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| molecular_geometry [2023/06/01 13:43] – [Counterpoise calculations] peterk | molecular_geometry [2025/02/17 06:37] (current) – molden: recommend to use subcommand orbital doll |
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| * **//group//** atomic group number (optional). Can be used if different basis sets are used for different atoms of the same kind. The basis set is then referred to by this group number and not by the atomic symbol. | * **//group//** atomic group number (optional). Can be used if different basis sets are used for different atoms of the same kind. The basis set is then referred to by this group number and not by the atomic symbol. |
| * **//atom//** chemical symbol of the new atom placed at position p0. This may optionally be appended (without blank) by an integer, which can act as sequence number, e.g., ''C1'', ''H2'', etc. Dummy centres with no charge and basis functions are denoted either ''Q'' or ''X'', optionally appended by a number, e.g, ''Q1''; note that the first atom in the z-matrix must not be called ''X'', since this may be confused with a symmetry specification (use ''Q'' instead). | * **//atom//** chemical symbol of the new atom placed at position p0. This may optionally be appended (without blank) by an integer, which can act as sequence number, e.g., ''C1'', ''H2'', etc. Dummy centres with no charge and basis functions are denoted X, optionally appended by a number, e.g, X1. |
| * **p1** atom to which the present atom is connected. This may be either a number //n//, where n refers to the n’th line of the Z-matrix, or an alphanumeric string as specified in the //atom// field of a previous card, e.g., ''C1'', ''H2'' etc. The latter form works only if the atoms are numbered in a unique way. | * **p1** atom to which the present atom is connected. This may be either a number //n//, where n refers to the n’th line of the Z-matrix, or an alphanumeric string as specified in the //atom// field of a previous card, e.g., ''C1'', ''H2'' etc. The latter form works only if the atoms are numbered in a unique way. |
| * **r** Distance of new atom from p1. This value is given in bohr, unless ''ANG'' has been specified directly before or after the symmetry specification. | * **r** Distance of new atom from p1. This value is given in bohr, unless ''ANG'' has been specified directly before or after the symmetry specification. |
| //file// specifies a file name to which the data is written; if blank, the data is written to the output stream. If //status// is omitted or set to ''NEW'', any old contents of the file are destroyed; otherwise the file is appended. | //file// specifies a file name to which the data is written; if blank, the data is written to the output stream. If //status// is omitted or set to ''NEW'', any old contents of the file are destroyed; otherwise the file is appended. |
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| A subcommand ''ORBITAL'' can be given, using the syntax given in section [[general program structure#selecting orbitals and density matrices (ORBITAL, DENSITY)|selecting orbitals and density matrices (ORBITAL, DENSITY)]], to specify a set of orbitals other than the default, latest set. | A subcommand ''ORBITAL'' can be given, using the syntax given in section [[general program structure#selecting orbitals and density matrices (ORBITAL, DENSITY)|selecting orbitals and density matrices (ORBITAL, DENSITY)]], to specify a set of orbitals other than the default. Using this keyword is recommended if several orbitals sets are computed with one input file, and especially necessary when orbitals such as natural orbitals from CCSD shall be exported. |
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| ==== Visualization of results using Molden ==== | ==== Visualization of results using Molden ==== |
| ''COUNTERPOISE'' [, //key1=value, key2=value,…...//] | ''COUNTERPOISE'' [, //key1=value, key2=value,…...//] |
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| Without any options, this will calculate the ghost-orbital corrections to dimer interaction energies using the last energy calculation to define the dimer and the methods to be used. First of all, the molecule is automatically partitioned into fragments. This is done by assigning all interatomic distances as either intra- or intermolecular, comparing the distance with the scaled sum of Bragg radii of the two atoms. The default scale factor is 1.4, but it can be changed with ''SCALE=''//scale//; for the S66 database of intermolecular interactions, correct partitioning is obtained with a scale factor in the range 1.2 to 1.9. If all of the distances are intramolecular, then it will be assumed that the system is not a non-bonded complex, and the counterpoise calculation will not be done at all. This gives support for running the same Molpro input for both dimers and monomers. At present, partitioning into more than two fragments is discovered, but there is no supporting implementation of the counterpoise correction. | Without any options, this will calculate the ghost-orbital corrections to dimer interaction energies using the last energy calculation to define the dimer and the methods to be used. First of all, the molecule is automatically partitioned into fragments. This is done by assigning all interatomic distances as either intra- or intermolecular, comparing the distance with the scaled sum of Bragg radii of the two atoms. The default scale factor is 1.4, but it can be changed with ''SCALE=''//scale//; for the S66 database of intermolecular interactions, correct partitioning is obtained with a scale factor in the range 1.2 to 1.95. If all of the distances are intramolecular, then it will be assumed that the system is not a non-bonded complex, and the counterpoise calculation will not be done at all. This gives support for running the same Molpro input for both dimers and monomers. At present, partitioning into more than two fragments is discovered, but there is no supporting implementation of the counterpoise correction. |
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| The counterpoise procedure performs four calculations. For each of the identified monomers, it calculates the energy at the dimer geometry using first the dimer basis set, and secondly just the basis functions tied to the monomer atoms. The difference between these, the counterpoise correction, is reported, and added to the previously-calculated dimer energy. | The counterpoise procedure performs four calculations. For each of the identified monomers, it calculates the energy at the dimer geometry using first the dimer basis set, and secondly just the basis functions tied to the monomer atoms. The difference between these, the counterpoise correction, is reported, and added to the previously-calculated dimer energy. |
| <code - examples/ohar_bsse.inp> | <code - examples/ohar_bsse.inp> |
| ***,OH(2Sig+)-Ar linear | ***,OH(2Sig+)-Ar linear |
| geometry={q1; !dummy center in center of mass | geometry={x1; !dummy center in center of mass |
| o,q1,ro;h,q1,rh,o,180; !geometry of OH | o,x1,ro;h,x1,rh,o,180; !geometry of OH |
| ar,q1,rar,o,theta,h,0} !geometry of Ar | ar,x1,rar,o,theta,h,0} !geometry of Ar |
| roh=1.8 !OH bond-length | roh=1.8 !OH bond-length |
| rar=7.5 !distance of Ar from center of mass | rar=7.5 !distance of Ar from center of mass |