. The 12th column is a switch to the constraint. '1' means that the constraint is applied, and '0' no constraint. Since for each atomic site a different direction of the magnetic field can be applied, this scheme provides a way of studying non-collinear spin configuration. It is noted that the keyword 'scf.NC.Zeeman.Spin' and the keyword 'scf.Constraint.NC.Spin' are mutually exclusive. Therefore, when 'scf.NC.Zeeman.Spin' is 'on', the keyword 'scf.Constraint.NC.Spin' must be switched off as follows:
scf.Constraint.NC.Spin off # on|off, default=off(6) Zeeman term for orbital magnetic moment
scf.NC.Zeeman.Orbital on # on|off, default=off scf.NC.Mag.Field.Orbital 1.0e+3 # default=0.0(Tesla)When you include the Zeeman term for orbital magnetic moment, switch on the keyword 'scf.NC.Zeeman.Orbital'. The magnitude of the uniform magnetic field can be specified by the keyword 'scf.NC.Mag.Field.Orbital' in units of Tesla. Moreover, we extend the scheme as a constraint scheme in which the direction of the magnetic field can be different from each atomic site atom by atom. Then, the direction of magnetic field for orbital magnetic moment can be controlled, for example, by the keyword 'Atoms.SpeciesAndCoordinates':
<Atoms.SpeciesAndCoordinates 1 Sc 0.000 0.000 0.000 6.6 4.4 10.0 50.0 160.0 20.0 1 on 2 Sc 2.000 0.000 0.000 6.6 4.4 80.0 50.0 160.0 20.0 1 on Atoms.SpeciesAndCoordinates>The 10th and 11th columns give the Euler angles, theta and phi, in order to specify the magnetic field for orbital magnetic moment. The 12th column is a switch to the constraint. '1' means that the constraint is applied, and '0' no constraint. Since for each atomic site a different direction of the magnetic field can be applied, this scheme provides a way of studying non-collinear orbital configuration. Also, it is noted that the direction of magnetic field for orbital magnetic moment can be different from that for spin moment.
<Atoms.SpeciesAndCoordinates 1 Sc 0.000 0.000 0.000 6.6 4.4 10.0 50.0 160.0 20.0 1 on 2 Sc 2.000 0.000 0.000 6.6 4.4 80.0 50.0 160.0 20.0 1 on Atoms.SpeciesAndCoordinates>The specification of each column is listed as:
1: sequential serial number 2: species name 3: x-coordinate 4: y-coordinate 5: z-coordinate 6: initial occupation for up spin 7: initial occupation for down spin 8: Euler angle, theta, of the magnetic field for spin magnetic moment 9: Euler angle, phi, of the magnetic field for spin magnetic moment Also, the 8th and 9th are used to generate the initial non-collinear spin charge distribution 10: the Euler angle, theta, of the magnetic field for orbital magnetic moment 11: the Euler angle, phi, of the magnetic field for orbital magnetic moment 12: switch for the constraint schemes specified by the keywords 'scf.Constraint.NC.Spin', 'scf.NC.Zeeman.Orbital' and 'scf.NC.Zeeman.Orbital'. '1' means that the constraint is applied, and '0' no constraint. 13: switch for enhancement of orbital polarization in the LDA+U method, 'on' means that the enhancement is made, 'off' no enhancement.(8) Constrained geometry optimization and molecular dynamics
<MD.Fixed.XYZ 1 1 1 1 2 1 0 0 MD.Fixed.XYZ>The example is for a system consisting of two atoms. If you have N atoms, then you have to provide N-th rows in this specification. The 1st column is the same sequential number to spefify atom as in the specification of the keyword 'Atoms.SpeciesAndCoordinates'. The 2nd, 3rd, 4th columns are switchs for the x-, y-, z-coordinates. '1' means that the coordinate is fixed, and '0' relaxed. It should be noted that the definition of the switch is opposite compared to the previous constraint schemes. In above example, the x-, y-, z-coordinates of the atom '1' are fixed, only the x-coordinate of the atom '2' is fixed. The default setting is that all the coordinates are relaxed. The fixing of atomic positions are valid all the geometry optimizer and molecular dynamics schemes. So, the previous constraint schemes such as 'Constraint_DIIS' are replaced by a combination of the keyword 'MD.Fixed.XYZ' and the geometry optimizer and molecular dynamics schemes specified by the keyword 'MD.Type'. Then, the following schemes are now available for the keyword 'MD.Type'.
