Benchmarks and examples

A set of TROVE benchmarks for a number of typical systems can be found here

Benchmarks.

PH3

This PH3 benchmark is to produce a small line list for phosphine (PH3) using a relatively large primitive basis set.

It includes the following input files:

ph3_P18_step1.inp
ph3_P18_step2.inp
ph3_P18_step3_J0.inp
ph3_P18_step3_J1.inp
ph3_P18_step3_J2.inp
ph3_P18_step3_J3.inp
ph3_P18_step3_J4.inp
ph3_P18_step3_J5.inp
ph3_P18_step3_J10.inp
ph3_P18_step3_J50.inp
ph3_P18_step4_intensity.inp

covering the following steps:

  • Step 1: Produce the initial smaller J=0 HAMILTONIAN matrix and diagonalize it using DSYEV (step1)

  • Step 2: Convert to J=0 representation; prepare matrix elements for J>0 calculations (step2)

  • Step 3: Generate a J=0-5 10, 50 energies and eigenfunctions (step3-step9) by diagonalising three double real, symmetric matrices for each J using DSYEV.

    Each calculation is independent, but depends on the checkpoints produced at steps 1-2. It requires checkpoints from steps 1-2.

  • Step 4: Intensity calculations between J=0-5 states (ph3_P18_step4_intensity.inp). It will depend on the checkpoints produced at steps 1-3.

Memory and time requirements:

  • Step1: 84 Gb 27032.7

  • Step2: 9.9 Gb 1220.9 s

  • Step3: 0.8 Gb 2.6 s

  • Step4: 6.8 Gb 73 s

  • Step5: 7.8 Gb 198 s

  • Step6: 8.4 Gb 502 s

  • Step7: 9.0 Gb 830 s

  • Step8: 9.6 Gb 1449 s

  • Step9: 19.3 Gb 9032 s

  • Step10: 32.5 Gb 12096 s

  • Step_intensity: 89 Gb 1592 s

Disk space used: 300 Gb

Here J is the rotational angular momentum.

There are three matrices to diagonalise for each symmetry \Gamma=A_1, A_2, E. The dimensions of the matrices are given approximately by

N(A) = (2J+1) x N_0(A) N(E) = (2J+1) x N_0(E)

where N_0 are the dimensions of the \Gamma=A_1, A_2 and E matrices at J=0, N_0=1000 and 2000, respectively (approximately).

The first step in this case is relatively expensive, 84 Gb and 27032.7 s on a 16 processor workstation.

The input file has the structure described in detail in the following.

  • Stand-alone keywords, memory, verbosity level, expansion order of KEO and PEF, sparse methods.

mem 64 gb
verbose 5

KinOrder  6   (Max order in the kinetic energy expansion)
PotOrder  8   (Max order in the potential energy expansion)

Natoms 4       (Number of atoms)
Nmodes 6       (Number of modes = 3*Natoms-6)

sparse

  • More stand-alone keywords:

  • Finite difference steps, general coordinates type (linear-ised or local), TROVE coordinates, Molecule type, the molecule name (only for printing), reference configuration:

dstep   0.01
COORDS  linear
TRANSFORM  R-ALPHA
MOLTYPE    XY3
MOLECULE   PH3
REFER-CONF RIGID

  • Molecular symmetry group

SYMGROUP C3v(M)

  • Primitive basis block:

PRIMITIVES
  Npolyads        18        (Number of primitive polyads)
  enercut        80000.     (energy cut for the primitive basis set)
END

  • Contracted basis block:

CONTRACTION
  Npolyads        18         (Number of contracted polyads)
  enercut       80000.0      (energy cut for the contracted basis set)
  degeneracy     1e-3        (threshold used to define degenerate energies)
  coeff_thresh   1e-14       (threshold used to define symmetry)
  enercut_matelem 10000.0
  exp_coeff_thresh   1.0d-6
END

  • Eigensolver (diagonalizer) block:

DIAGONALIZER
 syev
 enermax 15000
end

  • Zmatrix block defining the structure and masses:

ZMAT
    P   0  0  0  0   30.9737620
    H   1  0  0  0   1.00782505
    H   1  2  0  0   1.00782505
    H   1  2  3  0   1.00782505
end

  • Control block:

    control step 1 external end

  • Basis set block defining the order of the primitive basis set functions and how their grouped into the contracted basis sets:

