OpenMX

https://openmx-square.org/openmx_man3.9/
Admin
OpenMX is a software package for large-scale ab initio molecular dynamics simulations based on...
Tokens:108,171
Snippets:886
Trust Score:8.7
Update:8 months ago
Show doc for...
Tokens:
Raw
### Example kpoint.in File Structure

Source: https://openmx-square.org/openmx_man3.9/node179

This is an example of the 'kpoint.in' file content, which specifies the k-points and band indices for the MulPOnly calculation. Each line contains the x, y, and z coordinates of a k-point, followed by the band index.

```data
40 0.18 55   <- # of k-points; radius; state (band index) (outer circle in k-space)
40 0.15 56   <- # of k-points; radius; state (band index) (inner circle in k-space)
0            <- exit

80
0.00000000000000 0.18000000000000 0.00000000000000 55
0.00000000000000 0.17778390130712 0.02815820370724 55
0.00000000000000 0.17119017293313 0.05562305898749 55
0.00000000000000 0.16038117435391 0.08171828995312 55
0.00000000000000 0.14562305898749 0.10580134541265 55
0.00000000000000 0.12727922061358 0.12727922061358 55
0.00000000000000 0.10580134541265 0.14562305898749 55
0.00000000000000 0.08171828995312 0.16038117435391 55
0.00000000000000 0.05562305898749 0.17119017293313 55
0.00000000000000 0.02815820370724 0.17778390130712 55
0.00000000000000 0.00000000000000 0.18000000000000 55
0.00000000000000 -0.02815820370724 0.17778390130712 55
...
```

--------------------------------

### Specifying Fortran Library Paths

Source: https://openmx-square.org/openmx_man3.9/node14

Examples of how to explicitly specify the Fortran library path in the LIB variable to resolve linker errors.

```makefile
LIB= ... -L/opt/intel/fce/10.0.026/lib -lifcore (with the Intel compiler)
LIB= ... -L/opt/pgi/linux86-64/7.0/lib -pgf90libs (with the PGI compiler)
LIB= ... -L/usr/lib -lgfortran (with the GNU compiler)
```

--------------------------------

### Common Linker Errors

Source: https://openmx-square.org/openmx_man3.9/node14

Examples of common linker errors encountered during the build process, indicating missing libraries.

```shell
/usr/bin/ld: cannot find -lifcore

/usr/bin/ld: cannot find -lpgf90

     -lpgf90_rpm1, -lpgf902, -lpgf90rtl, -lpgftnrtl

      /usr/bin/ld: cannot find -lgfortran
```

--------------------------------

### JX Tool Output for Bulk Calculation

Source: https://openmx-square.org/openmx_man3.9/node125

This is an example output from the 'jx' tool for a bulk calculation. It provides details about the SCF solver, system properties, and the calculated exchange coupling constants (J) for a periodic structure, including contributions from different k-grid points.

```text
********************************************************************
********************************************************************
 jx: code for calculating an effective exchange coupling constant J 
 Copyright (C), 2003, Myung Joon Han, Jaejun Yu, and Taisuke Ozaki 
                 2019, Asako Terasawa and Taisuke Ozaki 
 This is free software, and you are welcome to         
redistribute it under the constitution of the GNU-GPL.
********************************************************************
********************************************************************

 Read the scfout file (Fe_Bulk_jx.scfout)
 ***
 The file format of the SCFOUT file:  3
 And it supports the following functions:
 - jx
 - polB
 - kSpin
 - Z2FH
 - calB
 ***

  Previous eigenvalue solver = Band
  atomnum                    = 2
  ChemP                      = -0.205912787451 (Hartree)
  E_Temp                     = 300.000000000000 (K)

  Jij calculation for a periodic structure
    Number of k-grids: 27 27 27 
    flag_periodic_sum = 0: coupling between site i at cell 0 and site j at cell R 
      Number of poles of Fermi-Dirac continued fraction (PRB.75.035123): 60

     i     j    c1    c2    c3            J [meV]            J [mRy]   time_eig [s] ...
 ---------------------------------------------------------------------------------- ...
     1     1    -2    -2    -2    -0.845809571401    -0.062165857439        0.51534 ...
     1     1    -2    -2    -1     0.274300677331     0.020160728111        0.00000 ...
     1     1    -2    -2     0     0.036006012552     0.002646393135        0.00000 ...
     1     1    -2    -2     1     0.274300705154     0.020160730156        0.00000 ...
     1     1    -2    -2     2    -0.845809596417    -0.062165859278        0.00000 ...
     1     1    -2    -1    -2     0.274300737539     0.020160732536        0.00000 ...
     1     1    -2    -1    -1    -0.206315672897    -0.015163922403        0.00000 ...
     1     1    -2    -1     0     0.149714301525     0.011003798302        0.00000 ...
     1     1    -2    -1     1    -0.206315540488    -0.015163912672        0.00000 ...
     1     1    -2    -1     2     0.274300804604     0.020160737465        0.00000 ...
     ...
     ..
     2     2     0    -1     2     0.149714016159     0.011003777328        0.00000 ...
     2     2     0     0    -2     0.401809366424     0.029532443987        0.00000 ...
     2     2     0     0    -1    11.452192349598     0.841720620155        0.00000 ...

  Elapsed time = 340.817975 (s)