NoMD Opt DIIS NVE NVT_VS NVT_NH(9) Initial velocity for molecular dynamics
<MD.Init.Velocity 1 3000.000 0.0 0.0 2 -3000.000 0.0 0.0 MD.Init.Velocity>The example is for a system consisting of two atoms. If you have N atoms, then you have to provide N-th rows in this specification. The 1st column is the same sequential number to spefify atom as in the specification of the keyword 'Atoms.SpeciesAndCoordinates'. The 2nd, 3rd, and 4th columns are x-, y-, and z-components of the velocity of each atom. The unit of the velocity is m/s. The keyword 'MD.Init.Velocity' is compatible with the keyword 'MD.Fixed.XYZ'.
MD.Opt.DIIS.History 4 # default=4 MD.Opt.StartDIIS 5 # default=5The keyword 'MD.Opt.DIIS.History' specifies the number of the previous steps to estimate an optimum structure which will give the minimum norm of forces used. The default value is 4. Also, the geometry optimization step which starts 'DIIS' is specified by the keyword 'MD.Opt.StartDIIS'. The geometry optimization steps before starting DIIS type methods is performed by the steepest decent method as in 'Opt'. The default value is 5. For the details, see 'Section 13 Geometry optimization' in the manual.
scf.Mixing.EveryPulay # default = 5The residual vectors in the Pulay-type mixing schemes tend to become linearly dependent each other as the mixing steps accumulate, and the linear dependence among the residual vectors makes the convergence difficult. A way of avoiding the linear dependence is to do the Pulay-type mixing occasionally during the Kerker mixing. With this prescription, you can specify the frequency using the keyword 'scf.Mixing.EveryPulay'. For example, in case of 'scf.Mixing.EveryPulay=5', the Pulay-mixing is made at every five SCF iteration, while Kerker-type mixing is used at the other steps. 'scf.Mixing.EveryPulay=1' corresponds to the conventional Pulay-type mixing. It is noted that the keyword 'scf.Mixing.EveryPulay' is supported for only 'RMM-DIISK', and the default value is five. For the details, see 'Section 11 SCF convergence' in the manual.
scf.Hubbard.U on # On|Off, default=offFor the details, see 'Section 29 LDA+U' in the manual.
scf.Constraint.NC.Spin on # on|off, default=off scf.Constraint.NC.Spin.v 0.2 # default=0.0(eV)You can switch on the keyword 'scf.Constraint.NC.Spin' and give a magnitude by 'scf.Constraint.NC.Spin.v' which determines the strength of constraint, when the constraint for the spin orientation is introduced. For the details, see 'Section 30 Constraint DFT for non-collinear spin orientation' in the manual.
scf.lapack.dste dstegr # dstegr|dstedc|dstevx, default=dstegrThese lapack routines, dstegr, dstedc, and dstevx, are based on a multiple relatively robust representation (MR3) scheme (I.S.Dhillon and B.N.Parlett, SIAM J.Matrix Anal.Appl. 25, 858 (2004)), a divide and conquer (DC) algorithm (J.J.M.Cuppen, Numer.Math. 36, 177 (1981); M.Gu and S.C.Eisenstat, SIAM J.Mat.Anal.Appl. 16, 172 (1995)), and QR and inverse iteration algorithm, respectively. For further details, see the lapack website . Based on our experiences, we find that the computational speed is as follows:
dstevx < dstedc < dstegrIn contrast to the computational speed, the computational robustness seems to be opposite as follows:
dstegr < dstedc < dstevxSo, an appropriate one (robuster and faster) on your computational environment should be selected by this keyword, scf.lapack.dste.
