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Molecule and Geometry Specification


Psi4 has a very flexible input parser that allows the user to provide geometries as Cartesian coordinates, Z-matrix variables, or a combination of both. The use of fixed values and variables are supported for both. For example, the geometry for H2 can be specified a number of ways, using the molecule optional_molecule_name {...} block.

molecule {
  H 1 0.9


molecule {
  H 1 r
  r = 0.9


molecule {
  H2 H1 0.9


molecule {
  H 0.0 0.0 0.0
  H 0.0 0.0 0.9


molecule {
  H 0.0 0.0 0.0
  H 0.0 0.0 r
  r = 0.9


molecule {
  H 0.0 0.0 -r
  H 0.0 0.0 r
  r = 0.45

Blank lines are ignored and, unlike regular Python syntax, indentation within the molecule block does not matter, although the molecule keyword itself must be aligned within the input according to standard Python syntax. For more examples of geometry specification, see the mints1 input file in the samples folder. It is also possible to mix Cartesian and Z-matrix geometry specifications, as demonstrated in the mints4 and mints6 sample input files. For example, consider the following geometry specification, taken from the mints6 input:

molecule alanine {
    N           -1.527107413251     0.745960643462     0.766603000356
    C           -0.075844098953     0.811790225041     0.711418672248
    C            0.503195220163    -0.247849447550    -0.215671574613
    O           -0.351261319421    -0.748978309671    -1.089590304723
    O            1.639498336738    -0.571249748886    -0.174705953194
    H           -1.207655674855    -0.365913941094    -0.918035522052
    # First, remove the H from the alpha carbon.  This line could be deleted
    # and is only included for completeness
    #H            0.429560656538     0.717651915252     1.673774709694
    # Now patch it, using a Z Matrix specification.  This patch can be applied
    # anywhere in the coord specification, as long as it appears lower than
    # the atoms referenced, as is usual for Z-Matrices
    C  2  rCC   3  aCCC   1  dCCCN
    H  7  rCH1  2  aHCC1  3  dHCCC1
    H  7  rCH2  2  aHCC2  3  dHCCC2
    H  7  rCH3  2  aHCC3  3  dHCCC3
    H            0.221781602033     1.772570540211     0.286988509018
    H           -1.833601608592     0.108401996052     1.481873213172
    H           -1.925572581453     1.640882152784     0.986471814808

    aCCC = 108.0
    rCC = 1.4
    dCCCN = 120
    rCH1 = 1.08
    rCH2 = 1.08
    rCH3 = 1.08
    aHCC1 = 109.0
    aHCC2 = 109.0
    aHCC3 = 109.0
    dHCCC1 = 0.0
    dHCCC2 = 120.0
    dHCCC3 = 240.0

Here, we remove the hydrogen from the alpha carbon of glycine and replace it with a methyl group. Applying this patch using Cartesian coordinates is difficult, because it depends on the orientation of the existing glycine unit. In this example, we use Z-Matrix coordinates to define the methyl group, and define the orientation in terms of the existing glycine Cartesian coordinates which is much easier to visualize than the corresponding Cartesian-only approach.

Molecule Keywords

In addition to specifying the geometry, additional information can be provided in the molecule block molecule optional_molecule_name {...}.

Charge & Multiplicity
If two integers charge multiplicity are encountered on any line of the molecule block, they are interpreted as the molecular charge and multiplicity (2 M_s + 1), respectively. For multi-fragment complexes, each fragment can have a charge multiplicity line.
By default, Ångström units are used; this is changed by adding a line that reads units spec, where spec is one of ang, angstrom, a.u., au, or bohr.
Certain computations require that the molecule is not reoriented. This can be achieved by adding either no_reorient or noreorient. To prevent even recentering of the molecule, add no_com or nocom.
A line reading pubchem:mol fetches the geometry for molecule mol from the PubChem database, where mol is either the IUPAC molecule name or the CID number. See PubChem Database for details.
The symmetry can be specified by a line reading symmetry symbol, where symbol is the Schönflies symbol of the (Abelian) point group to use for the computation, one of one of c1, c2, ci, cs, d2, c2h, c2v, or d2h. This need not be specified, as the molecular symmetry is automatically detected by Psi4. See Symmetry for details.
A line reading -- is interpreted as the separator between two non-covalently bound molecular fragments. See Non-Covalently Bonded Molecule Fragments for details.

