pair_style mgpt command
pair_style mgpt pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double pair_coeff * * parmin potin Omega volpress yes nbody 12
Within DFT quantum mechanics, generalized pseudopotential theory (GPT) (Moriarty1) provides a first-principles approach to multi-ion interatomic potentials in d-band transition metals, with a volume-dependent, real-space total-energy functional for the N-ion elemental bulk material in the form
where the prime on each summation sign indicates the exclusion of all self-interaction terms from the summation. The leading volume term E_vol as well as the two-ion central-force pair potential v_2 and the three- and four-ion angular-force potentials, v_3 and v_4, depend explicitly on the atomic volume Omega, but are structure independent and transferable to all bulk ion configurations, either ordered or disordered, and with of without the presence of point and line defects. The simplified model GPT or MGPT (Moriarty2, Moriarty3), which retains the form of E_tot and permits more efficient large-scale atomistic simulations, derives from the GPT through a series of systematic approximations applied to E_vol and the potentials v_n that are valid for mid-period transition metals with nearly half-filled d bands.
Both analytic (Moriarty2) and matrix (Moriarty3) representations of MGPT have been developed. In the more general matrix representation, which can also be applied to f-band actinide metals and permits both canonical and non-canonical d/f bands, the multi-ion potentials are evaluated on the fly during a simulation through d- or f-state matrix multiplication, and the forces that move the ions are determined analytically. Fast matrix-MGPT algorithms have been developed independently by Glosli (Glosli, Moriarty3) and by Oppelstrup (Oppelstrup)
The mgpt pair style calculates forces, energies, and the total energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm. Input potential and control data are entered through the pair_coeff command. Each material treated requires input parmin and potin potential files, as shown in the above examples, as well as specification by the user of the initial atomic volume Omega through pair_coeff. At the beginning of a time step in any simulation, the total volume of the simulation cell V should always be equal to Omega*N, where N is the number of metal ions present, taking into account the presence of any vacancies and/or interstitials in the case of a solid. In a constant-volume simulation, which is the normal mode of operation for the mgpt pair style, Omega, V and N all remain constant throughout the simulation and thus are equal to their initial values. In a constant-stress simulation, the cell volume V will change (slowly) as the simulation proceeds. After each time step, the atomic volume should be updated by the code as Omega = V/N. In addition, the volume term E_vol and the potentials v_2, v_3 and v_4 have to be removed at the end of the time step, and then respecified at the new value of Omega. In all simulations, Omega must remain within the defined volume range for E_vol and the potentials for the given material.
The default option volpress yes in the pair_coeff command includes all volume derivatives of E_tot required to calculate the stress tensor and pressure correctly. The option volpress no disregards the pressure contribution resulting from the volume term E_vol, and can be used for testing and analysis purposes. The additional optional variable nbody controls the specific terms in E_tot that are calculated. The default option and the normal option for mid-period transition and actinide metals is nbody 1234 for which all four terms in E_tot are retained. The option nbody 12, for example, retains only the volume term and the two-ion pair potential term and can be used for GPT series-end transition metals that can be well described without v_3 and v_4. The nbody option can also be used to test or analyze the contribution of any of the four terms in E_tot to a given calculated property.
The mgpt pair style makes extensive use of matrix algebra and includes optimized kernels for the BlueGene/Q architecture and the Intel/AMD (x86) architectures. When compiled with the appropriate compiler and compiler switches (-msse3 on x86, and using the IBM XL compiler on BG/Q), these optimized routines are used automatically. For BG/Q machines, building with the default Makefile for that architecture (e.g., “make bgq”) should enable the optimized algebra routines. For x-86 machines, there is a provided Makefile.mgptfast which enables the fast algebra routines, i.e. build LAMMPS with “make mgptfast”. The user will be informed in the output files of the matrix kernels in use. To further improve speed, on x86 the option precision single can be added to the pair_coeff command line, which improves speed (up to a factor of two) at the cost of doing matrix calculations with 7 digit precision instead of the default 16. For consistency the default option can be specified explicitly by the option precision double.
All remaining potential and control data are contained with the parmin and potin files, including cutoffs, atomic mass, and other basic MGPT variables. Specific MGPT potential data for the transition metals tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials), and vanadium (V6.1 potentials) are contained in the LAMMPS potentials directory. The stored files are, respectively, Ta4.mgpt.parmin, Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin, Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and V6.1.mgpt.potin . Useful corresponding informational “README” files on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the potentials directory. These latter files indicate the volume mesh and range for each potential and give appropriate references for the potentials. It is expected that MGPT potentials for additional materials will be added over time.
Useful example MGPT scripts are given in the examples/USER/mgpt directory. These scripts show the necessary steps to perform constant-volume calculations and simulations. It is strongly recommended that the user work through and understand these examples before proceeding to more complex simulations.
For good performance, LAMMPS should be built with the compiler flags “-O3 -msse3 -funroll-loops” when including this pair style. The src/MAKE/OPTIONS/Makefile.mgptfast is an example machine Makefile with these options included as part of a standard MPI build. Note that it as provided, it will build with whatever low-level compiler (g++, icc, etc) is the default for your MPI installation.
Mixing, shift, table tail correction, restart:
This pair style does not support the pair_modify mix, shift, table, and tail options.
This pair style does not write its information to binary restart files, since it is stored in potential files. Thus, you needs to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file.
This pair style can only be used via the pair keyword of the run_style respa command. It does not support the inner, middle, outer keywords.
This pair style is part of the USER-MGPT package and is only enabled if LAMMPS is built with that package. See the Making LAMMPS section for more info.
The MGPT potentials require the newtion setting to be “on” for pair style interactions.
The stored parmin and potin potential files provided with LAMMPS in the “potentials” directory are written in Rydberg atomic units, with energies in Rydbergs and distances in Bohr radii. The mgpt pair style converts Rydbergs to Hartrees to make the potential files compatible with LAMMPS electron units.
The form of E_tot used in the mgpt pair style is only appropriate for elemental bulk solids and liquids. This includes solids with point and extended defects such as vacancies, interstitials, grain boundaries and dislocations. Alloys and free surfaces, however, require significant modifications, which are not included in the mgpt pair style. Likewise, the hybrid pair style is not allowed, where MGPT would be used for some atoms but not for others.
Electron-thermal effects are not included in the standard MGPT potentials provided in the “potentials” directory, where the potentials have been constructed at zero electron temperature. Physically, electron-thermal effects may be important in 3d (e.g., V) and 4d (e.g., Mo) transition metals at high temperatures near melt and above. It is expected that temperature-dependent MGPT potentials for such cases will be added over time.
The options defaults for the pair_coeff command are volpress yes, nbody 1234, and precision double.
(Moriarty1) Moriarty, Physical Review B, 38, 3199 (1988).
(Moriarty2) Moriarty, Physical Review B, 42, 1609 (1990). Moriarty, Physical Review B 49, 12431 (1994).
(Moriarty3) Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang, Journal of Materials Research, 21, 563 (2006).
(Glosli) Glosli, unpublished, 2005. Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference Series, 46, 254 (2006).
(Oppelstrup) Oppelstrup, unpublished, 2015. Oppelstrup and Moriarty, to be published.