scf.EigenvalueSolver GDC # DC|GDC|Cluster|BandBy optimizing the shell size in the divide-conquer (DC) method (W.Yang, Phys.Rev.Lett. 66, 1438 (1991)), a generalized DC method has been developed. The details will be published elsewhere.
scf.Mixing.Type Rmm-diisk # Simple|Rmm-Diis|GR-Pulay|Kerker|Rmm-DiiskSo, five mixing schemes are available in OpenMX2.3. Although a mixing is performed for density matrices (real space) in previous three mixing schemes, Simple, Rmm-Diis, and GR-Pulay, the charge mixing is made in Fourier space in these newly supported schemes, Kerker and Rmm-Diisk. So, the charge sloshing, which comes from charge components with long wave length, can be significantly suppressed by introducing Kerker's metric defined by
scf.Kerker.factor 1.0 # default=1.0A larger significantly suppresses the charge sloshing, but leads to slower convergence. Since an optimum value depends on system, you may tune an appropriate value for your system. In addition, it should be noted that the relation between 'Kerker' and 'Rmm-Diisk' schemes is the same as that between 'Simple' and 'Rmm-Diis'. Since all the keywords for 'Simple' and 'Rmm-Diis' are valid for 'Kerker' and 'Rmm-Diisk' as well, you may tune these parameters to obtain the faster convergence for your systems.
LIB = -L/usr/local/lib -fftw3If you want to use FFTW2, you need to add '-Dfftw2' for the compile option as follows:
CC = gcc -Dfftw2Since the computational time for FFT is a small fraction in the total computational time, you can use either FFTW2 or FFTW3 without loosing significant efficiency.
For serial running % ./openmx -runtest For parallel running % ./openmx -runtest "mpirun -np 4 openmx"Then, OpenMX will run with several test files, and compare calculated results with the previous results which are stored in work/input_example. The comparison (difference in the total energy and force) is stored in a file 'runtest.result'. If the difference is within last seven digits, we may consider that the installation is successful. If you want to make reference files by youself, please execute OpeMX as follows:
% ./openmx -maketestThen, for *.dat files In work/input_example, OpenMX will generate *.out files in work/input_example. So, you can add a new dat file which is used in the next running test. But, please make sure that the previous out files in work/input_example will be overwritten.
level.of.fileout 0 # default=1 (0-2)Then, any Gaussian cube or grid file is not generated.
MD.Type NVT_VS # NOMD|Opt|NVE|NVT_VS|NVT_NHThen, in this NVT molecular dynamics the temperature for nuclear motion can be controlled by
<MD.TempControl 3 100 2 1000.0 0.0 400 10 700.0 0.4 700 40 500.0 0.7 MD.TempControl>The beginning of the description must be <MD.TempControl, and the last of the description must be MD.TempControl>. The first number '3' gives the number of the following lines to control the temperature. In this case you can see that there are three lines. Following the number '3', in the consecutive lines the first column means the number of MD steps and the second column gives interval of MD steps which determine ranges of MD steps and intervals at which the velocity scaling is made. For the above example, a velocity scaling is performed at every two MD steps until 100 MD steps, at every 10 MD steps from 100 to 400 MD steps, and at every 40 MD steps from 400 to 700 MD steps. The third and fourth columns give a given temperature T_give and a scaling parameter alpha in the interval. In this velocity scaling velocities are scaled by
1: MD step 2: MD time 14: kinetic energy of nuclear motion, Ukc (Hartree) 15: DFT total energy, Utot (Hartree) 16: Utot + Ukc (Hartree) 17: Fermi energy (Hartree) 18: Given temperature for nuclear motion (K) 19: Calculated temperature for nuclear motion (K) 22: Nose-Hoover Hamitonian (Hartree)which means that the first and second columns correspond to MD step and MD time, and so on. As an example, we show a result for the velocity scaling MD of a glycine molecule (input file) in the following figure.
