Merge pull request #1503 from etomica/master
Implement HMA compute in LAMMPS
This commit is contained in:
Axel Kohlmeyer
@ -217,6 +217,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
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"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
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"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
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"heat/flux/tally"_compute_tally.html -
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"heat/flux/tally"_compute_tally.html -
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"hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
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"hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
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"hma"_compute_hma.html - harmonically mapped averaging for atomic crystals
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"improper"_compute_improper.html - energy of each improper sub-style
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"improper"_compute_improper.html - energy of each improper sub-style
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"improper/local"_compute_improper_local.html - angle of each improper
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"improper/local"_compute_improper_local.html - angle of each improper
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"inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
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"inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
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184
doc/src/compute_hma.txt
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184
doc/src/compute_hma.txt
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@ -0,0 +1,184 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute hma command :h3
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[Syntax:]
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compute ID group-ID hma temp-ID keyword ... :pre
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ID, group-ID are documented in "compute"_compute.html command :l
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hma = style name of this compute command :l
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temp-ID = ID of fix that specifies the set temperature during canonical simulation :l
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keyword = {anharmonic} {u} {p Pharm} {cv} :l
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{anharmonic} = compute will return anharmonic property values
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{u} = compute will return potential energy
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{p} = compute will return pressure. the following keyword must be the difference between the harmonic pressure and lattice pressure as described below
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{cv} = compute will return the heat capacity :pre
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:ule
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[Examples:]
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compute 2 all hma 1 u
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compute 2 all hma 1 anharmonic u p 0.9
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compute 2 all hma 1 u cv :pre
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[Description:]
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Define a computation that calculates the properties of a solid (potential
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energy, pressure or heat capacity), using the harmonically-mapped averaging
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(HMA) method.
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This command yields much higher precision than the equivalent compute commands
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("compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html, etc.)
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commands during a canonical simulation of an atomic crystal. Specifically,
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near melting HMA can yield averages of a given precision an order of magnitude
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faster than conventional methods, and this only improves as the temperatures is
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lowered. This is particularly important for evaluating the free energy by
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thermodynamic integration, where the low-temperature contributions are the
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greatest source of statistical uncertainty. Moreover, HMA has other
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advantages, including smaller potential-truncation effects, finite-size
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effects, smaller timestep inaccuracy, faster equilibration and shorter
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decorrelation time.
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HMA should not be used if atoms are expected to diffuse. It is also
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restricted to simulations in the NVT ensemble. While this compute may be
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used with any potential in LAMMPS, it will provide inaccurate results
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for potentials that do not go to 0 at the truncation distance;
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"pair_lj_smooth_linear"_pair_lj_smooth_linear.html and Ewald summation should
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work fine, while "pair_lj"_pair_lj.html will perform poorly unless
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the potential is shifted (via "pair_modify"_pair_modify.html shift) or the cutoff is large. Furthermore, computation of the heat capacity with
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this compute is restricted to those that implement the single_hessian method
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in Pair. Implementing single_hessian in additional pair styles is simple.
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Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at
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buffalo.edu) if your desired pair style does not have this method. This is
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the list of pair styles that currently implement pair_hessian:
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"lj_smooth_linear"_pair_lj_smooth_linear.html :l
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:ule
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In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble
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averages, which leads to an accurate and precise measurement of the anharmonic contributions without contamination
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by noise produced by the already-known harmonic behavior.
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A detailed description of this method can be found in ("Moustafa"_#hma-Moustafa). The potential energy is computed by the formula:
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\begin\{equation\}
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\left< U\right>_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B T + \left< U + \frac\{1\}\{2\} F\bullet\Delta r \right>
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\end\{equation\}
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where \(N\) is the number of atoms in the system, \(k_B\) is Boltzmann's
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constant, \(T\) is the temperature, \(d\) is the
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dimensionality of the system (2 or 3 for 2d/3d), \(F\bullet\Delta r\) is the sum of dot products of the
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atomic force vectors and displacement (from lattice sites) vectors, and \(U\) is the sum of
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pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies.
