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File Formats

Examples for input files and formats.

Table of contents

  1. Input Atomic Coordinates
  2. Ensemble and Trajectory Files
  3. Atomlists
  4. Constraints
  5. Vibrational frequencies in the vibspectrum format

Input Atomic Coordinates

The program supports molecular [INPUT] files in the

  • Turbomole coord format (.coord extension, Bohr)
  • Xmol format (.xyz extension, Ångström)
  • MDL molfile format (V2000,V3000, .sdf/.mol extension, Ångström)

Example coordinates are shown for the caffeine molecule below. Atoms are typically specified line-by-line, each containing the Cartesian x-, y-, and z-coordinate and the atom type by its element symbol. Depending on the input file type the Cartesian coordinates can be in atomic units (Bohr) or Ångström. Some file formats additionally require the total number of atoms in the molecule. The order in which atoms are specified should not be changed since structure comparisons depend on it. For the caffeine example the atom order has been marked in the below figure for better comprehension.

caffeine

$coord
        0.88817153184985        4.85432985322531        0.00113383599811      O
       -5.90936424946312       -0.83828274793318       -0.00056691799905      O
       -1.83038924627610       -2.48026624585729        0.00000000000000      N
        4.19179168499859        0.26682940488766       -0.00056691799905      N
       -2.54678462441286        2.04033787859209       -0.00018897266635      N
        2.66810507621022       -3.66077849255219        0.00037794533270      N
        1.62119650462550        0.48981715118187       -0.00151178133081      C
        0.73642648076997       -1.93961544742699       -0.00075589066540      C
        0.05801460856977        2.68719131551167       -0.00113383599811      C
       -3.60200799331702       -0.47148680254582       -0.00075589066540      C
        4.73036378409903       -2.26729405087968        0.00056691799905      C
       -2.69777378482733       -5.09470308482382        0.00151178133081      C
        6.03314134592305        2.27919932885980        0.00056691799905      C
       -4.34051317341685        4.13491091242693        0.00132280866446      C
        6.64484586690134       -2.98331148368374        0.00151178133081      H
       -1.97495333603463       -6.04202306124154       -1.68884871917917      H
       -4.75946557471709       -5.21488970062308        0.00207869932986      H
       -1.97419744536923       -6.04013333457803        1.69262817250619      H
        7.93534020541253        1.47417577020440        0.00037794533270      H
        5.75761919838324        3.41889347962287       -1.69924221582848      H
        5.75724125305054        3.41719272562571        1.70150988782469      H
       -3.41794861629111        5.98117386267651       -0.00056691799905      H
       -5.54105652274496        3.97352825536315        1.67826624986351      H
       -5.54559186673738        3.97239441936504       -1.67221912454028      H
$end
   24
   (in this line a comment or an energy can be placed)
 O     0.470000     2.568800     0.000600
 O    -3.127100    -0.443600    -0.000300
 N    -0.968600    -1.312500     0.000000
 N     2.218200     0.141200    -0.000300
 N    -1.347700     1.079700    -0.000100
 N     1.411900    -1.937200     0.000200
 C     0.857900     0.259200    -0.000800
 C     0.389700    -1.026400    -0.000400
 C     0.030700     1.422000    -0.000600
 C    -1.906100    -0.249500    -0.000400
 C     2.503200    -1.199800     0.000300
 C    -1.427600    -2.696000     0.000800
 C     3.192600     1.206100     0.000300
 C    -2.296900     2.188100     0.000700
 H     3.516300    -1.578700     0.000800
 H    -1.045100    -3.197300    -0.893700
 H    -2.518600    -2.759600     0.001100
 H    -1.044700    -3.196300     0.895700
 H     4.199200     0.780100     0.000200
 H     3.046800     1.809200    -0.899200
 H     3.046600     1.808300     0.900400
 H    -1.808700     3.165100    -0.000300
 H    -2.932200     2.102700     0.888100
 H    -2.934600     2.102100    -0.884900
2519
  caffeine (this is a comment line)

