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#! A demonstration of mixed Cartesian/ZMatrix geometry specification, using variables, for
#! the benzene-hydronium complex.  Atoms can be placed using ZMatrix coordinates, whether they belong
#! to the same fragment or not.  Note that the Cartesian specification must come before the ZMatrix entries
#! because the former define absolute positions, while the latter are relative.

refENuc   = 268.617178206572646  #TEST

molecule dimer {
1 1
# This part is just a normal Cartesian geometry specification for benzene
C          0.710500000000    -0.794637665924    -1.230622098778
C          1.421000000000    -0.794637665924     0.000000000000
C          0.710500000000    -0.794637665924     1.230622098778
C         -0.710500000000    -0.794637665924     1.230622098778
H          1.254500000000    -0.794637665924    -2.172857738095
H         -1.254500000000    -0.794637665924     2.172857738095
C         -0.710500000000    -0.794637665924    -1.230622098778
C         -1.421000000000    -0.794637665924     0.000000000000
H          2.509000000000    -0.794637665924     0.000000000000
H          1.254500000000    -0.794637665924     2.172857738095
H         -1.254500000000    -0.794637665924    -2.172857738095
H         -2.509000000000    -0.794637665924     0.000000000000
# And the hydronium part is specified using a zmatrix, referencing the benzene coordinates
X  1  CC  3  30   2  A2
O  13 R   1  90   2  90
H  14 OH  13 TDA  1  0
H  14 OH  15 TDA  13 A1
H  14 OH  15 TDA  13 -A1

CC    = 1.421
CH    = 1.088
A1    = 120.0
A2    = 180.0
OH    = 1.05
R     = 4.0
units angstrom
}

dimer.update_geometry()
dimer.print_out()
compare_values(refENuc, dimer.nuclear_repulsion_energy(), 9, "Nuclear repulsion energy")   #TEST