```

--------------------------------

### jx.config File Example for OpenMX

Source: https://openmx-square.org/openmx_man3.9/node123

An example configuration file ('jx.config') for the jx execution in OpenMX. This file specifies parameters for periodic summation, number of poles, k-grid dimensions, and ij pairs.

```config
Flag.PeriodicSum           off       # default - off
Num.Poles                  60 
Num.Kgrid                  27 27 27
Num.ij.pairs               236
Bunch.ij.pairs             236
<ijpairs.cellid
  1 1 -2 -2 -2
  1 1 -2 -2 -1
  1 1 -2 -2 0
   ...
   ...
  2 2 0 -1 2
  2 2 0 0 -2
  2 2 0 0 -1
ijpairs.cellid>
```

--------------------------------

### kSpin Tool Output Header

Source: https://openmx-square.org/openmx_man3.9/node179

This is a typical output header from the kSpin tool, indicating the start of the calculation. It includes copyright information, licensing details, and a citation for the relevant research paper.

```text
******************************************************************
******************************************************************
 kSpin:
 code for evaluating spin related properties
 in momentum space of solid state materials.
 Copyright (C), 2019, 
 Hiroki Kotaka, Naoya Yamaguchi and Fumiyuki Ishii.
 This software includes the work that is distributed
 in version 3 of the GPL (GPLv3). 
 
 Please cite the following article:
 H. Kotaka, F. Ishii, and M. Saito,
 Jpn. J. Appl. Phys. 52, 035204 (2013).
 DOI: 10.7567/JJAP.52.035204.
******************************************************************
******************************************************************


 Input filename is "Au111Surface.scfout"  


 Start "MulPOnly" Calculation (6).  

 ########### ORBITAL DATA ##################
 ClaOrb_MAX[0]:   2
```

--------------------------------

### OpenMX SCF Calculation Output Example (Text)

Source: https://openmx-square.org/openmx_man3.9/node16

Demonstrates the typical output format for the SCF history during an OpenMX calculation. It shows the convergence of the calculation by listing the SCF iteration number, the normalized residual (NormRD), and the electronic energy (Uele) at each step. This helps in assessing the stability and convergence of the simulation.

```text
***********************************************************
***********************************************************
                  SCF history at MD= 1
***********************************************************
***********************************************************

   SCF=   1  NormRD=  1.000000000000  Uele= -3.523169099731
   SCF=   2  NormRD=  0.181517404404  Uele= -3.686855123738
   SCF=   3  NormRD=  0.449067381009  Uele= -4.193062144919
   SCF=   4  NormRD=  0.541215648203  Uele= -4.381387140154
   SCF=   5  NormRD=  0.509921689399  Uele= -4.352426233337
   SCF=   6  NormRD=  0.004026023243  Uele= -3.886371199720
   SCF=   7  NormRD=  0.000838640096  Uele= -3.889312346884
   SCF=   8  NormRD=  0.000420666755  Uele= -3.889396659132
   SCF=   9  NormRD=  0.000241013350  Uele= -3.889362708861
   SCF=  10  NormRD=  0.000573725679  Uele= -3.889427222948
   SCF=  11  NormRD=  0.000000150516  Uele= -3.889316043314
   SCF=  12  NormRD=  0.000000001917  Uele= -3.889316014533
   SCF=  13  NormRD=  0.000000000005  Uele= -3.889316014156
   SCF=  14  NormRD=  0.000000000001  Uele= -3.889316014146

```

--------------------------------

### OpenMX Installation: FUJITSU Compilers on FX100

Source: https://openmx-square.org/openmx_man3.9/node14

Configuration for OpenMX installation using FUJITSU compilers (mpifccpx, mpifrtpx) on FX100 machines. Specifies linking with ScaLAPACK and BLACS libraries.

```makefile
CC = mpifccpx -Kfast -Dnosse -Dkcomp
FC = mpifrtpx -Kfast -Dkcomp
LIB = -lfftw3 -SCALAPACK -SSL2BLAMP
```