gnuplot> "gly_VS.ene" u 1:18 w l,"gly_VS.ene" u 1:19 w l
MD.Type NVT_NH # NOMD|Opt|NVE|NVT_VS|NVT_NHThen, in this NVT molecular dynamics the temperature for nuclear motion can be controlled by
<MD.TempControl 4 1 1000.0 100 1000.0 400 700.0 700 600.0 MD.TempControl>The beginning of the description must be <MD.TempControl, and the last of the description must be MD.TempControl>. The first number '4' gives the number of the following lines to control the temperature. In this case you can see that there are four lines. Following the number '4', in the consecutive lines the first and second columns give the number of MD steps and a given temperature for nuclear motion. The temperature between the interval is given by a linear interpolation. Although the same keyword 'MD.TempControl' as used in the velocity scaling MD is utilized in this specification, it is noted that the format is different from each other. In addition to the specification of 'MD.TempControl', you must specify a mass of heat bath by the following keyword:
NH.Mass.HeatBath 30.0 # default = 20.0In this specification, we use a unit that the weight of a proton is 1.0. Calculated quantities at every MD step are stored in an output file '*.ene' as explained in 'Velocity scaling molecular dynamics'. As an example, we show a result for Nose-Hoover MD of a glycine molecule (input file) in the following figure.
gnuplot> "gly_NH.ene" u 1:18 w l,"gly_NH.ene" u 1:19 w l
MD.Type NVE # NOMD|Opt|NVE|NVT_VS|NVT_NHIt should be noted that the old option 'Constant_Energy_MD' is not available anymore.
scf.SpinOrbit.Coupling on # On|Off, default=offIf you use a fully relativistic j-dependent pseudo potential, and set the keyword 'OFF', then the j-dependent pseudo potential are automatically averaged with a weight of j-degeneracy when it is read by OpenMX, which corresponds to a scalar relativistic pseudo potential. See also the Section 'Relativistic effects' in the manual for the details.
scf.SpinPolarization NC # On|Off|NCIf the option 'NC' is specified, wave functions are expressed by a two components spinor. An initial spin orientation of each site is given by
<Atoms.SpeciesAndCoordinates 1 Cr 1.07400 1.07400 0.00000 4.0 8.0 90.0 90.0 1 2 Cr -1.07400 1.07400 0.00000 4.0 8.0 90.0 -90.0 1 3 Cr -1.07400 -1.07400 0.00000 4.0 8.0 90.0 90.0 1 4 Cr 1.07400 -1.07400 0.00000 4.0 8.0 90.0 -90.0 1 5 Cr 0.00000 0.00000 1.90000 7.0 5.0 0.0 0.0 1 Atoms.SpeciesAndCoordinates>The Euler angles, theta and phi, to determine the spin orientation are given by the 8th and 9th columns in the specifination of '<Atoms.SpeciesAndCoordinates'. The final 10th column is a switch for determining whether the spin orientation is relaxed during the SCF calculation. '1' means that the spin orientation is relaxed. '0' means that the spin orientation is fixed at the initial orientation. See also the Section 'Non-collinear DFT' in the manual for the details.
scf.system.charge 1.0 # default=0.0The plus and minus signs correspond to hole and electron dopings, respectively. A partial charge doping is also possible. The excess charge given by the keyword 'scf.system.charge' is compensated by a uniform background opposite charge, since FFT is used to solve Poisson's equation in OpenMX.
