Cart

here a much better manual in french Cart

Basically, this program converts geometries from one program to another one (like Babel). But also, it can also calculate distances, angles, zmatrix, adds dummy atoms... (sorry it can't make coffee, maybe the next version).

What does-it do?

Read cartesian coordinates from g92, monstergauss (an old ab initio program), exthuc (extended Hückel), ampac, gamess, molpro.

Write cartesian coordinates for xmol, rasmol, molecule, chem3d, molplt.

Read a zmatrix.

Write zmatrix for g92, monstergauss, exthuc.

Calculate rotational constants.

list of commands.

How does-it work?

The program reads "namelist" (here, only 4 letters of a word -French-) which correspond to a command and then it does it.
So, when you add a dummy atom, you can use it for another command.

download a copy of cart cart.tar.gz
uncompress and compile it.


gunzip cart.tar.gz
tar xvf cart.tar
cd cart
make

There are more examples in cart/examples

a simple example: read (lecture) and write (ecriture) cartesian coordinates.

 $lect na=4 prog='molpro' $end
  1   O     8.00    1.374606665    1.374606665   -0.344635602
  2   O     8.00    1.374606665   -1.374606665    0.344635602
  4   O     8.00   -1.374606665   -1.374606665   -0.344635602
  3   O     8.00   -1.374606665    1.374606665    0.344635602
 $eras $end
 $fini

With the first namelist ($lect), the program reads the number of atoms (na) and the format of the cartesian coordinates (prog='molpro').

With $eras, it's write the same geometry in xyz for rasmol.

The last one ($fini) is use to specify the end of the file.

you get:


           4

 O         0.727410         0.727410        -0.182373
 O         0.727410        -0.727410         0.182373
 O        -0.727410        -0.727410        -0.182373
 O        -0.727410         0.727410         0.182373

List of namelists (or commands):

$lect read cartesian coordinates
$lecz read a zmatrix

$puri orient the coordinates such the 2 first atoms are on the z-axis
$rota rotational constants

$oper (operation) beginning of a sub commands list (compulsory if you're using commands in the following list)

$dist calculate a distance (2 atoms)
$angl calculate a valence angle (3 atoms)
$dihe calculate a dihedral angle (4 atoms)
$prod add a dummy atom, vector product of "3 atoms"
$proj add a dummy atom, projection of a vector on a plan (5 atoms)
$fict add a dummy atom, like in a zmatrix
$biss add a dummy atom, bisector of "3 atoms"
$fic2 add a dummy atom, between 2 atoms
$zmat make a zmatrix.

$fiop end of the sub commands (compulsory)

$cart write cartesian coordinates without specific format
$e_3d write cartesian coordinates for chem3d
$xmol write cartesian coordinates for xmol
$emol write cartesian coordinates for molecule
$eras write cartesian coordinates for rasmol
$eplt write cartesian coordinates for molplt

$fini end of the data file (compulsory)

$lect

You need to specify the number of atoms "nb=??" and the format of xyz with a program name (prog='g92', 'monst', 'ampac', 'gamess', 'exthuc' and 'molpro') in the namelist.
You can also specify the unit (bohr=.true. or .false.) and a convention flag (convert=.true. or .false.). If convert=.true. then it does the conversion (Bohr->Ångström or the reverse).

Then you need to give "na" lines which define your cartesian coordinates.

the complete example:

 $lect na=3 prog='gamess' convert=f $end
 O           8.0     0.0000000000        0.5000000000       -0.1344680200
 H           1.0     1.4326043750        0.5000000000        1.0670525220
 H           1.0    -1.4326043750        0.5000000000        1.0670525220
 $puri $end
 $cart $end
 $rota $end
 $fini

Also example for the rotational constants (the units MUST be in Bohr).

you get:


  8   0.000000000   0.000000000   0.000000000
  1   0.000000000   0.000000000   1.869761190
  1  -1.841201533   0.000000000  -0.325551565
 txx,tyy,tzz,txy,txz,tyz   (masse au * bohr^2)
   6372.11125974603        12251.4586000692        5879.34734032315     
  0.000000000000000E+000  -1393.44696872439       0.000000000000000E+000



 moments of inertia in masse au * bohr^2
   4710.66798520812        7540.79061486106        12251.4586000692     

 moments of inertia in kg * cm^2
  1.201661451093768E-043  1.923607739093903E-043  3.125269190187670E-043

 rotational constants in cm-1
   23.2954828331759        14.5524906852527        8.95707921517093

$cart $e_3d $xmol $emol $eras $eplt $rota $oper $fiop $fini
For these namelists you don't need other data.

