- Description
- Input
- Options
- Availability
- Related Keywords
- Examples
Description
This keyword requests a classical trajectory calculation [Bunker71, Raff85, Hase91, Thompson98] using the Atom Centered Density Matrix Propagation molecular dynamics model [Iyengar01, Schlegel01, Schlegel02]. This method provides equivalent functionality to Born-Oppenheimer molecular dynamics (see the BOMD keyword) at considerably reduced computational cost [Schlegel02].
ADMP belongs to the extended Lagrangian approach to molecular dynamics using Gaussian basis functions and propagating the density matrix. The best known method of this type is Car-Parrinello (CP) molecular dynamics [Car85], in which the Kohn-Sham molecular orbitals, ψi, are chosen as the dynamical variables to represent the electronic degrees of freedom in the system. CP calculations are usually carried out in a plane wave basis (although Gaussian orbitals are sometimes added as an adjunct [Martyna91, Lippert97, Lippert99]). Unlike plane wave CP, it is not necessary to use pseudopotentials on hydrogen or to use deuterium rather than hydrogen in the dynamics. Fictitious masses for the electronic degrees of freedom are set automatically [Schlegel02] and can be small enough that thermostats are not required for good energy conservation.
ADMP can be performed with semi-empirical, HF, and pure and hybrid DFT models (see the Availability tab for more details). It can be applied to molecules, clusters and periodic systems. PBC calculations use only the Γ point (i.e., no K-integration).
Input
Although most jobs will not require it, ADMP calculations can accept some input. The first section below provides the optional initial Cartesian velocities for the ReadVelocity and ReadMWVelocity options.
| Initial velocity for atom 1: x y z | Optional initial Cartesian velocities |
| Initial velocity for atom 2: x y z | (ReadVelocity and ReadMWVelocity options) |
| … | |
| Initial velocity for atom N: x y z | |
| … |
First, the initial velocity for each atom is read if the ReadVelocity or ReadMWVelocity option is included. Each initial velocity is specified as a Cartesian velocity in atomic units (Bohr/sec) or as a mass-weighed Cartesian velocity (in amu1/2*Bohr/sec), respectively. One complete set of velocities is read for each requested trajectory computation.
This information (if present) may be immediately followed by the Morse parameters for each diatomic product (no intervening blank line):
| Atom1, Atom2, E0, Len, De, Be | |
| … | |
| Terminate entire trajectory input subsection with a blank line. |
The Morse parameter data is used to determine the vibrational excitation of diatomic fragments using the EBK quantization rules. It consists of the atomic symbols for the two atoms, the bond length between them (Len, in Angstroms), the energy at that distance (E0 in Hartrees), and the Morse curve parameters De (Hartrees) and Be (Angstroms-1). This input subsection is terminated by a blank line.
Options
MaxPoints=n
Specifies the maximum number of steps that may be taken in each trajectory (the default is 50). If a trajectory job is restarted, the maximum number of steps will default to the number specified in the original calculation.
Lowdin
Use the Löwdin basis for the orthonormal set. The alternative is Cholesky, which uses the Cholesky basis and is the default.
NKE=N
Set the initial nuclear kinetic energy to N microHartrees. NuclearKineticEnergy is a synonym for this option. The default is 100000 (corresponding to 0.1 Hartree).
DKE=N
Set the initial density kinetic energy to N microHartrees. DensityKineticEnergy is a synonym for this option.
ElectronMass=N
Set the fictitious electron mass to |N/10000| amu (the default is N=1000, resulting in a fictitious mass of 0.1 amu). EMass is a synonym for this option. If NFullSCF
Do the dynamics with converged SCF results at each point.
ReadVelocity
Read initial Cartesian velocities from the input stream. Note that the velocities must have the same symmetry orientation as the molecule. This option suppresses the fifth-order anharmonicity correction.
ReadMWVelocity
Read initial mass-weighted Cartesian velocities from the input stream. Note that the velocities must have the same symmetry orientation as the molecule. This option suppresses the fifth-order anharmonicity correction.
StepSize=n
Sets the step size in dynamics to n*0.0001 femtoseconds. The default is 1000 (a step size of 0.1 femtoseconds).
BandGap
Whether to diagonalize the Fock matrix in order to report the band gap at each step. The default is NoBandGap.
