#! /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 SigU and EpsU 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 SigU and EpsU 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.


$ADFBIN/adf << eor
Title 3D-RISM test

SYMMETRY C(s)

NOBECKEGRID

ATOMS  internal
  C   0  0  0   0.0       0.0            0.0          SigU=3.50    EpsU=0.066
  O   1  0  0   1.208031  0.0            0.0          SigU=2.96    EpsU=0.200
  O   1  2  0   1.341959  123.553475     0.0          SigU=2.96    EpsU=0.200
  C   1  2  3   1.495685  124.769221   180.0          SigU=3.50    EpsU=0.066
  N   4  1  2   1.427005  115.495309     0.0          SigU=3.25    EpsU=0.170
  H   3  1  2   0.992780  105.645766     0.0          SigU=1.00    EpsU=0.046
  H   4  1  2   1.107716  107.591718   123.973836     SigU=1.00    EpsU=0.046
  H   4  1  2   1.107716  107.591718  -123.973836     SigU=1.00    EpsU=0.046
  H   5  4  1   1.028574  109.800726    57.697485     SigU=1.00    EpsU=0.046
  H   5  4  1   1.028574  109.800726   -57.697485     SigU=1.00    EpsU=0.046
End

Basis
  Type DZP
  Core small
End

XC
  LDA
End
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

Gradient

eor

# The densf utility can be used to convert the 3D-RISM grid data stored in the TAPE21 file to 
# the TAPE41 format suitable for visualization by ADFview. 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)


$ADFBIN/densf << eor
RISM
eor

mv TAPE41 glycine.t41
mv TAPE21 glycine.t21
rm -f RISMDATA