$dist $angl $dihe $prod $proj

You need to specify the number of operation "nb=??" (nb=1 default) in the namelist. Then on the next line(s) ("nb" lines) the atoms involve in the "nb" operation(s).

example:

 $dist nb=2 $end
1 2
1 3
 $angl $end
3 2 1
 $dihe nb=1 $end
   5 1 2 3
 $prod $end
3 2 1
 $proj $end
1 2 3  4 5

$dist: calculate 2 distances (nb=2) between atoms 1-2 and 1-3.
$angl: calculate 1 valence angle (nb=1, default) between atoms 3, 2 and 1.
$dihe: calculate 1 dihedral angle (nb=1) between atoms 5 1 2 3 (the angle between the plans 5-1-2 and 1-2-3).
$prod: add a dummy atom # at 1.000 (Ångström or Bohr) from 2 such the vector #-2 is perpendicular to the vectors 3-2 and 1-2 (vector product).
$proj: add a dummy atom # from 4 such the vector 4-# is the projection of the vector 4-5 on the plan 1-2-3.

the complete example:

 $lect na=5 prog='molpro' convert=.false. $end
  1   O     8.00    0.000000000    0.000000000    0.000000000
  2   O     8.00    0.000000000    0.000000000    0.500000000
  3   O     8.00    0.000000000    0.500000000    0.000000000
  5   O     8.00    0.000000000    0.000000000    0.000000000
  4   O     8.00    0.500000000    0.000000000    0.500000000
 $oper $end
 $dist nb=2 $end
1 2
1 3
 $angl $end
3 2 1
 $dihe nb=1 $end
   5 1 2 3
 $prod $end
3 2 1
 $proj $end
1 2 3  4 5
 $fiop
 $cart $end
 $fini

you get:


 oper           5
 dist           5
   1   2     0.50000000
   1   3     0.50000000
 angl           5
   3   2     0.70710678   1   45.000
 dihe           5
   5   1     0.70710678   2   45.000   3   90.000
 prod           5
point : 6 -1.00000000  0.00000000  0.50000000
 proj           6
point : 7  0.00000000  0.00000000  0.50000000
 fiop           7
  8   0.000000000   0.000000000   0.000000000
  8   0.000000000   0.000000000   0.500000000
  8   0.000000000   0.500000000   0.000000000
  8   0.000000000   0.000000000   0.000000000
  8   0.500000000   0.000000000   0.500000000
  0  -1.000000000   0.000000000   0.500000000
  0   0.000000000   0.000000000   0.500000000

$biss

You need to specify the number of operation "nb=??" and "norm=??" in the namelist (nb=1 and norm=1.000 default). Then on the next ligne(s) ("nb" lines) the atoms involve in the "nb" operation(s)

example:

 $biss nb=1 norm=0.5 $end
2 1 3

$biss: add 1 dummy atom # (nb=1) at 0.5 (norm=0.5) from 1, such the vector 1-# is the bisector of the vectors 1-2 and 1-3.

the complete example:

 $lect na=5 prog='molpro' convert=.false. $end
  1   O     8.00    0.000000000    0.000000000    0.000000000
  2   O     8.00    0.000000000    0.000000000    0.500000000
  3   O     8.00    0.000000000    0.500000000    0.000000000
  5   O     8.00    0.000000000    0.000000000    0.000000000
  4   O     8.00    0.500000000    0.000000000    0.500000000
 $oper $end
 $biss nb=1 norm=0.5 $end
2 1 3
 $fiop
 $cart $end
 $fini

you get:
oper 5 biss 5 fiop 6 8 0.000000000 0.000000000 0.000000000 8 0.000000000 0.000000000 0.500000000 8 0.000000000 0.500000000 0.000000000 8 0.000000000 0.000000000 0.000000000 8 0.500000000 0.000000000 0.500000000 0 0.000000000 0.353553391 0.353553391

$fic2
Add a dummy atom between 2 atoms.
You need to specify "n1=??" and "n2=??" the first and the second atom, respectively and also "r=??" for the position of this atom between the two atoms (r=0.0 add an atom in n1 and r=1.0 add an atom in n2).

example:

$fic2 n1=1 n2=2 r=0.2 $end

$fic2: add 1 dummy atom # at 0.2*distance(1-2) (r=0.2) from 1.

the complete example:
$lect na=5 prog='molpro' convert=.false. $end 1 O 8.00 0.000000000 0.000000000 0.000000000 2 O 8.00 0.000000000 0.000000000 0.500000000 3 O 8.00 0.000000000 0.500000000 0.000000000 5 O 8.00 0.000000000 0.000000000 0.000000000 4 O 8.00 0.500000000 0.000000000 0.500000000 $oper $end $fic2 n1=1 n2=2 r=0.2 $end $fiop $cart $end $fini

you get:
oper 5 fic2 5 6 0.000000000000000E+000 0.000000000000000E+000 0.100000001490116 fiop 6 8 0.000000000 0.000000000 0.000000000 8 0.000000000 0.000000000 0.500000000 8 0.000000000 0.500000000 0.000000000 8 0.000000000 0.000000000 0.000000000 8 0.500000000 0.000000000 0.500000000 0 0.000000000 0.000000000 0.100000001