 24 25  0     0  0  0  0  0  0999 V2000
    0.4700    2.5688    0.0006 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1271   -0.4436   -0.0003 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9686   -1.3125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2182    0.1412   -0.0003 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3477    1.0797   -0.0001 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4119   -1.9372    0.0002 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8579    0.2592   -0.0008 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3897   -1.0264   -0.0004 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0307    1.4220   -0.0006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9061   -0.2495   -0.0004 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5032   -1.1998    0.0003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4276   -2.6960    0.0008 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1926    1.2061    0.0003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2969    2.1881    0.0007 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5163   -1.5787    0.0008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0451   -3.1973   -0.8937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5186   -2.7596    0.0011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0447   -3.1963    0.8957 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1992    0.7801    0.0002 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0468    1.8092   -0.8992 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0466    1.8083    0.9004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8087    3.1651   -0.0003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9322    2.1027    0.8881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9346    2.1021   -0.8849 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  2  0  0  0  0
  2 10  2  0  0  0  0
  3  8  1  0  0  0  0
  3 10  1  0  0  0  0
  3 12  1  0  0  0  0
  4  7  1  0  0  0  0
  4 11  1  0  0  0  0
  4 13  1  0  0  0  0
  5  9  1  0  0  0  0
  5 10  1  0  0  0  0
  5 14  1  0  0  0  0
  6  8  1  0  0  0  0
  6 11  2  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
 11 15  1  0  0  0  0
 12 16  1  0  0  0  0
 12 17  1  0  0  0  0
 12 18  1  0  0  0  0
 13 19  1  0  0  0  0
 13 20  1  0  0  0  0
 13 21  1  0  0  0  0
 14 22  1  0  0  0  0
 14 23  1  0  0  0  0
 14 24  1  0  0  0  0
M  END

$$$$

Ensemble and Trajectory Files

Ensemble (.xyz) and trajectory (.trj) files in CREST are given in the .xyz format as specified above. The files simply consists out of all the structures pasted after another.

If the ensemble is to be processed by CREST, e.g., with the CREGEN sorting routine, an energy in atomic units (Eh, Hartree) should be provided in the comment line. An example for an n-butane ensemble can be seen here:

  14
         -1.95933513
 C         -1.9450668421        0.1311167672       -0.0001772545
 C         -0.5674743975       -0.5132672899        0.0001933101
 C          0.5674752787        0.5132638115        0.0001915171
 C          1.9450638093       -0.1311175361       -0.0001779077
 H         -2.0853782627        0.7646639932        0.8782051254
 H         -2.7466842224       -0.6116573212       -0.0004139053
 H         -2.0848832626        0.7646834243       -0.8786240987
 H         -0.4586079390       -1.1740559621       -0.8706321703
 H         -0.4589068044       -1.1737556210        0.8712831745
 H          0.4588981405        1.1737728909        0.8712658721
 H          0.4586137126        1.1740687810       -0.8706234929
 H          2.0850227749       -0.7644118141       -0.8787988057
 H          2.0852599026       -0.7649044717        0.8780496213
 H          2.7466915989        0.6116467123       -0.0000648118
  14
         -1.95861370
 C         -1.5634429064        0.0307829908        0.5671856584
 C         -0.6780400299       -0.3575310612       -0.6072767893
 C          0.6780374832        0.3575328640       -0.6072807936
 C          1.5634444854       -0.0307786855        0.5671868578
 H         -1.7381548026        1.1085042885        0.5904194743
 H         -1.1085086806       -0.2426226956        1.5210355320
 H         -2.5399702240       -0.4581336702        0.5235479812
 H         -1.2059135035       -0.1493891533       -1.5491742664
 H         -0.5130824651       -1.4435518231       -0.6080674515
 H          0.5130888273        1.4435548434       -0.6080686466
 H          1.2059008586        0.1493974488       -1.5491848268
 H          1.1087081819        0.2429933207        1.5210259608
 H          2.5401620514        0.4577301888        0.5232639016
 H          1.7377812886       -1.1085555327        0.5906966592
  14
         -1.95476831
 C         -1.8280514558        0.1026283679       -0.3378109356
 C         -0.6096777513       -0.4807999039        0.3626338277
 C          0.6096679585        0.4807861256        0.3626336492
 C          1.8280554740       -0.1026120684       -0.3378127654
 H         -2.6737183814       -0.5895996214       -0.3384876099
 H         -1.6051787878        0.3482893729       -1.3783393521
 H         -2.1588537968        1.0236078559        0.1469845806
 H         -0.3239394543       -1.4268049722       -0.1182711212
 H         -0.8704029060       -0.7659987748        1.3922403082
 H          0.8703773548        0.7659540027        1.3922522276
 H          0.3239374558        1.4268002601       -0.1182574316
 H          1.6052556663       -0.3480468876       -1.3784082402
 H          2.1587507058       -1.0237028671        0.1468484919
 H          2.6738409543        0.5894715887       -0.3381226983