Multiple Molecules

To facilitate more elaborate computations, it is possible to provide a name for each molecule and tell Psi4 which one should be used in a given calculation. For example, consider the following input file:

molecule h2 {
  H 1 0.9

set basis cc-pvdz
set reference rhf
energy('scf')  # on H2


molecule h {

set basis cc-pvdz
set reference uhf
energy('scf')  # on H

Here, two separate jobs are performed on two different molecules; the first is performed on H2, while the second is for H atom. The last molecule to be specified is the “active” molecule by default. To explicitly activate a named molecule, the activate command is provided. With it, the above input file can be equivalently written as follows. Alternatively, the molecule can be specified directly to the computing function. Below, the third calculation is the same as the first.

molecule h2 {
  H 1 0.9

molecule h {

set basis cc-pvdz
set reference rhf
energy('scf')  # on H2


set basis cc-pvdz
set reference uhf
energy('scf')  # on H

# --------------------------------------
# equivalent to previous input ends here


set reference rhf
energy('scf', molecule=h2)  # on H2

Job Control Keywords provides more details about the job control and calculation keywords used in the above examples.

Ghost Atoms

While many common computations, particularly SAPT and counterpoise corrections, can be greatly simplified using the notation described in Non-Covalently Bonded Molecule Fragments, manual specification of ghost atoms is sometimes required. Either

molecule he2 {
    Gh(He) 1 2.0


molecule he2 {
    @He 1 2.0

will generate a helium dimer with the second atom ghosted, i.e., possessing basis functions but no electrons or nuclear charge. See dfmp2_1 and ghosts for a demonstration of both mechanisms for specifying ghost atoms.

Isotopic Substitution


Use of isotopic substitution in Psi4 is not well developed, and the syntax is subject to change.

At present, isotopes can only be specified at creation-time of the molecule

The syntax for a deuterium- and tritium-substituted water is below. Note that asymmetric isotopic substitution such as this will change the molecule’s point group symmetry.

molecule dto {
  units au
  O                   0.00000000    0.00000000    0.00000000
  H@2.014101779       0.00000000    1.93042809   -1.10715266
  H_label@3.01604927  0.00000000   -1.93042809   -1.10715266

The masses used by Psi4 can be found at psi4/include/masses.h. See freq-isotope for about the only use to which isotopologs can presently be put in Psi4.

PubChem Database

Obtaining rough starting guess geometries can be burdensome. The Z-matrix coordinate system was designed to provide chemists with an intuitive method for guessing structures in terms of bond lengths and angles. While Z-matrix input is intuitive for small molecules with few degrees of freedom, it quickly becomes laborious as the system size grows. To obtain a reasonable starting guess geometry, Psi4 can take a chemical name as input; this is then used to attempt to retrieve Cartesian coordinates from the [PubChem] database.

For example, to run a computation on benzene, we can use the following molecule specification:

molecule benzene {

If the computer is connected to the internet, the above code will instruct Psi4 to search PubChem for a starting structure. The search is actually performed for compounds whose name contains “benzene”, so multiple entries will be returned. If the name provided (“benzene” in the above example) exactly matches one of the results, that entry will be used. If no exact match is found the results, along with a unique chemical identifier (CID), are printed to the output file, prompting the user to provide a more specific name. For example, if we know that we want to run a computation on a compound whose name(s) contain “benzene”, but we’re not sure of the exact IUPAC name, the following input can be used:

molecule benzene {

Appending the “*” prevents an exact match from being found and, at the time of writing, the following results are displayed in the output file:

Chemical ID     IUPAC Name
         241   benzene
        7371   benzenesulfonic acid
       91526   benzenesulfonate
         244   phenylmethanol
         727   1,2,3,4,5,6-hexachlorocyclohexane
         240   benzaldehyde
       65723   benzenesulfonohydrazide
       74296   N-phenylbenzenesulfonamide
         289   benzene-1,2-diol
         243   benzoic acid
        7370   benzenesulfonamide
      636822   1,2,4-trimethoxy-5-[(E)-prop-1-enyl]benzene
        7369   benzenesulfonyl chloride
       12932   N-[2-di(propan-2-yloxy)phosphinothioylsulfanylethyl]benzenesulfonamide
        7505   benzonitrile
       78438   N-[anilino(phenyl)phosphoryl]aniline
       12581   3-phenylpropanenitrile
      517327   sodium benzenesulfonate
      637563   1-methoxy-4-[(E)-prop-1-enyl]benzene
      252325   [(E)-prop-1-enyl]benzene