Voronoi.charge on # on|off, default = offThe result is stored in *.out.
scf.ProExpn.VNA on # on|off, default = onIf the keyword is 'on', this means the projector expansion, otherwise the real space grid integration of the neutral atom.
eq.type dirac # sch|sdirac|diracwhere 'sch', 'sdirac', and 'dirac' mean the Schrodinger equation (no relativistic effect), a scalar relativistic treatment, and a full relativistic treatment of Dirac equation, respectively. Although eq.type=dirac means the scalar relativistic treatment in ADPACK1.3, the scalar relativistic treatment is specified by 'sdirac' in ADPACK1.5. In the scalar relativistic treatment, the coupled Dirac equations are averaged with a weight of j-degeneracy, and solved by taking account of both the majority and minority components of radial wave function. Thus, the scalar relativistic treatment includes explicitly kinematic relativistic effects (Darwin and mass velocity terms), and implicitly averaged spin-orbit coupling (no energy splitting). On the other hand, in the full relativistic treatment, j-dependent Dirac equations are solved including both the majority and minority components of radial wave function. Thus, energy splitting by spin-orbit coupling is also considered.
System.UseRestartfile YES # NO|YES, default=NO
System.Restartfile C0_Rest # default=nullIf the keyword, System.UseRestartfile, is specified as YES, a restart file which contains informations of all electron calculation is used in order to skip all electron calculation. If there is no restart file, a restart file is generated in case of System.UseRestartfile=YES. If System.UseRestartfile=YES, then the name specified by the keyword, System.Restartfile, is refered to as a restart file.
scf.XcType GGA-PBEYou can specify either the non-spin or spin polarization calculation based on GGA using the keyword, scf.SpinPolarization.
scf.Electric.Field 1.0 0.0 0.0The sign of electric field is for electrons. When the uniform external electric field is applied to a periodic system, discontinuities of the potential are introduced. For molecular systems, the discontinuities are located in the vacuum resion. Thus, numerical instabilities may not be induced. On the other hand, you might meet numerical instabilities due to the discontinuities for bulk systems.
orbitalOpt.Method speciesThe PAOs for proteins, DNA, and RNA were optimized using the constrained orbital optimization scheme.
<Atoms.SpeciesAndCoordinates 1 C 0.300000 0.000000 0.000000 2.0 2.0 0 2 H -0.889981 -0.629312 0.000000 0.5 0.5 0 3 H 0.000000 0.629312 -0.889981 0.5 0.5 1 4 H 0.000000 0.629312 0.889981 0.5 0.5 1 5 H 0.889981 -0.629312 0.000000 0.5 0.5 1 Atoms.SpeciesAndCoordinates>In the final column, 0 means that the atom is fixed at the initial position, and 1 means that the atom is relaxed. If you specify the other keywords for MD.type, then you do not need add the number in the final column.
<Atoms.SpeciesAndCoordinates 1 C 0.000000 0.000000 0.000000 2.0 2.0 2 H -0.889981 -0.629312 0.000000 0.5 0.5 3 H 0.000000 0.629312 -0.889981 0.5 0.5 4 H 0.000000 0.629312 0.889981 0.5 0.5 5 H 0.889981 -0.629312 0.000000 0.5 0.5 Atoms.SpeciesAndCoordinates>Please don't forget to attach a sequential serial number for identifying atoms in the first column.
rho_inp = rho_opt + alpha*R_opt,where alpha is a parameter, ranging from 0 to 1, which can vary automatically. When 'scf.Mixing.Type=Rmm-Diis' or 'scf.Mixing.Type=Gr-Pulay' is used, the following recipes are helpful to obtain the convergence of SCF calculations:
<log.deri.R 0 2.0 1 2.0 log.deri.R>The beginning of the description must be <log.deri.R, and the last of the description must be log.deri.R>. The first column is the angular momentum number L, and the second column is the radius at which the logarithmic derivatives of radial wave functions are evaluated.
<pseudo.NandL 0 3 0 1.8 1 3 1 2.3 2 4 0 1.8 3 4 1 2.3 pseudo.NandL>