Input description

Relevant Keywords in QUILD block

name default description
CVG_ENR 1.0e-5 Convergence criterion for energy (when IDCVG \(\geq\) 2)
CVG_GRD 1.0e-4 Convergence criterion for maximum component of gradient; depending on the value of IDELOCAL, either the delocalized or Cartesian gradient is checked
CVG_STP 1.0e-4 Convergence criterion for maximum component of step (when IDCVG \(\geq\) 2)
DIFSTEP 1.0e-5 Stepsize for numerical differentiation (with numerical gradients/Hessian))
I_ADD_DUMMIES 1 Index to do (1) or do not (0) add dummy atoms for avoiding (nearly-)linear angles
ICREATE 7 Index which method to use for generating the primitive coordinates
IDCVG 1 Index how to signal convergence:
    1. check nr. of negative Hessian eigenvalues is correct and max. component and rms value of gradient are less than the convergence criterion (see CVG_GRD)
    3. same as 1, but both max. component of step and change in energy should be less than their respective convergence criteria (see CVG_STP and CVG_ENR)
    2. same as 3, but only of the additional criteria has to be fulfilled
IDELOCAL 1 Kind of coordinates to use in the geometry optimization:
    1. adapted delocalized coordinates
    0. Cartesian coordinates
IDIIS 3 Kind of GDIIS equations to use:
    0. original GDIIS
    1. same as 0, but with Farkas-Schlegel rules applied
    2. use gradient as error vector
    3. same as 2, but with Farkas-Schlegel rules applied
    4. use ‘energy’ vector as error vector
    5. same as 4, but with Farkas-Schlegel rules applied
IDSTEP 5 Step to take:
    1. RSO for minimizations, RFO (Baker) for TransitionStates
    3. RFO (Baker) always
    5. Generalized RSO (Swart) using image-function for TransitionStates
IEXCST 1 Number of excited state to use for numerical gradients By default for singlet excited state; triplet excited state can be used by adding ONLYTRIP keyword to EXCITATIONS block on input
IHOPT 3 Index for force constants method to use for initial Hessian:
    0. Baker (0.5 bonds, 0.2 angles, 0.1 dihedrals)
    1. Thomas Fischer
    2. simplification of Lindh
    3. Swart-Bickelhaupt scheme
    7. Swart generalized scheme (works well for close to minima)
IHUPD -1 cq. 4 Index for Hessian update scheme:
    1. BFGS for Hessian (-1 BFGS for inverse Hessian)
    2. Powell-symmetric-Broyden, PSB (for Transition States)
    3. Murtagh-Sargent (Symmetric Rank-One, SR1)
    4. Bofill weighted combi of PSB and SR1 (for Transition State)
    5. Farkas-Schlegel weighted combi of BFGS and SR1
    6. Bakken-Halgaker combi of BFGS and SR1
IQUILD_OUTPUT 1 Amount of output requested, debug output \(\geq\) 2
IRESTART 0 Index if ADF/ORCA jobs should restart from t21.files from previous geometry
    < 0 ORCA uses restart, ADF not
    > 0 both ORCA and ADF use restart
ITRUST 0 Index if dynamic trust radius should be used (1) or not (0)
MXDIIS 5 Maximum number of GDIIS vectors to use
MXGEO 50 Maximum number of geometry cycles (overrides value read from ITERATIONS in GEOMETRY block)
NR_REGIONS 1 Number of different regions for multi-level approach
NRLT 0 Number of LinearTransit steps
RTRUST 0.20 Trust radius value
SMETAGGA
String for functional from METAGGA post-SCF scheme to use for numerical gradients, should be given exactly as on METAGGA output
TRUST_ALFA 1.20 Factor to increase trust radius with if \(\Delta\) energy agrees with model prediction
TRUST_BETA 0.70 Factor to decrease trust radius with if \(\Delta\) energy does not agree with model
TRUST_GOOD 0.80 Lower threshold for increasing trust radius
TRUST_RMIN 0.40 Upper threshold for increasing trust radius

The other keywords that are printed in the output are for debug purposes, under development, or of technical nature. More information about them can be obtained (if needed) from SCM or M. Swart.