--------------------------------

### Identifying Fortran Compiler Path

Source: https://openmx-square.org/openmx_man3.9/node14

Commands to locate the installation path of the Fortran compiler, necessary for correctly specifying library paths.

```shell
%which ifort (with the Intel compiler)
/opt/intel/fce/10.0.026/bin/ifort

%which pgf90 (with the PGI compiler)
/opt/pgi/linux86-64/7.0/bin/pgf90

%which gfortran (with the GNU compiler)
/usr/bin/gfortran
```

--------------------------------

### OpenMX Installation: Intel Compilers with MKL

Source: https://openmx-square.org/openmx_man3.9/node14

Configuration for OpenMX installation using Intel C and FORTRAN compilers (icc, ifort) linked with Intel MKL for ScaLAPACK and BLACS. Assumes FFTW3 is installed in /usr/local/fftw3/.

```makefile
MKLROOT = /opt/intel/mkl
CC = mpicc -O3 -xHOST -ip -no-prec-div -qopenmp -I/usr/local/fftw3/include
FC = mpif90 -O3 -xHOST -ip -no-prec-div -qopenmp
LIB= -L/usr/local/fftw3/lib -lfftw3 \
   -L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 \
   -lmkl_intel_thread -lmkl_core -lmkl_blacs_open mpi_lp64 \
   -lmpi_usempif08 -lmpi_usempi_ignore_tkr \
   -lmpi_mpifh -liomp5 -lpthread -lm -ldl
```

--------------------------------

### JX Tool Output for Cluster Calculation

Source: https://openmx-square.org/openmx_man3.9/node125

This is an example output from the 'jx' tool after processing an SCF output file from a cluster calculation. It displays information about the calculation, system parameters, and the calculated exchange coupling constants (J) in meV and mRy units.

```text
********************************************************************
********************************************************************
 jx: code for calculating an effective exchange coupling constant J 
 Copyright (C), 2003, Myung Joon Han, Jaejun Yu, and Taisuke Ozaki 
                 2019, Asako Terasawa and Taisuke Ozaki 
 This is free software, and you are welcome to         
redistribute it under the constitution of the GNU-GPL.
********************************************************************
********************************************************************

 Read the scfout file (Fe_Cluster_jx.scfout)
 ***
 The file format of the SCFOUT file:  3
 And it supports the following functions:
 - jx
 - polB
 - kSpin
 - Z2FH
 - calB
 ***

  Previous eigenvalue solver = Cluster
  atomnum                    = 2
  ChemP                      = -0.089740215968 (Hartree)
  E_Temp                     = 300.000000000000 (K) 

 Evaluation of J based on cluster calculation
 
     i     j            J [meV]            J [mRy]
 -------------------------------------------------
     1     1   1591.520791120630    116.974621661729
     1     2    106.511867492210      7.828477938772
     2     2   1591.520746009061    116.974618346089

  Elapsed time = 0.036225 (s)