$fict
Add a dummy atom(s) like in a zmatrix (from a distance, a valence angle and a dihedral angle).
You need to specify the number of operation "nb=??" (nb=1 default) in the namelist. Then on the next line(s) ("nb" lines):
the first atom number, a distance, the second atom number, the valence angle, the third atom number and the dihedral angle.

example:

$fict $end 1 2.0 2 90. 3 45.

$fict: add a dummy atom # at 2.0 (second number) from 1 such the valence angle #-1-2 is 90. (fourth number) and the dihedral angle #-1-2-3 is 45. (last number).

the complete example:
$lect na=5 prog='molpro' convert=.false. $end 1 O 8.00 0.000000000 0.000000000 0.000000000 2 O 8.00 0.000000000 0.000000000 0.500000000 3 O 8.00 0.000000000 0.500000000 0.000000000 5 O 8.00 0.000000000 0.000000000 0.000000000 4 O 8.00 0.500000000 0.000000000 0.500000000 $oper $end $fict $end 1 2.0 2 90. 3 45. $fiop $cart $end $fini

you get:
oper 5 fict 5 point : 6 1.41421356 1.41421356 0.00000000 fiop 6 8 0.000000000 0.000000000 0.000000000 8 0.000000000 0.000000000 0.500000000 8 0.000000000 0.500000000 0.000000000 8 0.000000000 0.000000000 0.000000000 8 0.500000000 0.000000000 0.500000000 0 1.414213563 1.414213562 0.000000000

$puri
Rotate the geometry such the first atom is on the origin and the second on the z-axis.

the complete example:
$lect na=4 prog='molpro' convert=f $end 1 O 8.00 -1.300720025 1.300720025 -0.237043517 2 O 8.00 -1.300720025 -1.300720025 0.237043517 3 O 8.00 1.300720025 1.300720025 0.237043517 4 O 8.00 1.300720025 -1.300720025 -0.237043517 $puri $end $cart $end $fini

you get:
8 0.000000000 0.000000000 0.000000000 8 0.000000000 0.000000000 2.644286076 8 2.601440050 0.466405284 0.084997806 8 2.601440050 -0.466405284 2.559288269

$zmat
Write a zmatrix for some programs.
You need to specify the number of atoms "nb=??" (nb= number of atoms previously defined, default) involve in the zmatrix. Also the name of the program (prog='g92' (default) or prog='monster' or prog='exthuc').
Then you need to give nb lines which define your zmatrix.

the first atom (position on the origin).

the second and the first atom (define the first distance).

3 atoms (define one distance and an angle).

4 atoms (define one distance, a valence angle and a dihedral angle).

same as before.....

the complete example:
$lect na=4 prog='molpro' $end 1 O 8.00 1.374606665 1.374606665 -0.344635602 2 O 8.00 1.374606665 -1.374606665 0.344635602 4 O 8.00 -1.374606665 -1.374606665 -0.344635602 3 O 8.00 -1.374606665 1.374606665 0.344635602 $oper $end $zmat nb=4 prog='g92' $end 1 2 1 3 2 1 4 3 2 1 $fiop $fini

you get:
oper 4 zmat 4 g92 O1 O2 O1 R1 O3 O2 R2 O1 A4 O4 O3 R3 O2 A5 O1 DH6 R1 1.49984751 R2 1.49984751 R3 1.49984751 A4 86.6094972 A5 86.6094972 DH6 -27.3367493 fiop 4

$lecz
Read a zmatrix.
You need to specify the number of atoms "nb=??" involve in the zmatrix.
Then you need to give nb lines which define your zmatrix.

Z (atomic number) of the first atom (position on the origin).

Z of the second atom, the first atom (1) and a distance (define the z-axis).

Z of the third atom, the number of the second atom (1 or 2), a distance, the number of the second atom (2 or 1) and a valence angle (define the xz plan).

Z of the fourth atom, n1, a distance, n2 a valence angle, n3 and a dihedral angle.

same as before.....

the complete example:
$lecz nb=4 $end 0. 0. 1 1. 1. 2 4.1 1 90. 1. 3 1.34 2 110. 1 90. $cart $end $fini

you get:
0 0.000000000 0.000000000 0.000000000 0 0.000000000 0.000000000 1.000000000 1 4.100000000 0.000000000 1.000000001 1 4.558306992 1.259188112 1.000000001

Background: Régis Loisel ici ou là (in French)