Note that some of these results do not contain the string “benzene”; these compounds have synonyms containing that text. We can now replace the “benzene*” in the input file with one of the above compounds using either the IUPAC name or the CID provided in the list, viz:

molecule benzene {


molecule benzene {

Some of the structures in the database are quite loosely optimized and do not have the correct symmetry. Before starting the computation, Psi4 will check to see if the molecule is close to having each of the possible symmetries, and will adjust the structure accordingly so that the maximum symmetry is utilized.

The standard keywords, described in Molecule Keywords, can be used in conjuction to specify charge, multiplicity, symmetry to use, etc. .


For efficiency, Psi4 can utilize the largest Abelian subgroup of the full point group of the molecule. Concomitantly, a number of quantities, such as SOCC and DOCC, are arrays whose entries pertain to irreducible representations (irreps) of the molecular point group. Ordering of irreps follows the convention used in Cotton’s Chemical Applications of Group Theory, as detailed in Table Irreps. We refer to this convention as “Cotton Ordering” hereafter.

Ordering of irreducible representations (irreps) used in Psi4
Point Group 1 2 3 4 5 6 7 8
C_1 A              
C_i A_g A_u            
C_2 A B            
C_s A' A''            
D_2 A B_1 B_2 B_3        
C_{2v} A_1 A_2 B_1 B_2        
C_{2h} A_g B_g A_u B_u        
D_{2h} A_g B_{1g} B_{2g} B_{3g} A_u B_{1u} B_{2u} B_{3u}

For example, water (C_{2v} symmetry) has three doubly occupied A_1 orbitals, as well as one each of B_1 and B_2 symmetry; the corresponding DOCC array is therefore:

DOCC = [3, 0, 1, 1]

Although Psi4 will detect the symmetry automatically, and use the largest possible Abelian subgroup, the user might want to run in a lower point group. To do this the molecule keyword symmetry symbol can be used (see Molecule Keywords). In most cases the standard Schönflies symbol (one of c1, c2, ci, cs, d2, c2h, c2v, d2h will suffice for symbol. For certain computations, the user might want to specify which particular subgroup is to be used by appending a unique axis specifier. For example when running a computation on a molecule with D_{2h} symmetry in C_{2v}, the C_2 axis can be chosen as either the x, the y, or the z; these can be specified by requesing the symmetry as c2vx, c2vy, or c2vz, respectively. Likewise the c2x, c2y, c2z, c2hx, c2hy, and c2hz labels are valid. For C_s symmetry the labels csx, csy, and csz request the yz, xz, and xy planes be used as the mirror plane, respectively. If no unique axis is specified, Psi4 will choose an appropriate subgroup.

Certain types of finite difference computations, such as numerical vibrational frequencies, might lower the symmetry of the molecule. When this happens symmetry-dependent arrays, such as SOCC, are automatically remapped to the lower symmetry. For example, if we were to investigate the ^2B_1 state of water cation, we can specify

SOCC = [0, 0, 1, 0]

in the input file. If any ensuing computations lower the symmetry, the above array will be appropriately remapped. For example, reducing the symmetry to C_s (with the molecular plane defining the mirror plane), the above array will be automatically interpreted as:

SOCC = [0, 1]

Some caution is required, however. The ^2A_1 state can be obtained with the

SOCC = [1, 0, 0, 0]

specification, which would become

SOCC = [1, 0]

under the above-mentioned reduction in symmetry. The ^2B_2 state, whose singly-occupied orbitals are

SOCC = [0, 0, 0, 1]

would be mapped to

SOCC = [1, 0]

which is the same occupation as the ^2A_1 state. In this case, the ^2A_1 state is lower in energy, and is not problematic. The distorted geometries for the ^2B_2 state are excited states that are subject to variational collapse. One way to obtain reliable energies for these states is to use a multi-state method; in this case it’s easier to run the entire computation in the lowest symmetry needed during the finite difference procedure.