```

--------------------------------

### OpenMX MPI_Comm_spawn Example (C)

Source: https://openmx-square.org/openmx_man3.9/node214

This C code is an example of using MPI_Comm_spawn to call OpenMX as a library. It groups MPI processes into three new communication groups and runs OpenMX with different input files ('Methane.dat', 'C60.dat', 'Fe2.dat') in each group. It includes necessary MPI headers and functions for process management.

```c
/**********************************************************************                                                                   
                                                                                                                                          
  example_mpi_spawn.c:                                                                                                                    
                                                                                                                                          
  An example of calling OpenMX as library by MPI_Comm_spawn, where                                                                        
  a given MPI processes are grouped to three new MPI communication                                                                        
  groups and OpenMX runs with an input file: 'Methane.dat', 'C60.dat',                                                                
  or 'Fe2.dat' in each MPI group.                                                                                                        
                                                                                                                                          
  Log of example_mpi_spawn.c:                                                                                                             
                                                                                                                                          
     25/Sep./2019  Released by Taisuke Ozaki                                                                                              
                                                                                                                                          
***********************************************************************/

#include "mpi.h"
#include <stdio.h>
#include <stdlib.h>

void Make_Comm_Worlds(
   MPI_Comm MPI_Curret_Comm_WD,
   int myid0,
   int numprocs0,
   int Num_Comm_World,
   int *myworld1,
   MPI_Comm *MPI_CommWD,     /* size: Num_Comm_World */
   int *NPROCS1_ID,          /* size: numprocs0 */
   int *Comm_World1,         /* size: numprocs0 */
   int *NPROCS1_WD,          /* size: Num_Comm_World */
   int *Comm_World_StartID   /* size: Num_Comm_World */
   );

int main(int argc, char *argv[])
{
  int i,j;
  int numprocs0,myid0,ID0;
  int numprocs1,myid1;
  int num;
  int Num_Comm_World1;
  int myworld1;
  int *NPROCS1_ID,*NPROCS1_WD;
  int *Comm_World1;
  int *Comm_World_StartID;
  MPI_Comm *MPI_CommWD;
  MPI_Comm comm;
  MPI_Comm *intercomm;

  MPI_Init(&argc,&argv);
  MPI_Comm_size(MPI_COMM_WORLD,&numprocs0);
  MPI_Comm_rank(MPI_COMM_WORLD,&myid0);

  /* set Num_Comm_World1 */

  Num_Comm_World1 = 3;

  /* allocation of arrays */

  NPROCS1_ID = (int*)malloc(sizeof(int)*numprocs0);
  Comm_World1 = (int*)malloc(sizeof(int)*numprocs0);
  NPROCS1_WD = (int*)malloc(sizeof(int)*Num_Comm_World1);
  Comm_World_StartID = (int*)malloc(sizeof(int)*Num_Comm_World1);
  MPI_CommWD = (MPI_Comm*)malloc(sizeof(MPI_Comm)*Num_Comm_World1);
  intercomm = (MPI_Comm*)malloc(sizeof(MPI_Comm)*Num_Comm_World1);

  /* Make_Comm_Worlds */

  Make_Comm_Worlds(MPI_COMM_WORLD, myid0, numprocs0, Num_Comm_World1, 
                   &myworld1, MPI_CommWD,
                   NPROCS1_ID, Comm_World1, NPROCS1_WD, Comm_World_StartID);

  /* get numprocs1 and myid1 */

  MPI_Comm_size(MPI_CommWD[myworld1],&numprocs1);
  MPI_Comm_rank(MPI_CommWD[myworld1],&myid1);

  /*                                                                                                                                      
  printf("numprocs0=%2d myid0=%2d myworld1=%2d numprocs1=%2d myid1=%2d\n",                                                                
          numprocs0,myid0,myworld1,numprocs1,myid1);                                                                                      
  */

  /* MPI_Comm_spawn */

  char command[] = "./openmx";
  char **argvin;
  char *inputfiles[] = { "Methane.dat", "C60.dat", "Fe2.dat" };

  argvin=(char **)malloc(2 * sizeof(char *));

```

--------------------------------

### OpenMX Installation: GNU Compilers with ScaLAPACK/BLACS

Source: https://openmx-square.org/openmx_man3.9/node14

Configuration for OpenMX installation using GNU C and FORTRAN compilers (gcc, g++, gfortran) linked with ScaLAPACK and BLACS libraries. Includes paths for FFTW3 and a custom OpenMPI installation.

```makefile
CC = mpicc -O3 -ffast-math -fopenmp -Dkcomp -I/usr/local/include -I/home/ytl/openmx-3.0.1/ompi/include
FC = mpif90 -O3 -ffast-math -fopenmp -Dkcomp -I/home/ytl/openmx-3.0.1/ompi/include
LIB= -L/usr/local/lib -lfftw3 -L/home/ytl/openmx-3.0.1/ompi -lmpi -lmpi_mpifh \
   -L/home/ytl/Packages/lapack-3.7.0 -llapack -lrefblas -lgfortran
```

--------------------------------

### Install MPI Version (make install command)

Source: https://openmx-square.org/openmx_man3.9/node7

This snippet shows the command to execute after configuring the 'makefile' for the MPI version installation.

```bash
% make install
```

--------------------------------

### OpenMX Installation: GNU Compilers with MKL

Source: https://openmx-square.org/openmx_man3.9/node14

Configuration for OpenMX installation using GNU C and FORTRAN compilers (gcc, g++, gfortran) linked with Intel MKL for ScaLAPACK and BLACS. Assumes FFTW3 is installed in /usr/local/fftw3/.

```makefile
MKLROOT=/opt/intel/mkl
CC = mpicc -O3 -ffast-math -fopenmp -I/usr/local/fftw3/include -I/$MKLROOT/include
FC = mpif90 -O3 -ffast-math -fopenmp -I/$MKLROOT/include
LIB= -L/usr/local/fftw3/lib -lfftw3 \
   -L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 \
   -lmkl_intel_thread -lmkl_core -lmkl_blacs_open mpi_lp64 \
   -lmpi_usempif08 -lmpi_usempi_ignore_tkr \
   -lmpi_mpifh -liomp5 -lpthread -lm -ldl
```