CONSTR subblock in QUILD block

Constraints can be supplied in the CONSTR subblock of QUILD. Below are the different option that are possible:

QUILD
  CONSTR
    dist   1 2         0.9
    angle  1 2 3     120.0
    dihed  1 2 3 4   100.0
    x      1           0.0   ! only with idelocal=0
    y      1           0.0   ! only with idelocal=0
    z      1           0.0   ! only with idelocal=0
  SUBEND
END

The units of these constraints are determined by the parameters in the UNITS block. The numbers in this subblock refer like usual to the atom numbers, as they are found in the ATOMS block.

A special case is observed for LinearTransit calculations, as given in the example below.

QUILD
  nrlt 11
  CONSTR
    dist   1 2         1.0    2.0
    angle  1 2 3     120.0   70.0
  SUBEND
END

Here there are two LinearTransit coordinates, i.e. the distance between atoms 1 and 2 and the angle 1-2-3. The distance between atoms 1 and 4 is a simple constraint throughout the whole calculation.

FROZEN subblock in QUILD block

Another way to introduce constraints is by freezing certain atoms. This can be achieved with the FROZEN subblock of QUILD, where either all three Cartesian (x, y, z) coordinates of an atom (or a series of atoms) can be frozen, or only one of the three:

QUILD
  FROZEN
    x      1-37   ! the X-coordinates of atoms 1 to 37 are kept frozen
    xyz   48-256  ! the X,Y,Z-coordinates of atoms 48 to 256 are kept frozen
  SUBEND
END

SYMROT subblock in QUILD block

Sometimes, one wants to lower the symmetry because of more convenient descriptions of d-orbitals of transition metals for instance. In that case, if one still wants to maintain the higher symmetry for the geometry, one can use the SYMROT subblock to rotate the coordinates. For instance, for Fe(II)(Cl)4 2- with Td geometric symmetry, the Fe d-orbitals are not conveniently separated. This might be better done within C2v symmetry:

Symmetry C(2v)

QUILD
 Symgeo T(d)
 Symrot
   -0.7071067811865475 -0.7071067811865475  0.0
   -0.7071067811865475  0.7071067811865475  0.0
    0.0                 0.0                 1.0
 Subend
End

Atoms
 Fe               0.000000000    0.000000000    0.000000000
 Cl              -1.326583289    1.326583289    1.326583289
 Cl              -1.326583289   -1.326583289   -1.326583289
 Cl               1.326583289    1.326583289   -1.326583289
 Cl               1.326583289   -1.326583289    1.326583289
End

This transforms the coordinates from Td symmetry:

Atomic coordinates

 atom       nr    x (Bohrs)   y (Bohrs)   z (Bohrs)       x (angs)    y (angs)    z (angs)
--------------------------------------------------------------------------------------------
 FE          1      0.00000     0.00000     0.00000        0.00000     0.00000     0.00000
 CL          2     -2.50688     2.50688     2.50688       -1.32658     1.32658     1.32658
 CL          3     -2.50688    -2.50688    -2.50688       -1.32658    -1.32658    -1.32658
 CL          4      2.50688     2.50688    -2.50688        1.32658     1.32658    -1.32658
 CL          5      2.50688    -2.50688     2.50688        1.32658    -1.32658     1.32658

to C2v symmetry:

SYMMETRY C(2V)
Atoms
 FE               0.000000000    0.000000000    0.000000000
 CL               0.000000000    1.876072079    1.326583289
 CL               1.876072079    0.000000000   -1.326583289
 CL              -1.876072079    0.000000000   -1.326583289
 CL               0.000000000   -1.876072079    1.326583289
End

The particular rotation matrix to be used depends on the choice made by the user for how to represent the molecule in the lower symmetry (see AMSinput how to impose symmetry).

TSRC subblock in QUILD block

The Transition State Reaction Coordinates that are used to construct the special initial Hessian, should be given in the TSRC subblock of QUILD. Similar to the CONSTR subblock, the distances, angles, or dihedrals should be specified, one per line, with atom numbers. The atom numbers should refer to the atoms as they are found in the ATOMS block.