Restart
Restart an ADMP calculation from the checkpoint file. Note that options set in the original job will continue to be in effect and cannot be modified.
ReadIsotopes
This option allows you to specify alternatives to the default temperature, pressure, frequency scale factor and/or isotopes—298.15 K, 1 atmosphere, no scaling, and the most abundant isotopes (respectively). It is useful when you want to rerun an analysis using different parameters from the data in a checkpoint file.
Be aware, however, that all of these can be specified in the route section (Temperature, Pressure and Scale keywords) and molecule specification (the Iso parameter), as in this example:
#T Method/6-31G(d) JobType Temperature=300.0 … … 0 1 C(Iso=13) …
ReadIsotopes input has the following format:
| temp pressure [scale] | Values must be real numbers. |
| isotope mass for atom 1 | |
| isotope mass for atom 2 | |
| … | |
| isotope mass for atom n |
Where temp, pressure, and scale are the desired temperature, pressure, and an optional scale factor for frequency data when used for thermochemical analysis (the default is unscaled). The remaining lines hold the isotope masses for the various atoms in the molecule, arranged in the same order as they appeared in the molecule specification section. If integers are used to specify the atomic masses, the program will automatically use the corresponding actual exact isotopic mass (e.g., 18 specifies 18O, and Gaussian uses the value 17.99916).
Availability
Semi-empirical, HF, and DFT methods.
Related Keywords
Examples
The following sample ADMP input file will calculate a trajectory for H2CO dissociating to H2 + CO, starting at the transition state:
# B3LYP/6-31G(d) ADMP Geom=Crowd Dissociation of H2CO → H2 + CO 0 1 C O 1 r1 H 1 r2 2 a H 1 r3 3 b 2 180. r1 1.15275608 r2 1.74415774 r3 1.09413376 a 114.81897892 b 49.08562961
Final blank line
At the beginning of an ADMP calculation, the parameters used for the job are displayed in the output:
TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ -------------------------------------------------------------------- INPUT DATA FOR L121 -------------------------------------------------------------------- General parameters: Maximum Steps = 50 Random Number Generator Seed = 398465 Time Step = 0.10000 femtosec Ficticious electronic mass = 0.10000 amu MW individual basis funct. = True Initial nuclear kin. energy = 0.10000 hartree Initial electr. kin. energy = 0.00000 hartree Initial electr. KE scheme = 0 Multitime step - NDtrC = 1 Multitime step - NDtrP = 1 No Thermostats chosen to control nuclear temperature Integration parameters: Follow Rxn Path (DVV) = False Constraint Scheme = 10 Projection of angular mom. = True Rotate density with nuclei = True -------------------------------------------------------------------- TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ
The molecular coordinates and velocities appear at the beginning of each trajectory step (some output digits are truncated here):
Cartesian coordinates: I= 1 X= -1.1971360D-01 Y= 0.0000000D+00 Z= -1.0478570D+00 I= 2 X= -1.1971360D-01 Y= 0.0000000D+00 Z= 1.1305362D+00 I= 3 X= 2.8718451D+00 Y= 0.0000000D+00 Z= -2.4313539D+00 I= 4 X= 4.5350603D-01 Y= 0.0000000D+00 Z= -3.0344227D+00 MW Cartesian velocity: I= 1 X= -4.0368385D+12 Y= 1.4729976D+13 Z= 1.4109897D+14 I= 2 X= 4.4547606D+13 Y= -6.3068948D+12 Z= -2.2951936D+14 I= 3 X= -3.0488505D+13 Y= 6.0922004D+12 Z= 1.8527270D+14 I= 4 X= -1.3305097D+14 Y= -3.1794401D+13 Z= 2.4220839D+14 Cartesian coordinates after ADCart: I= 1 X= -1.1983609D-01 Y= 4.2521779D-04 Z= -1.0437931D+00 I= 2 X= -1.1859803D-01 Y= -1.5769743D-04 Z= 1.1248052D+00 I= 3 X= 2.8688210D+00 Y= 6.0685035D-04 Z= -2.4129040D+00 I= 4 X= 4.4028377D-01 Y= -3.1670730D-03 Z= -3.0103048D+00 TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ
After the trajectory computation is complete, summary information is displayed in the output for each time step in the trajectory:
Trajectory summary for trajectory 1 Energy/Fock evaluations 51 Gradient evaluations 51 Trajectory summary Time (fs) Kinetic (au) Potent (au) Delta E (au) Delta A (h-bar) 0.000000 0.1000000 -114.3576722 0.0000000 0.0000000000000000 0.100000 0.0988486 -114.3564837 0.0000371 -0.0000000000000081 0.200000 0.0967812 -114.3543446 0.0001088 -0.0000000000000104 0.300000 0.0948898 -114.3524307 0.0001313 -0.0000000000000115 …
You can also use GaussView or other visualization software to display the trajectory path as an animation.
