How to run BAGEL

Command

BAGEL runs by

$ BAGEL input.json

Normally you will want to run in parallel using mpirun. BAGEL sends output to the standard I/O stream, so you have to pipe the output in order to save it as a file:

$ mpirun BAGEL input.json > output.out

Environment variables

The folowing commands can be used to control the number of threads used by each MPI process of BAGEL:

$ export BAGEL_NUM_THREADS=16
$ export MKL_NUM_THREADS=16

The default value for $BAGEL_NUM_THREADS is copied from $OMP_NUM_THREADS or the number of available CPU cores. It is generally recommended to set this variable such that BAGEL_NUM_THREADS times the number of MPI processes equals the number of available cores on your machine.

When you run BAGEL with Intel MPI using a large number (>16) of processes, you have to set:

$ export I_MPI_SCALABLE_OPTIMIZATION=off

owing to the problem in Intel’s MPI scalable optimization.

Test input and output

This is an example input file for a simple Hartree–Fock calculation:

{ "bagel" : [

{
  "title" : "molecule",
  "basis" : "svp",
  "df_basis" : "svp-jkfit",
  "angstrom" : "false",
  "geometry" : [
    { "atom" : "F",  "xyz" : [ -0.000000,     -0.000000,      2.720616]},
    { "atom" : "H",  "xyz" : [ -0.000000,     -0.000000,      0.305956]}
  ]
},

{
  "title" : "hf"
}

]}

from which you should get an output file as follows:

===============================================================
  BAGEL - Freshly leavened quantum chemistry
===============================================================

*** Geometry ***

Symmetry: c1

{ "atom" : "F", "xyz" : [     -0.000000,     -0.000000,      2.720616 ] },
{ "atom" : "H", "xyz" : [     -0.000000,     -0.000000,      0.305956 ] },

Number of auxiliary basis functions:       95

Since a DF basis is specified, we compute 2- and 3-index integrals:
  o Being stored without compression. Storage requirement is 0.000 GB
     - 3-index ints prep                         0.00
     - 3-index ints                              0.02
     - 2-index ints                              0.00
     - computing inverse                         0.02
      elapsed time:        0.05 sec.


Number of basis functions:       19
Number of electrons      :       10


  * METHOD: MOLECULE                             0.13

     - Overlap matrix                            0.00
     - Hcore matrix                              0.00
     - Overlap orthog                            0.00

*** RHF ***

=== Nuclear Repulsion ===

   3.7272328195

    * DIIS with orbital gradients will be used.

     - SCF startup                               0.07

=== RHF iteration (svp) ===

             o Fock build                                  0.00
    0        -99.70639103          0.06595513           0.00
             o DIIS                                        0.00
             o Diag                                        0.00
             o Post process                                0.00
             o Fock build                                  0.00
    1        -99.78677680          0.04496384           0.00
             o DIIS                                        0.00
             o Diag                                        0.00
             o Post process                                0.00
             o Fock build                                  0.00
    2        -99.84655378          0.00434989           0.00
             o DIIS                                        0.00
             o Diag                                        0.00
             o Post process                                0.00
             o Fock build                                  0.00
    3        -99.84766336          0.00089762           0.00
             o DIIS                                        0.00
             o Diag                                        0.00
             o Post process                                0.00
             o Fock build                                  0.00
    4        -99.84772173          0.00015090           0.00
             o DIIS                                        0.00
             o Diag                                        0.00
             o Post process                                0.00
             o Fock build                                  0.00
    5        -99.84772349          0.00002429           0.00
             o DIIS                                        0.00
             o Diag                                        0.00
             o Post process                                0.00
             o Fock build                                  0.00
    6        -99.84772354          0.00000255           0.00
             o DIIS                                        0.00
             o Diag                                        0.00
             o Post process                                0.00
             o Fock build                                  0.00
    7        -99.84772354          0.00000043           0.00
             o DIIS                                        0.00
             o Diag                                        0.00
             o Post process                                0.00
             o Fock build                                  0.00
    8        -99.84772354          0.00000012           0.00
             o DIIS                                        0.00
             o Diag                                        0.00
             o Post process                                0.00
             o Fock build                                  0.00
    9        -99.84772354          0.00000004           0.00
             o DIIS                                        0.00
             o Diag                                        0.00
             o Post process                                0.00
             o Fock build                                  0.00
   10        -99.84772354          0.00000000           0.00

  * SCF iteration converged.

  * Permanent dipole moment:
         (    0.000000,    -0.000000,     1.055510) a.u.


  * METHOD: HF                                   0.08



===============================================================