QUILD
  TSRC
    dist   1 2
    angle  1 2 3
    dihed  1 2 3 4
  SUBEND
END

REGION subblocks in QUILD block

The definition of the different regions should be given in REGION subblocks of QUILD. Although the program counts the number of regions itself, it should be regarded good practice to make sure that the NR_REGIONS keyword corresponds to the correct number of REGION subblocks.

QUILD
  NR_REGIONS 2
  REGION 1
    1-11
  SUBEND
  REGION 2
    12 14 13 15 16 17 19 18 22 21 20
  SUBEND
END

The order in which the atom numbers are given does not matter, and in order that the input is easier to make and read, shortcuts are introduced. For instance, the “1-11” shortcut corresponds to “1 2 3 4 5 6 7 8 9 10 11” etc. Unlike other multi-level approaches, there is no need to have a shell structure for the different regions. I.e., the regions can overlap, or be defined as given above for DNA.

ADDREMOVE subblock in QUILD block

There is no ADDREMOVE subblock of QUILD active yet, but in the future it will be added to be able to control how the capping atoms will be added in the case of regions with dangling bonds. I.e., which elements should be added, and so on. For the moment, only hydrogens will be added, which works without problems for QM/QM and/or QM/MM calculations on DNA, or simple peptides. Future developments should decide whether this needs to be adapted.

DESCRIPTION subblocks in QUILD block

In case of multi-level jobs, where different regions are treated with different methodologies, the different methodologies should be given in the DESCRIPTION subblocks.

QUILD
  DESCRIPTION 1 ADF [NUMFREQ]
    XC
      GGA OPBE
    END
    BASIS
      type TZ2P
      core NONE
    END
  SUBEND
  DESCRIPTION 2 ADF NUMGRAD
    XC
      HYBRID B3LYP
    END
    basis
      type DZ
      core NONE
    end
  SUBEND
  DESCRIPTION 3 ORCA NUMFREQ
    %method method hf
     runtyp gradient
    end
    %basis basis sto_3g
    end
    %coords
      mult 2
      charge -1
    end
  SUBEND
  DESCRIPTION 4 NEWMM NUMFREQ
    QMMM
      FORCE_FIELD_FILE $AMSRESOURCES/ForceFields/amber95.ff
      QMMM_INFO
       -1    OW  QM  -0.8340  HOH     1  O         2      3
        2    HW  QM   0.4170  HOH     1  H1       -1
        3    HW  QM   0.4170  HOH     1  H2       -1
        4    OW  MM  -0.8340  HOH     2  O         5      6
        5    HW  MM   0.4170  HOH     2  H1        4
        6    HW  MM   0.4170  HOH     2  H2        4
      SUBEND
    END
  SUBEND
  DESCRIPTION 5 DFTB NUMFREQ
    CHARGE 0
    GEOMETRY
      runtype SP
      iterations 1
    END  1
  SUBEND
  DESCRIPTION 6 MOPAC NUMFREQ
    AUX(0) BONDS CHARGE=0 SCFCRT=1.0D-8 PM3 1SCF GRAD
    Coordinates generated by AMSinput (c) SCM 1998-2009
  SUBEND
  DESCRIPTION 7 GENERIC NUMGRAD NUMFREQ
  ! input-description specific for GENERIC program
  ! for the system under study (see above)
  SUBEND
END

Description 1 here applies to OPBE/TZ2P(ae) with ADF, description 2 to B3LYP/DZ(ae) with ADF, description 3 to UHF/STO-3G through the ORCA interface, and finally descriptions 4 to 7 apply to description for NEWMM, DFTB, MOPAC and GENERIC respectively.

The input for multi-level approaches has been explained above. The standard input should be given for ADF, DFTB and NEWMM. See the corresponding User Manuals for ADF, DFTB and ADF-QM/MM respectively for them. Also for ORCA should standard input be used, the only exception being the total charge and multiplicity, which should be given as a partial %coords block. The QUILD program will then add the atomic coordinates to this block for the “black-box” inputfiles.