- Description
- Input
- Options
- Availability
- Related Keywords
- Examples
This keyword requests a classical trajectory calculation [Bunker71, Raff85, Hase91, Thompson98] using the Atom Centered Density Matrix Propagation molecular dynamics model [Iyengar01, Schlegel01, Schlegel02]. This method provides equivalent functionality to Born-Oppenheimer molecular dynamics (see the BOMD keyword) at considerably reduced computational cost [Schlegel02].
ADMP belongs to the extended Lagrangian approach to molecular dynamics using Gaussian basis functions and propagating the density matrix. The best known method of this type is Car-Parrinello (CP) molecular dynamics [Car85], in which the Kohn-Sham molecular orbitals, ψi, are chosen as the dynamical variables to represent the electronic degrees of freedom in the system. CP calculations are usually carried out in a plane wave basis (although Gaussian orbitals are sometimes added as an adjunct [Martyna91, Lippert97, Lippert99]). Unlike plane wave CP, it is not necessary to use pseudopotentials on hydrogen or to use deuterium rather than hydrogen in the dynamics. Fictitious masses for the electronic degrees of freedom are set automatically [Schlegel02] and can be small enough that thermostats are not required for good energy conservation.
ADMP can be performed with semi-empirical, HF, and pure and hybrid DFT models (see the Availability tab for more details). It can be applied to molecules, clusters and periodic systems. PBC calculations use only the Γ point (i.e., no K-integration).
Although most jobs will not require it, ADMP calculations can accept some input. The first section below provides the optional initial Cartesian velocities for the ReadVelocity and ReadMWVelocity options.
| Initial velocity for atom 1: x y z | Optional initial Cartesian velocities |
| Initial velocity for atom 2: x y z | (ReadVelocity and ReadMWVelocity options) |
| … | |
| Initial velocity for atom N: x y z | |
| … |
First, the initial velocity for each atom is read if the ReadVelocity or ReadMWVelocity option is included. Each initial velocity is specified as a Cartesian velocity in atomic units (Bohr/sec) or as a mass-weighed Cartesian velocity (in amu1/2*Bohr/sec), respectively. One complete set of velocities is read for each requested trajectory computation.
This information (if present) may be immediately followed by the Morse parameters for each diatomic product (no intervening blank line):
| Atom1, Atom2, E0, Len, De, Be | |
| … | |
| Terminate entire trajectory input subsection with a blank line. |
The Morse parameter data is used to determine the vibrational excitation of diatomic fragments using the EBK quantization rules. It consists of the atomic symbols for the two atoms, the bond length between them (Len, in Angstroms), the energy at that distance (E0 in Hartrees), and the Morse curve parameters De (Hartrees) and Be (Angstroms-1). This input subsection is terminated by a blank line.
MaxPoints=n
Specifies the maximum number of steps that may be taken in each trajectory (the default is 50). If a trajectory job is restarted, the maximum number of steps will default to the number specified in the original calculation.
Lowdin
Use the Löwdin basis for the orthonormal set. The alternative is Cholesky, which uses the Cholesky basis and is the default.
NKE=N
Set the initial nuclear kinetic energy to N microHartrees. NuclearKineticEnergy is a synonym for this option. The default is 100000 (corresponding to 0.1 Hartree).
DKE=N
Set the initial density kinetic energy to N microHartrees. DensityKineticEnergy is a synonym for this option.
ElectronMass=N
Set the fictitious electron mass to |N/10000| amu (the default is N=1000, resulting in a fictitious mass of 0.1 amu). EMass is a synonym for this option. If N<0, then uniform scaling is used for all basis functions. By default, core functions are weighted more heavily than valence functions.FullSCF
Do the dynamics with converged SCF results at each point.