BASIS
  0,'JKtau', Jrot 0
  1,'numerov','linear', 'morse',   range 0, 9, resc 2.0, points 2000, borders -0.5,2.10
  1,'numerov','linear', 'morse',   range 0, 9, resc 2.0, points 2000, borders -0.5,2.10
  1,'numerov','linear', 'morse',   range 0, 9, resc 2.0, points 2000, borders -0.5,2.10
  2,'numerov','linear', 'linear',  range 0,18, resc 1.0, points 2000, borders -1.6,1.30
  2,'numerov','linear', 'linear',  range 0,18, resc 1.0, points 2000, borders -1.6,1.30
  2,'numerov','linear', 'linear',  range 0,18, resc 1.0, points 2000, borders -1.6,1.30
END

  • Equilibrium structure block:

EQUILIBRIUM
re          1       1.41182210
re          1       1.41182210
re          1       1.41182210
alphae      0      93.3685 deg
alphae      0      93.3685 deg
alphae      0      93.3685 deg
end

  • “Special” parameters block, mostly used to define the Morse stretching parameters and in some cases harmonic frequencies or Laguerre structural parameter.

SPECPARAM
beta        0        1.8000000
beta        0        1.8000000
beta        0        1.8000000
END

  • Potential energy function block:

POTEN
NPARAM   109    (obsolete)
POT_TYPE  poten_xy3_morbid_10
COEFF  list  (powers or list)
VE           0  0.00000000000000E+00
FA1          1 -0.34350288027976E+03
FA2          1  0.28963515335650E+06
FA3          1 -0.66897678674464E+06
FA4          1  0.26097579162907E+07
......
end

  • Dipole moment function block

DIPOLE
rank 3
NPARAM  127 0 0
DMS_TYPE  XY3_MB
COEFF   list  (powers or list)
COORDS  linear
Order   2 2 2
parameters
charge   0     0.00000000
order    0     4.00000000
alphae   0    93.40000000
re14     0     1.41200000
beta     0     1.00000000
gamma    0     0.00000000
delta    0     0.00000000
mu0      0     0.33369443
F1       0    -1.05840018
F3       0     0.13117597
F4       0     0.17351923
F5       0    -0.21359267
.....
end

H3+

This is another pyramid-type molecule but with a non-rigid umbrella degree of freedom treated using a non-rigid reference configuration and linearised coordinates to represent the KEO. The PEF is empirical from [20YuTeMi]. The calculation steps are as in the example of PH3.

SiH2 Refinement

Two directories SiH2-1 and SiH2-2 provide examples of the TROVE refinement for a rigid XY2 type system:

./trove.x <SiH2_step1.inp    >  SiH2_step1.out
./trove.x <SiH2_step2.inp    >  SiH2_step2.out
./trove.x <SiH2_step3_J0.inp >  SiH2_step3_J0.out
./trove.x <SiH2_step3_J1.inp >  SiH2_step3_J1.out
./trove.x <SiH2_step3_J2.inp >  SiH2_step3_J2.out
./trove.x <SiH2_step4.inp    >  SiH2_step4.out
./trove.x <SiH2_step5.inp    >  SiH2_step5.out

H2CO

H2CO-1: A typical TROVE line list pipeline for H2CO treated as a rigid molecule using a non-exact KEO (linearised coordinates).

In order to run this benchmark on COSMOS submit using, e.g.

The actual running script is run_trove_benchmark.csh for the following jobs:

./trove.x <file1.inp >file1.out
./trove.x <file2.inp >file2.out
./trove.x <file3.inp >file3.out
./trove.x <file4.inp >file4.out
./trove.x <file5.inp >file5.out
./trove.x <file6.inp >file6.out
./trove.x <file7.inp >file7.out
./trove.x <file8.inp >file8.out
./trove.x <file_intensity.inp > file_intensity.out

with the steps as in the PH3 example.

HCN

An example of a linear molecule with an exact KEO.

The TROVE package must be compiled with pot_HCN.f90 (module pot_user), which defines the potential energy function of HCN as the general type and a PEF from [16MaKyPo].

This benchmark contains the following jobs:

./trove.x <HCN_step1.inp     >  HCN_step1.out
./trove.x <HCN_step2.inp     >  HCN_step2.out
./trove.x <HCN_step3_J0.inp  >  HCN_step3_J0.out
./trove.x <HCN_step3_J1.inp  >  HCN_step3_J1.out
./trove.x <HCN_step3_J2.inp  >  HCN_step3_J2.out

This TROVE calculation represents the following steps:

  • Step 1: Produce the initial smaller J=0 HAMILTONIAN matrix and diagonalize it using DSYEV (HCN_step1.inp)

  • Step 2: Convert to J=0 representation; prepare matrix elements for J>0 calculations (HCN_step2.inp)

  • Step 3: Generate a J=0-2 energies and eigenfunctions (HCN_step3_J<0,1,2>.inp) by diagonalising double real, symmetric matrices for each J using DSYEV.