--------------------------------

### OpenMX Eigenvalues Output Example (Text)

Source: https://openmx-square.org/openmx_man3.9/node16

Displays the eigenvalues for the SCF Kohn-Sham equations calculated by OpenMX. It includes the chemical potential, the total number of states, and the HOMO level. The eigenvalues are listed for both spin-up and spin-down electrons, providing insights into the electronic band structure of the system.

```text
***********************************************************
***********************************************************
           Eigenvalues (Hartree) for SCF KS-eq.
***********************************************************
***********************************************************

   Chemical Potential (Hartree) =   0.00000000000000
   Number of States             =   8.00000000000000
   HOMO =  4
   Eigenvalues
                Up-spin            Down-spin
          1  -0.69897506408475  -0.69897506408475
          2  -0.41523055776668  -0.41523055776668
          3  -0.41523055768741  -0.41523055768741
          4  -0.41522182758055  -0.41522182758055
          5   0.21221759603691   0.21221759603691
          6   0.21221759685634   0.21221759685634

```

--------------------------------

### OpenMX Total Energy Output Example (Text)

Source: https://openmx-square.org/openmx_man3.9/node16

Presents the breakdown of the total energy components calculated by OpenMX for a given step. It lists various energy contributions such as kinetic energy, Coulomb energy, exchange-correlation energy, and core-core interaction, along with their definitions. This section is crucial for understanding the energetic properties of the system.

```text
*******************************************************
        Total energy (Hartree) at MD = 1
*******************************************************

  Uele.         -3.889316014146

  Ukin.          5.533759381370
  UH0.         -14.855519969177
  UH1.           0.041396138425
  Una.          -5.040606545149
  Unl.          -0.134650846490
  Uxc0.         -1.564720263874
  Uxc1.         -1.564720263874
  Ucore.         9.551521413583
  Uhub.          0.000000000000
  Ucs.           0.000000000000
  Uzs.           0.000000000000
  Uzo.           0.000000000000
  Uef.           0.000000000000
  UvdW           0.000000000000
  Uch            0.000000000000
  Utot.         -8.033540955187

  Note:

  Utot = Ukin+UH0+UH1+Una+Unl+Uxc0+Uxc1+Ucore+Uhub+Ucs+Uzs+Uzo+Uef+UvdW

  Uene:   band energy
  Ukin:   kinetic energy
  UH0:    electric part of screened Coulomb energy
  UH1:    difference electron-electron Coulomb energy
  Una:    neutral atom potential energy
  Unl:    non-local potential energy
  Uxc0:   exchange-correlation energy for alpha spin
  Uxc1:   exchange-correlation energy for beta spin
  Ucore:  core-core Coulomb energy
  Uhub:   DFT+U energy
  Ucs:    constraint energy for spin orientation
  Uzs:    Zeeman term for spin magnetic moment
  Uzo:    Zeeman term for orbital magnetic moment
  Uef:    electric energy by electric field
  UvdW:   semi-empirical vdW energy

  (see also PRB 72, 045121(2005) for the energy contributions)


  Chemical potential (Hartree)       0.000000000000

```

--------------------------------

### Orbital Optimization Progress Log

Source: https://openmx-square.org/openmx_man3.9/node73

Example output log showing the history of the orbital optimization process, including iteration number, gradient norm, and total energy.

```log
***********************************************************
***********************************************************
         History of orbital optimization   MD= 1
*********     Gradient Norm ((Hartree/borh)^2)     ********
              Required criterion=  0.000100000000
***********************************************************

   iter=   1  Gradient Norm=  0.057098961101  Uele= -3.217161102876
   iter=   2  Gradient Norm=  0.044668461503  Uele= -3.220120116009
   iter=   3  Gradient Norm=  0.034308306321  Uele= -3.223123238394
   iter=   4  Gradient Norm=  0.025847573248  Uele= -3.226177980300
   iter=   5  Gradient Norm=  0.019106400842  Uele= -3.229294858054
   iter=   6  Gradient Norm=  0.013893824906  Uele= -3.232489198284
   iter=   7  Gradient Norm=  0.010499500005  Uele= -3.235304178159
   iter=   8  Gradient Norm=  0.008362635043  Uele= -3.237652870812
   iter=   9  Gradient Norm=  0.006959703539  Uele= -3.239618540761
   iter=  10  Gradient Norm=  0.005994816379  Uele= -3.241268535418
   iter=  11  Gradient Norm=  0.005298095979  Uele= -3.242657118263
   iter=  12  Gradient Norm=  0.003059655878  Uele= -3.250892948269
   iter=  13  Gradient Norm=  0.001390201488  Uele= -3.255123241210
   iter=  14  Gradient Norm=  0.000780925380  Uele= -3.255179362845
   iter=  15  Gradient Norm=  0.000726631072  Uele= -3.255263012792
   iter=  16  Gradient Norm=  0.000390930576  Uele= -3.250873416989
   iter=  17  Gradient Norm=  0.000280785975  Uele= -3.250333677139
   iter=  18  Gradient Norm=  0.000200668585  Uele= -3.252345643243
   iter=  19  Gradient Norm=  0.000240367596  Uele= -3.254238199726
   iter=  20  Gradient Norm=  0.000081974594  Uele= -3.258146794679
```

