#! /bin/sh


# == Expert option ==

# Computing solvent effects with the 3D-RISM model is illustrated on the glycine
# example.

# All subkeys in the RISM block are discussed in the User's Guide. The things to
# pay attention to here are adf.SigU and EpsUadf. parameters for each atom in the ATOMS
# block, the solvent parameters in the SOLVENT sub-block and the FFT box
# parameters in the SOLUTE sub-block. Both adf.SigU and EpsUadf. values as well as the
# solvent parameters may be obtained from force field parameter lists.
# Parameters for some common solvents are available in the ADF User's Guide.

# One should take into account the following when choosing FFT box parameters in
# the SOLUTE block:

# - the box should be at least twice as large as your model in each dimension,
# - the number of grid points in each dimension must be a power of 2, and
# - accuracy of the results and the memory usage depend on the number of grid-
#   points

# Note: the 3D-RISM part in ADF has not been parallelized, thus calculating on
# more than 1 processor will not reduce the elapsed time. In this example only
# the gradients are calculated, no geometry optimization is performed.


# == Remarks for different solvent than water ==

# The default values for the RISM1D subblock key are only applicable if the
# solvent is water. You must change the FLUIDPARAM subkey of the subblock key
# RISM1D when modeling a different solvent, at least the dielectric constant and
# the density. In that case you may also have to change other subkeys of the
# subblock key RISM1D. For a different solvent than water, of course, you also
# have to change the description of the subblock SOLVENT. You may have to change
# the boxsize.


$AMSBIN/ams <<eor
System
  atoms
     C  0.0                  0.0                0.0                   adf.SigU=3.50    adf.EpsU=0.066
     O  1.208031058311462    0.0                0.0                   adf.SigU=2.96    adf.EpsU=0.200
     O -0.741720974445343    1.118348836898804  0.0                   adf.SigU=2.96    adf.EpsU=0.200
     C -0.8529478907585144  -1.228639006614685  0.0                   adf.SigU=3.50    adf.EpsU=0.066
     N -0.1451586186885834  -2.467742681503296  0.0                   adf.SigU=3.25    adf.EpsU=0.170
     H -0.09300804138183594  1.869869947433472  0.0                   adf.SigU=1.00    adf.EpsU=0.046
     H -1.528575420379639   -1.167157530784607  0.8756611347198486    adf.SigU=1.00    adf.EpsU=0.046
     H -1.528575420379639   -1.167157530784607 -0.8756611347198486    adf.SigU=1.00    adf.EpsU=0.046
     H  0.4767249822616577  -2.513782262802124  0.8179888725280762    adf.SigU=1.00    adf.EpsU=0.046
     H  0.4767249822616577  -2.513782262802124 -0.8179888725280762    adf.SigU=1.00    adf.EpsU=0.046
  end
end

Task SinglePoint

Properties
  Gradients Yes
End

Engine ADF
  title 3D-RISM test
  basis
    core small
    type DZP
  end
  nobeckegrid
  Relativity Level=None
  rism glycine 1N
    RISM1D
    SUBEND
    SOLVENT1 water
      UNITS      uWeight=g/mol  ULJsize=A  ULJenergy=kcal/mol Ucoord=A Udens=1/A3
      Parameters Weight=18.015   nAtoms=2
      1    -0.8476   3.166    0.1554       0.000000  0.00000  0.000000
      2     0.4238   1.000    0.0460      -0.816490  0.00000  0.577359
                                           0.816490  0.00000  0.577359
      DenSpe=0.03333
    SUBEND
    SOLUTE  CO
      BOXSIZE 32.0 32.0 32.0
      BOXGRID   64   64   64
    SUBEND
  end
  symmetry C(s)
  xc
    lda
  end
EndEngine
eor


# The densf utility can be used to convert the 3D-RISM grid data stored in the adf.rkf file to 
# the TAPE41 format suitable for visualization by AMSview. The following fields are created 
# for each solvent site: Huv (solvent total correlation function), Uuv (solvent potential in RT), 
# Guv (solvent pair distribution function), Cuv (solvent direct correlation), 
# and PMF (potentials of mean force in kcal/mol)


$AMSBIN/densf << eor
adffile ams.results/adf.rkf
RISM
eor