Non-Covalently Bonded Molecule Fragments

Psi4 has an extensive range of tools for treating non-covalent intermolecular forces, including counterpoise corrections and symmetry adapted perturbation theory methods. These require the definition of which fragments are interacting within the complex. Psi4 provides a very simple mechanism for doing so: simply define the complex’s geometry using the standard Cartesian, Z-matrix, or mixture thereof, specifications and then place two dashes between nonbonded fragements. For example, to study the interaction energy of ethane and ethyne molecules, we can use the following molecule block:

molecule eneyne {
  0 1
  C  0.000000 -0.667578  -2.124659
  C  0.000000  0.667578  -2.124659
  H  0.923621 -1.232253  -2.126185
  H -0.923621 -1.232253  -2.126185
  H -0.923621  1.232253  -2.126185
  H  0.923621  1.232253  -2.126185
  0 1
  C 0.000000 0.000000 2.900503
  C 0.000000 0.000000 1.693240
  H 0.000000 0.000000 0.627352
  H 0.000000 0.000000 3.963929

In this case, the charge and multiplicity of each interacting fragment is explicitly specified. If the charge and multiplicity are specified for the first fragment, it is assumed to be the same for all fragments. When considering interacting fragments, the overall charge is simply the sum of all fragment charges, and any unpaired electrons are assumed to be coupled to yield the highest possible M_s value.

Having defined a molecule containing fragments like eneyne above, it is a simple matter to perform calculations on only a subset of the fragments. For instance, the commands below run a scf first on the ethene fragment alone (extract_subsets(1) pulls out fragment 1 as Real atoms and discards remaining fragments) and next on the ethene fragment with the ethyne fragment ghosted (extract_subsets(1,2) pulls out fragment 1 as Real atoms and sets fragment 2 as Ghost atoms). For beyond bimolecular complexes, arrays can be used, e.g. extract_subsets(2,[1,3]):

mA = eneyne.extract_subsets(1)


mAcp = eneyne.extract_subsets(1,2)

If the molecule contains fragments but is not conveniently ordered for the -- marker, the auto_fragments() function can be applied, as shown in pywrap-basis, to return as active molecule the previous active molecule, only fragmented.

Advanced Python

A named molecule in an input file is a full-fledged instance of the powerful C++ Molecule class. Thus, all member functions (that have been exported via Boost Python) documented thereat are accessible through the handle option_molecule_name in molecule optional_molecule_name {...}.

  • The molecular geometry can be got and set and manipulated as a psi4.Matrix object. Below shows how to access coordinates in an input file in Python.

    molecule formaldehyde {
    C  0.0 0.0 0.0
    O  0.0 1.2 0.0
    H -0.8 -0.3 0.0
    H  0.8 -0.3 0.0                         # set geometry in angstroms
    formaldehyde.update_geometry()          # update the molecule internals since pre-energy()-like call
    formaldehyde.print_out()                # print molecule to output file
    geom1psi = formaldehyde.geometry()      # get coordinates in bohr as a psi4.Matrix
    geom1psi.print_out()                    # print coordinates array to output file
    geom1py = mat2arr(geom1psi)             # get coordinates as a Python array
    print geom1py                           # print coordinates to screen
    geom2py = [[ 0.0,  0.0, 0.0],
              [ 0.0,  1.5, 0.0],
              [-0.8, -0.3, 0.0],
              [ 0.8, -0.3, 0.0]]            # define alternate coordinates in angstroms as Python array
    geom2psi = psi4.Matrix(4, 3)            # initialize psi4.Matrix
    geom2psi.set(geom2py)                   # load Python array into psi4.Matrix
    geom2psi.scale(1.0/psi_bohr2angstroms)  # scale into bohr
    geom2psi.print_out()                    # print alternate coord array to output file
    formaldehyde.set_geometry(geom2psi)     # load alternate coordinates into molecule
    formaldehyde.update_geometry()          # update the molecule internals
    formaldehyde.print_out()                # print new molecule to output file
    compare_values(28.9950517332, formaldehyde.nuclear_repulsion_energy(), 4, "geom2 took")
  • Molecules can be initited from XYZ files and fragmented for SAPT computations.