--------------------------------

### Run analysis_example with SCF Output

Source: https://openmx-square.org/openmx_man3.9/node213

This command executes the compiled 'analysis_example' program, taking the system's SCF output file as input. The results, including Hamiltonian, overlap, and density matrices, are printed to standard output or can be redirected to a file like 'HS.out'.

```bash
% ./analysis_example System.Name.scfout
  or 
% ./analysis_example System.Name.scfout > HS.out
```

--------------------------------

### Compile and Run OpenMX Example with MPI_Comm_spawn (C)

Source: https://openmx-square.org/openmx_man3.9/node214

This snippet shows the compilation and execution commands for the 'example_mpi_spawn.c' program. The program demonstrates calling OpenMX as a library using MPI_Comm_spawn, creating separate MPI communication groups for different input files.

```bash
% make example_mpi_spawn

% mpirun -np 24 -machinefile machine0 --oversubscribe ./example_mpi_spawn
```

--------------------------------

### Define Initial Structure for NEB Calculation (OpenMX Input)

Source: https://openmx-square.org/openmx_man3.9/node157

Specifies the atomic species and coordinates for the precursor structure in an NEB calculation. This block is crucial for defining the starting point of the reaction pathway.

```OpenMX Input
<Atoms.SpeciesAndCoordinates
  1    C   -0.66829065594143    0.00000000101783   -2.19961193219289     2.0     2.0
  2    C    0.66817412917689   -0.00000000316062   -2.19961215251205     2.0     2.0
  3    H    1.24159214112072   -0.92942544650857   -2.19953308980064     0.5     0.5
  4    H    1.24159212192367    0.92942544733979   -2.19953308820323     0.5     0.5
  5    H   -1.24165800644131   -0.92944748269232   -2.19953309891389     0.5     0.5
  6    H   -1.24165801380425    0.92944749402510   -2.19953309747076     0.5     0.5
  7    C   -0.66829065113509    0.00000000341499    2.19961191775648     2.0     2.0
  8    C    0.66817411530651   -0.00000000006073    2.19961215383949     2.0     2.0
  9    H    1.24159211310925   -0.92942539308841    2.19953308889301     0.5     0.5
  10    H    1.24159212332935    0.92942539212392    2.19953308816332     0.5     0.5
  11    H   -1.24165799549343   -0.92944744948986    2.19953310195071     0.5     0.5
  12    H   -1.24165801426648    0.92944744880542    2.19953310162389     0.5     0.5
  Atoms.SpeciesAndCoordinates>
```

--------------------------------

### Configure Temperature Control for MD in OpenMX (Method 1)

Source: https://openmx-square.org/openmx_man3.9/node21

Sets up temperature control for MD simulations using a specific method. This example uses 3 temperature control points with associated parameters.

```input
<MD.TempControl
     3
     100   2  1000.0  0.0  
     400  10   700.0  0.4  
     700  40   500.0  0.7  
   MD.TempControl>
```