ReadVelocity
Read initial Cartesian velocities from the input stream. Note that the velocities must have the same symmetry orientation as the molecule. This option suppresses the fifth-order anharmonicity correction.
ReadMWVelocity
Read initial mass-weighted Cartesian velocities from the input stream. Note that the velocities must have the same symmetry orientation as the molecule. This option suppresses the fifth-order anharmonicity correction.
StepSize=n
Sets the step size in dynamics to n*0.0001 femtoseconds. The default is 1000 (a step size of 0.1 femtoseconds).
BandGap
Whether to diagonalize the Fock matrix in order to report the band gap at each step. The default is NoBandGap.
Restart
Restart an ADMP calculation from the checkpoint file. Note that options set in the original job will continue to be in effect and cannot be modified.
[include-page id="/isotopes"]The following sample ADMP input file will calculate a trajectory for H2CO dissociating to H2 + CO, starting at the transition state:
# B3LYP/6-31G(d) ADMP Geom=Crowd Dissociation of H2CO → H2 + CO 0 1 C O 1 r1 H 1 r2 2 a H 1 r3 3 b 2 180. r1 1.15275608 r2 1.74415774 r3 1.09413376 a 114.81897892 b 49.08562961Final blank line
At the beginning of an ADMP calculation, the parameters used for the job are displayed in the output:
TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ -------------------------------------------------------------------- INPUT DATA FOR L121 -------------------------------------------------------------------- General parameters: Maximum Steps = 50 Random Number Generator Seed = 398465 Time Step = 0.10000 femtosec Ficticious electronic mass = 0.10000 amu MW individual basis funct. = True Initial nuclear kin. energy = 0.10000 hartree Initial electr. kin. energy = 0.00000 hartree Initial electr. KE scheme = 0 Multitime step - NDtrC = 1 Multitime step - NDtrP = 1 No Thermostats chosen to control nuclear temperature Integration parameters: Follow Rxn Path (DVV) = False Constraint Scheme = 10 Projection of angular mom. = True Rotate density with nuclei = True -------------------------------------------------------------------- TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ
The molecular coordinates and velocities appear at the beginning of each trajectory step (some output digits are truncated here):
Cartesian coordinates: I= 1 X= -1.1971360D-01 Y= 0.0000000D+00 Z= -1.0478570D+00 I= 2 X= -1.1971360D-01 Y= 0.0000000D+00 Z= 1.1305362D+00 I= 3 X= 2.8718451D+00 Y= 0.0000000D+00 Z= -2.4313539D+00 I= 4 X= 4.5350603D-01 Y= 0.0000000D+00 Z= -3.0344227D+00 MW Cartesian velocity: I= 1 X= -4.0368385D+12 Y= 1.4729976D+13 Z= 1.4109897D+14 I= 2 X= 4.4547606D+13 Y= -6.3068948D+12 Z= -2.2951936D+14 I= 3 X= -3.0488505D+13 Y= 6.0922004D+12 Z= 1.8527270D+14 I= 4 X= -1.3305097D+14 Y= -3.1794401D+13 Z= 2.4220839D+14 Cartesian coordinates after ADCart: I= 1 X= -1.1983609D-01 Y= 4.2521779D-04 Z= -1.0437931D+00 I= 2 X= -1.1859803D-01 Y= -1.5769743D-04 Z= 1.1248052D+00 I= 3 X= 2.8688210D+00 Y= 6.0685035D-04 Z= -2.4129040D+00 I= 4 X= 4.4028377D-01 Y= -3.1670730D-03 Z= -3.0103048D+00 TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ-TRJ
After the trajectory computation is complete, summary information is displayed in the output for each time step in the trajectory:
Trajectory summary for trajectory 1 Energy/Fock evaluations 51 Gradient evaluations 51 Trajectory summary Time (fs) Kinetic (au) Potent (au) Delta E (au) Delta A (h-bar) 0.000000 0.1000000 -114.3576722 0.0000000 0.0000000000000000 0.100000 0.0988486 -114.3564837 0.0000371 -0.0000000000000081 0.200000 0.0967812 -114.3543446 0.0001088 -0.0000000000000104 0.300000 0.0948898 -114.3524307 0.0001313 -0.0000000000000115 …
You can also use GaussView or other visualization software to display the trajectory path as an animation.
Last updated on: 19 June 2019.