Numerical versus analytical Hessians for multi-level vibrational frequencies

The descriptions on the previous page indicate for some of the programs, whether the gradients and Hessians can be obtained analytically (no extra keywords necessary) or numerically. In the latter case, depending on if it is for the gradients or Hessian, one should add NUMGRAD or NUMFREQ to the DESCRIPTION line (see previous page). The QUILD program will then take care of preparing the correct number of jobs etc.

Use of a GENERIC description for use with user-provided QM-program

The 2009.01 version of QUILD allows the user to create his/her own script for use with a QM-program (e.g. HONDO, Molcas, etc.) for which no standard interface is available yet within QUILD. For this purpose (and with the GENERIC description above), the QUILD program writes a generalized inputfile for this script that consists of the following:

Line 1:

NAT IQRUN
NAT    number of atoms
IQRUN  type of job:
       0 single-point energy
       1 single-point energy+grad
       2 single-point energy+grad+Hess

Line 2 to NAT+1

ATOM X  Y  Z
ATOM   atomname
X      Cartesian X-coordinate (in Å)
Y      Cartesian Y-coordinate (in Å)
Z      Cartesian Z-coordinate (in Å)

Remaining lines

User provided lines on input (within DESCRIPTION block)

The user should then make sure that his/her script runs their program, and extract data from it in the following manner (the QUILD program reads these lines as free format, e.g. spaces or upper/lowercase are not important):

# ----------------------------------------------
# lines starting with # will be ignored by QUILD
# ----------------------------------------------
# ---------------
# number of atoms
# ---------------
[nat]     3
# ----------------------
# total energy (Hartree)
# ----------------------
[energy]  -74.964263362500
# ----------------------------
# cartesian coordinates (Bohr)
# ----------------------------
[xyz]       0.0000000    0.0000000    0.0000000
[xyz]       0.0000000   -1.4572640   -1.1166010
[xyz]       0.0000000    1.4572640   -1.1166010
# --------------------
# expectation value S2
# --------------------
[s2]        0.000000000000
[sz]        0.000000000000
# ------------------------------
# energy gradient (Hartree/Bohr)
# ------------------------------
[grad]      0.0000000      0.0000000     -0.0424023
[grad]      0.0000000    0.0073465    0.0212011
[grad]      0.0000000   -0.0073465    0.0212011
# ------------------------------
# Hessian matrix (Hartree/Bohr2)
# ------------------------------
[hess]    -0.03797442   0.00000000   0.00000000   0.01898721   0.00000000   0.00000000
[hess]     0.01898721   0.00000000   0.00000000   0.00000000   0.93011207   0.00000000
[hess]     0.00000000  -0.46505603  -0.37088899   0.00000000  -0.46505603   0.37088899
[hess]     0.00000000   0.00000000   0.62917145   0.00000000  -0.24554704  -0.31458572
[hess]     0.00000000   0.24554704  -0.31458572   0.01898721   0.00000000   0.00000000
[hess]    -0.01201427   0.00000000   0.00000000  -0.00697295   0.00000000   0.00000000
[hess]     0.00000000  -0.46505603  -0.24554704   0.00000000   0.49190911   0.30821802
[hess]     0.00000000  -0.02685307  -0.06267097   0.00000000  -0.37088899  -0.31458572
[hess]     0.00000000   0.30821802   0.29686554   0.00000000   0.06267097   0.01772018
[hess]     0.01898721   0.00000000   0.00000000  -0.00697295   0.00000000   0.00000000
[hess]    -0.01201427   0.00000000   0.00000000   0.00000000  -0.46505603   0.24554704
[hess]     0.00000000  -0.02685307   0.06267097   0.00000000   0.49190911  -0.30821802
[hess]     0.00000000   0.37088899  -0.31458572   0.00000000  -0.06267097   0.01772018
[hess]     0.00000000  -0.30821802   0.29686554

# ------------------------------------------------------
# example of data for S2-correction
# in this case the Sz and S2 values should also be given
# ------------------------------------------------------
# ---------------
# number of atoms
# ---------------
[nat]     2
# ----------------------
# total energy (Hartree)
# ----------------------
[energy]  -74.362823992381
# ----------------------------
# cartesian coordinates (Bohr)
# ----------------------------
[xyz]       0.0000000    0.0000000    0.0000000
[xyz]       0.0000000    1.4572640   -1.1166010
# --------------------
# expectation value S2
# --------------------
[s2]        0.753292786229
[sz]        0.500000000000