--------------------------------

### OpenMX Eigenchannel Analysis Output Example

Source: https://openmx-square.org/openmx_man3.9/node133

This section shows the standard output generated by OpenMX during the eigenchannel calculation. It includes messages indicating the start and end of the calculation, file names for transmission eigenvalues and eigenvectors, and the format of the generated cube files for real and imaginary parts of eigenchannels.

```text
**************************************************
 Calculation of transmission eigenchannels starts
**************************************************

  File index : negf-8zgnr-0.3.traneval#k_#E_#spin negf-8zgnr-0.3.tranevec#k_#E_#spin 

  myid0 =   0, #k :    0, N_{ort} / N_{nonort} : 380 / 380 
  PE    0 generates ./negf-8zgnr-0.3.traneval0_0_0 . Sum(eigenval) :   0.031643 
  PE    0 generates ./negf-8zgnr-0.3.traneval0_0_1 . Sum(eigenval) :   0.000508 

  Eigenchannel calculation finished 
  They are written in plottable files. 
  File index : negf-8zgnr-0.3.tranec#k_#E_#spin_#branch_r.cube(.bin)  
               negf-8zgnr-0.3.tranec#k_#E_#spin_#branch_i.cube(.bin)  

  ./negf-8zgnr-0.3.tranec0_0_0_0_r.cube     ./negf-8zgnr-0.3.tranec0_0_0_0_i.cube 
  ./negf-8zgnr-0.3.tranec0_0_0_1_r.cube     ./negf-8zgnr-0.3.tranec0_0_0_1_i.cube 
  ./negf-8zgnr-0.3.tranec0_0_0_2_r.cube     ./negf-8zgnr-0.3.tranec0_0_0_2_i.cube 
  ./negf-8zgnr-0.3.tranec0_0_0_3_r.cube     ./negf-8zgnr-0.3.tranec0_0_0_3_i.cube 
  ./negf-8zgnr-0.3.tranec0_0_0_4_r.cube     ./negf-8zgnr-0.3.tranec0_0_0_4_i.cube 
  ./negf-8zgnr-0.3.tranec0_0_1_0_r.cube     ./negf-8zgnr-0.3.tranec0_0_1_0_i.cube 
  ./negf-8zgnr-0.3.tranec0_0_1_1_r.cube     ./negf-8zgnr-0.3.tranec0_0_1_1_i.cube 
  ./negf-8zgnr-0.3.tranec0_0_1_2_r.cube     ./negf-8zgnr-0.3.tranec0_0_1_2_i.cube 
  ./negf-8zgnr-0.3.tranec0_0_1_3_r.cube     ./negf-8zgnr-0.3.tranec0_0_1_3_i.cube 
  ./negf-8zgnr-0.3.tranec0_0_1_4_r.cube     ./negf-8zgnr-0.3.tranec0_0_1_4_i.cube
```

--------------------------------

### Compile analysis_example Utility

Source: https://openmx-square.org/openmx_man3.9/node213

This command compiles the 'analysis_example' program from the OpenMX source code. It is typically run from the 'source' directory and generates an executable file named 'analysis_example' in the 'work' directory.

```bash
% make analysis_example
```

--------------------------------

### Configure Temperature Control for MD in OpenMX (Method 2)

Source: https://openmx-square.org/openmx_man3.9/node21

Sets up temperature control for MD simulations using a different configuration. This example uses 4 temperature control points with associated target temperatures.

```input
<MD.TempControl
     4
     1    1000.0
     100  1000.0
     400   700.0
     700   600.0
   MD.TempControl>
```

--------------------------------

### OpenMX Input File Configuration for Methane

Source: https://openmx-square.org/openmx_man3.9/node20

This snippet shows a typical OpenMX input file for a methane molecule. It includes sections for system settings, atomic species definition, atom coordinates, unit vectors, SCF parameters, and MD/geometry optimization settings. The format is keyword-based and flexible.

```plaintext
#
# File Name
#

System.CurrrentDirectory         ./    # default=./
System.Name                      met
level.of.stdout                   1    # default=1 (1-3)
level.of.fileout                  1    # default=1 (0-2)

#
# Definition of Atomic Species
#

Species.Number       2
<Definition.of.Atomic.Species
 H   H5.0-s1          H_PBE19
 C   C5.0-s1p1        C_PBE19
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number         5
Atoms.SpeciesAndCoordinates.Unit   Ang # Ang|AU
<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>
Atoms.UnitVectors.Unit             Ang # Ang|AU
<Atoms.UnitVectors
  10.0   0.0   0.0
   0.0  10.0   0.0
   0.0   0.0  10.0
Atoms.UnitVectors>

#
# SCF or Electronic System
#

scf.XcType                 GGA-PBE     # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization        off        # On|Off|NC
scf.ElectronicTemperature  300.0       # default=300 (K)
scf.energycutoff           120.0       # default=150 (Ry)
scf.maxIter                 100        # default=40
scf.EigenvalueSolver        cluster    # DC|Cluster|Band
scf.Kgrid                  1 1 1       # means n1 x n2 x n3
scf.Mixing.Type           rmm-diis     # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight     0.30        # default=0.30
scf.Min.Mixing.Weight      0.001       # default=0.001
scf.Max.Mixing.Weight      0.400       # default=0.40
scf.Mixing.History          7          # default=5
scf.Mixing.StartPulay       5          # default=6
scf.criterion             1.0e-10      # default=1.0e-6 (Hartree)

#
# MD or Geometry Optimization
#

MD.Type                     nomd       # Nomd|Opt|NVE|NVT_VS|NVT_NH
                                       # Constraint_Opt|DIIS
MD.maxIter                    1        # default=1
MD.TimeStep                 1.0        # default=0.5 (fs)
MD.Opt.criterion         1.0e-4        # default=1.0e-4 (Hartree/Bohr)