    # >>> cat
    #O          0.00000000      -0.05786571      -1.47979303
    #N          0.00000000       0.01436394       1.46454628
    #H          0.00000000       0.82293384      -1.85541474
    #H          0.81348351       0.39876776       1.92934049
    #H          0.00000000       0.07949567      -0.51934253
    #H          0.00000000      -0.98104857       1.65344779
    #H         -0.81348351       0.39876776       1.92934049
    # >>> cat
    # 6 au
    # stuff
    #     C     0.00000000000000     0.00000000000000     5.26601138679877
    #     C     0.00000000000000     0.00000000000000    -3.15195886530135
    #     H     0.00000000000000     0.00000000000000     7.28558683837122
    #     H     0.00000000000000     0.00000000000000    -1.12178201232889
    #     N     0.00000000000000     0.00000000000000     3.08339310458383
    #     N     0.00000000000000     0.00000000000000    -5.33865984413460
    sapt = {'mol1': -0.0105313323529,
            'mol2': -0.00839486625709}
    nre = {'mol1': 38.8138764635,
           'mol2': 72.3451968428}
    set basis jun-cc-pvdz
    for mol in ['mol1', 'mol2']:
        filen = mol + '.xyz'
        p4mol = Molecule.init_with_xyz(filen)           # create molecule from file above
        fragmentedmol = auto_fragments(molecule=p4mol)  # fragment with BFS algorithm
        activate(fragmentedmol)                         # activate returned molecule (for sapt)
        e = energy('sapt0')                             # run SAPT that requires 2 fragments
        compare_values(sapt[mol], e, 5, '%s sapt ok' % mol)
        compare_values(nre[mol], p4mol.nuclear_repulsion_energy(), 4, '%s ok' % mol)
        clean()                                         # clean scratch between loop calcs
  • The essential element, mass and coordinate information of the molecule is accessible

    molecule eneyne {
    0 1
    C_ene        0.000000  -0.667578  -2.124659
    C_ene        0.000000   0.667578  -2.124659
    H_ene@2.014  0.923621  -1.232253  -2.126185
    H_ene       -0.923621  -1.232253  -2.126185
    H_ene       -0.923621   1.232253  -2.126185
    Gh(H_ene)    0.923621   1.232253  -2.126185
    0 1
    X            9.0        9.0        9.0
    C_yne        0.000000   0.000000   2.900503
    C_yne        0.000000   0.000000   1.693240
    H_yne        0.000000   0.000000   0.627352
    H_yne        0.000000   0.000000   3.963929
    for iat in range(eneyne.natom()):
        print """{:4} {:4} {:12} {:8.4f} {:12.6f} {:12.6f} {:12.6f}   {:12.6f}""".format(
                                      eneyne.Z(iat),       # atomic number
                                      eneyne.symbol(iat),  # element symbol
                                      eneyne.label(iat),   # input element label
                                      eneyne.charge(iat),  # element charge
                                      eneyne.x(iat),       # x-coordinate
                                      eneyne.y(iat),       # y-coordinate
                                      eneyne.z(iat),       # z-coordinate
                                      eneyne.mass(iat),    # mass
    # 6.0 C    C_ENE          6.0000    -0.031900    -1.218981    -3.948079      12.000000
    # 6.0 C    C_ENE          6.0000    -0.031900     1.304098    -3.948079      12.000000
    # 1.0 H    H_ENE          1.0000     1.713491    -2.286062    -3.950962       2.014000
    # 1.0 H    H_ENE          1.0000    -1.777290    -2.286062    -3.950962       1.007825
    # 1.0 H    H_ENE          1.0000    -1.777290     2.371180    -3.950962       1.007825
    # 0.0 H    H_ENE          0.0000     1.713491     2.371180    -3.950962       1.007825
    # 6.0 C    C_YNE          6.0000    -0.031900     0.042559     5.548101      12.000000
    # 6.0 C    C_YNE          6.0000    -0.031900     0.042559     3.266705      12.000000
    # 1.0 H    H_YNE          1.0000    -0.031900     0.042559     1.252468       1.007825
    # 1.0 H    H_YNE          1.0000    -0.031900     0.042559     7.557685       1.007825