Spin-contamination correction per region

Previously, the spin-contamination correction was done for the complete system, but starting from version 2009.01 it can be performed for different regions, as in the following example:

QUILD
  DESCRIPTION 1 ADF
    Occupations smearq=0.0  &
       AA1           4.0     //      5.0
       AA2           0.0     //      0.0
       EE1           8.0     //      8.0
       EE2           6.0     //      4.0
      AAA1           0.0     //      0.0
      AAA2           4.0     //      4.0
      EEE1           6.0     //      6.0
      EEE2           4.0     //      4.0
    End
    CHARGE 0.0 1.0
    Unrestricted
  SUBEND

  DESCRIPTION 2 ADF
    Occupations smearq=0.0  &
       AA1           5.0     //      4.0
       AA2           0.0     //      0.0
       EE1           8.0     //      8.0
       EE2           6.0     //      4.0
      AAA1           0.0     //      0.0
      AAA2           4.0     //      4.0
      EEE1           6.0     //      6.0
      EEE2           4.0     //      4.0
    End
    CHARGE 0.0 3.0
    Unrestricted
  SUBEND

  INTERACTIONS
    TOTAL  description 1
    S2CORR region 1 spin-splus-description 2 for contaminated-description 1
  SUBEND

END
SYMMETRY D(5H)

Note that this in this case, the spin-contaminated system (doublet) consists of a triplet-alfa in the EE2-irrep coupled with a doublet-beta in the AA1-irrep. This is corrected for by a pure quartet, and the corresponding energies corrected:

Values for S2correction  1 :
s2cont        1.75396
s2pure        0.75000
s2plus        3.78716
a_s2          0.33056
jobsigns  job  2   -0.49378     job  1    1.49378

INTERACTIONS subblock in QUILD block

One of the most important input-parts for multi-level jobs is the INTERACTIONS subblock of QUILD, where one should define how the different descriptions should be applied to the different regions. At the part where we explained the multi-level approaches, we already showed some examples of how to combine different methodologies. Below is another example input where all possible options are given.

QUILD
  INTERACTIONS
    TOTAL     description 1
    REPLACE   region 1 region 2    description 3 for description 2
    REPLACE   region 1             description 4 for description 3
    INTXN     region 1 region 2    description 3 for description 2
    S2CORR    region 1  spin-splus-description 2 for contaminated-description 1
  SUBEND
END

If an INTERACTIONS subblock is present (if none is present it means no multi-level setup is done, i.e. pure QM or MM), there should always be a line with the description of the total system, as shown in the first line of the INTERACTIONS subblock. Then if you want to replace the interactions for one (or more) region(s), you could do so as indicated in the second and third line. Finally, if you want to replace the interaction between two regions, as we need for DNA where we replace the BP86 \(\pi\)-stacking by LDA \(\pi\)-stacking, the fourth line of the INTERACTIONS subblock should be used. Finally, the last line can be used for spin-contamination corrections for one (or more) regions.

Note that in all cases it is not necessary at all to add the “region”, “description” and “for” words in the INTERACTIONS subblock; they are ignored when reading the input. The program reads the line, uses the last two integers for the descriptions and the ones before for the regions. Therefore, a completely equivalent input would be as shown below. However, for better readability, it is to be advised to always use the additional text anyway.

QUILD
  INTERACTIONS
    TOTAL             1
    REPLACE   1 2   3 2
    REPLACE   1     4 3
    INTXN     1 2   3 2
    S2CORR    1     2 1
    S2CORR    1 3   2 1
  SUBEND
END

Note that in the last line, it is indicated that the spin-contamination correction is applied to regions 1 and 3 together.

INLINE options in the QUILD block

Similar to the situation in ADF, one can use the INLINE directive to read specific input-lines from a file rather than from input. In general, this should make no difference, but in rare instances (for instance if the $ sign is needed in inputfiles for one of the programs), it might become useful.