```

--------------------------------

### OpenMX Bulk Calculation and JX Analysis

Source: https://openmx-square.org/openmx_man3.9/node125

This snippet outlines the process for a bulk calculation using OpenMX, followed by using the 'jx' tool to compute exchange coupling constants for periodic systems. It involves running OpenMX with a specific input file and then processing the SCF output.

```bash
% mpirun -np 28 ./openmx Fe_Bulk_jx.dat

% mpirun -np 112 ./jx Fe_Bulk_jx.scfout Fe_Bulk_jx.config | tee jx.log
```

--------------------------------

### Extract Total Energies from Output

Source: https://openmx-square.org/openmx_man3.9/node193

Demonstrates how to extract the initial and final state total energies from the output files of OpenMX calculations. These energies are crucial for determining binding energies.

```text
Initial state: -10499.900104007471 (Hartree)
Final state:   -10489.553360141708 (Hartree)
```

--------------------------------

### Configure kSpin Calculation Type and Input Files

Source: https://openmx-square.org/openmx_man3.9/node179

This snippet shows the relevant keywords in an OpenMX input file to configure the kSpin calculation. It specifies the output file names, the calculation type ('MulPOnly'), and the k-point data file.

```input
Filename.scfout       Au111Surface.scfout 
Filename.outdata      Au111Surface_MO     
Calc.Type             MulPOnly               # FermiLoop, GridCalc,
                                                   BandDispersion, or MulPOnly 
                                                   default: MulPOnly
Filename.kpointdata   kpoint.in
```

--------------------------------

### Run MulPCalc for k-space spin density matrix analysis

Source: https://openmx-square.org/openmx_man3.9/node177

This snippet shows the command to execute MulPCalc for analyzing the k-space spin density matrix. It requires an input file (e.g., Au111Surface_GC.dat) as an argument. The output can be further analyzed by MulPCalc.

```bash
% ./MulPCalc Au111Surface_GC.dat

```

--------------------------------

### Example Memory Usage Output Format in OpenMX

Source: https://openmx-square.org/openmx_man3.9/node217

This is an example of the detailed memory usage output generated by OpenMX when 'memory.usage.fileout' is enabled. It lists memory consumption for various internal components and provides a total memory usage figure.

```text
Memory: SetPara_DFT: Spe_PAO_XV                             0.01 MBytes
Memory: SetPara_DFT: Spe_PAO_RV                             0.01 MBytes
Memory: SetPara_DFT: Spe_Atomic_Den                         0.01 MBytes
Memory: SetPara_DFT: Spe_PAO_RWF                            0.57 MBytes
Memory: SetPara_DFT: Spe_RF_Bessel                          1.03 MBytes
Memory: SetPara_DFT: Spe_VPS_XV                             0.01 MBytes
Memory: SetPara_DFT: Spe_VPS_RV                             0.01 MBytes
Memory: SetPara_DFT: Spe_Vna                                0.01 MBytes
Memory: SetPara_DFT: Spe_VH_Atom                            0.01 MBytes
Memory: SetPara_DFT: Spe_Atomic_PCC                         0.01 MBytes
Memory: SetPara_DFT: Spe_VNL                                0.11 MBytes
Memory: SetPara_DFT: Spe_VNLE                               0.00 MBytes
Memory: SetPara_DFT: Spe_VPS_List                           0.00 MBytes
.....
....
...
Memory: Poisson: array0                                     4.00 MBytes
Memory: Poisson: array1                                     4.00 MBytes
Memory: Poisson: request_send                               0.00 MBytes
Memory: Poisson: stat_send                                  0.00 MBytes
Memory: Poisson: request_recv                               0.00 MBytes
Memory: Poisson: stat_recv                                  0.00 MBytes
Memory: Force: Hx                                           0.00 MBytes
Memory: Force: Hy                                           0.00 MBytes
Memory: Force: Hz                                           0.00 MBytes
Memory: Force: CDM0                                         0.00 MBytes
Memory: Data_Grid_Copy_B2C_1: Work_Array_Snd_Grid_B2C       0.72 MBytes
Memory: Data_Grid_Copy_B2C_1: Work_Array_Rcv_Grid_B2C       0.72 MBytes
Memory: total                                             256.99 MBytes
```
Tokens:
Raw