From 439af71a6addabbefa19dc9ff6f2c63444412e7e Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 22 Oct 2015 23:53:39 +0000 Subject: [PATCH] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14178 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/doc2/Section_packages.html | 29 +++++ doc/doc2/pair_mgpt.html | 221 +++++++++++++++++++++++++++++++++ 2 files changed, 250 insertions(+) create mode 100644 doc/doc2/pair_mgpt.html diff --git a/doc/doc2/Section_packages.html b/doc/doc2/Section_packages.html index 16186a05d0..f6197d0145 100644 --- a/doc/doc2/Section_packages.html +++ b/doc/doc2/Section_packages.html @@ -216,6 +216,7 @@ serial. USER-H5MD dump output via HDF5 Pierre de Buyl (KU Leuven) dump h5md - - lib/h5md USER-INTEL Vectorized CPU and Intel(R) coprocessor styles W. Michael Brown (Intel) Section accelerate examples/intel - - USER-LB Lattice Boltzmann fluid Colin Denniston (U Western Ontario) fix lb/fluid USER/lb - - +USER-MGPT Fast MGPT multi-ion potentials Tomas Oppelstrup & John Moriarty (LLNL) pair_style mgpt USER/mgpt - - USER-MISC single-file contributions USER-MISC/README USER-MISC/README - - - USER-MOLFILE VMD molfile plug-ins Axel Kohlmeyer (Temple U) dump molfile - - VMD-MOLFILE USER-OMP OpenMP threaded styles Axel Kohlmeyer (Temple U) Section accelerate - - - @@ -597,6 +598,34 @@ Western Ontario. Contact them directly if you have questions.

+

USER-MGPT package +

+

This package contains a fast implementation for LAMMPS of +quantum-based MGPT multi-ion potentials. The MGPT or model GPT method +derives from first-principles DFT-based generalized pseudopotential +theory (GPT) through a series of systematic approximations valid for +mid-period transition metals with nearly half-filled d bands. The +MGPT method was originally developed by John Moriarty at Lawrence +Livermore National Lab (LLNL). +

+

In the general matrix representation of MGPT, which can also be +applied to f-band actinide metals, 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. The mgpt pair style in this package calculates forces +and energies using an optimized matrix-MGPT algorithm due to Tomas +Oppelstrup at LLNL. +

+

See this doc page to get started: +

+

pair_style mgpt +

+

The persons who created the USER-MGPT package are Tomas Oppelstrup +(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov) +Contact them directly if you have any questions. +

+
+

USER-MISC package

The files in this package are a potpourri of (mostly) unrelated diff --git a/doc/doc2/pair_mgpt.html b/doc/doc2/pair_mgpt.html new file mode 100644 index 0000000000..11ec3c2fff --- /dev/null +++ b/doc/doc2/pair_mgpt.html @@ -0,0 +1,221 @@ + +

LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

pair_style mgpt command +

+

Syntax: +

+
pair_style mgpt 
+
+

Examples: +

+
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 
+
+

Description: +

+

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 +smulations, 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, the here provided Makefile.mpi_fastmgpt +(build with "make mpi_fastmgpt") enables the fast algebra routines. +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. +

+
+ +

Mixing, shift, table tail correction, restart: +

+

The (mgpt) 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. +

+
+ +

Restrictions: +

+

The mgpt pair style is part of the USER-MGPT package and is only +enabled if LAMMPS is built with that package. +

+

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. +

+

Related commands: +

+

pair_coeff +

+

Default: +

+

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. +

+