Atomlists

Atomlists are used for some argument such as --notopo. They are used to specify atoms or types of atoms of your input structure. Effectively, atomlists are a single string consisting out of the respective number of the atom, or the element symbol. The only important thing to notice is that no whitespaces should be present in the atomlist, and arguments are separated by a comma ,. As an example,

  1,3,4,5,6

would select atom 1 (one of the oxygens) and all the nitrogen atoms in the caffeine exmple from above. Alternatively a range of atoms could be specified, as for example

  1,3-6

Finally, atomlists are compatible with element symbols, so the same atoms would be selected by

  1,n

Constraints

Files for constraining must be in xtb’s input format. An example would be

$constrain
  atoms: 1-26
  force constant=0.5
  reference=coord.ref
$metadyn
  atoms: 27-41
$end

See Example 4 for a more detailed guide.


Vibrational frequencies in the vibspectrum format

Construction of vibspectrum files is straightforward. They are declared by the $vibrational spectrum keyword and ended by the $end keyword. Within this block, each mode is assigned one line containing the mode number, symmetry label, frequency in cm-1, intensity (arbitrary units), in that order. For a molecule with N atoms, 3N lines have to be present. The modes must be arragend to their frequencies in ascending order. Comment lines starting with # are ignored.

For thymine (15 atoms), a vibspectrum file would look something like this:

$vibrational spectrum
#  mode     symmetry     wave number   IR intensity    selection rules
#                         cm**(-1)      (km*mol⁻¹)       IR     RAMAN
     1                      -0.00         0.00000        -       -
     2                      -0.00         0.00000        -       -
     3                      -0.00         0.00000        -       -
     4                       0.00         0.00000        -       -
     5                       0.00         0.00000        -       -
     6                       0.00         0.00000        -       -
     7        a             70.05         0.38846       YES     YES
     8        a            105.13         0.44816       YES     YES
     9        a            147.88         4.81587       YES     YES
    10        a            261.06         3.14819       YES     YES
    11        a            301.90         0.50209       YES     YES
    12        a            360.79         7.68669       YES     YES
    13        a            377.25        25.99351       YES     YES
    14        a            431.27        13.50432       YES     YES
    15        a            522.33         2.07831       YES     YES
    16        a            583.19         4.66771       YES     YES
    17        a            587.91       102.69438       YES     YES
    18        a            664.09        13.87677       YES     YES
    19        a            685.26        10.36450       YES     YES
    20        a            720.79       217.35379       YES     YES
    21        a            755.25         2.31369       YES     YES
    22        a            777.49         2.22428       YES     YES
    23        a            860.72        15.31103       YES     YES
    24        a            958.79         1.79962       YES     YES
    25        a           1006.53         1.51584       YES     YES
    26        a           1035.98         6.36000       YES     YES
    27        a           1126.59        38.23933       YES     YES
    28        a           1153.10        45.04718       YES     YES
    29        a           1212.04        55.76099       YES     YES
    30        a           1273.30        29.07111       YES     YES
    31        a           1303.81        96.17203       YES     YES
    32        a           1327.48        68.41479       YES     YES
    33        a           1400.54        60.93027       YES     YES
    34        a           1410.68       139.45727       YES     YES
    35        a           1454.52         5.40728       YES     YES
    36        a           1472.57         1.05534       YES     YES
    37        a           1663.21       141.68596       YES     YES
    38        a           1739.67       685.35070       YES     YES
    39        a           1779.98       830.38911       YES     YES
    40        a           3016.25         8.53182       YES     YES
    41        a           3034.18         7.87679       YES     YES
    42        a           3052.46        20.26137       YES     YES
    43        a           3076.43        17.81182       YES     YES
    44        a           3398.16        26.97265       YES     YES
    45        a           3444.01        49.06620       YES     YES
$end

Note that some additional information was present (IR and RAMAN coloumns), which is ignored by CREST. Not also, that the first six entries correspond to the translation and rotation and hence have a frequency of zero.


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Copyright © 2022-2023 Philipp Pracht.

CREST is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.