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The pressure is computed by the formula:
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\begin\{equation\}
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\left< P\right>_\{HMA\} = \Delta \hat P + \left< P_\{vir\} + \frac\{\beta \Delta \hat P - \rho\}\{d(N-1)\} F\bullet\Delta r \right>
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\end\{equation\}
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where \(\rho\) is the number density of the system, \(\Delta \hat P\) is the
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difference between the harmonic and lattice pressure, \(P_\{vir\}\) is
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the virial pressure computed as the sum of pair, bond, angle, dihedral,
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improper, kspace (long-range), and fix contributions to the force on each
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atom, and \(k_B=1/k_B T\). Although the method will work for any value of \(\Delta \hat P\)
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specified (use pressure "units"_units.html), the precision of the resultant
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pressure is sensitive to \(\Delta \hat P\); the precision tends to be
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best when \(\Delta \hat P\) is the actual the difference between the lattice
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pressure and harmonic pressure.
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\begin\{equation\}
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\left<C_V \right>_\{HMA\} = \frac\{d\}\{2\} (N-1) k_B + \frac\{1\}\{k_B T^2\} \left( \left<
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U_\{HMA\}^2 \right> - \left<U_\{HMA\}\right>^2 \right) + \frac\{1\}\{4 T\}
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\left< F\bullet\Delta r + \Delta r \bullet \Phi \bullet \Delta r \right>
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\end\{equation\}
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where \(\Phi\) is the Hessian matrix. The compute hma command
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computes the full expression for \(C_V\) except for the
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\(\left<U_\{HMA\}^2\right>^2\) in the variance term, which can be obtained by
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passing the {u} keyword; you must add this extra contribution to the \(C_V\)
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value reported by this compute. The variance term can cause significant
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round-off error when computing \(C_V\). To address this, the {anharmonic}
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keyword can be passed and/or the output format can be specified with more
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digits.
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thermo_modify format float '%22.15e' :pre
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The {anharmonic} keyword will instruct the compute to return anharmonic
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properties rather than the full properties, which include lattice, harmonic
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and anharmonic contributions.
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When using this keyword, the compute must be first active (it must be included
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via a "thermo_style custom"_thermo_style.html command) while the atoms are
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still at their lattice sites (before equilibration).
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The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover ("fix nvt"_fix_nh.html) or
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Berendsen ("fix temp/berendsen"_fix_temp_berendsen.html) thermostat used for the simulation. While using this command, Langevin thermostat
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("fix langevin"_fix_langevin.html)
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should be avoided as its extra forces interfere with the HMA implementation.
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NOTE: Compute hma command should be used right after the energy minimization, when the atoms are at their lattice sites.
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The simulation should not be started before this command has been used in the input script.
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The following example illustrates the placement of this command in the input script:
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min_style cg
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minimize 1e-35 1e-15 50000 500000
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compute 1 all hma thermostatid u
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fix thermostatid all nvt temp 600.0 600.0 100.0 :pre
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NOTE: Compute hma should be used when the atoms of the solid do not diffuse. Diffusion will reduce the precision in the potential energy computation.
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NOTE: The "fix_modify energy yes"_fix_modify.html command must also be specified if a fix is to contribute potential energy to this command.
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An example input script that uses this compute is included in
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examples/USER/hma/ along with corresponding LAMMPS output showing that the HMA
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properties fluctuate less than the corresponding conventional properties.
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[Output info:]
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This compute calculates a global vector that includes the n properties
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requested as arguments to the command (the potential energy, pressure and/or heat
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capacity). The elements of the vector can be accessed by indices 1-n by any
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command that uses global vector values as input. See the "Howto
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output"_Howto_output.html doc page for an overview of LAMMPS output options.
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The vector values calculated by this compute are "extensive". The
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scalar value will be in energy "units"_units.html.
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[Restrictions:]
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This compute is part of the USER-MISC package. It is enabled only
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if LAMMPS was built with that package. See the "Build
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package"_Build_package.html doc page for more info.
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Usage restricted to canonical (NVT) ensemble simulation only.
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[Related commands:]
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"compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html
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"dynamical matrix"_dynamical_matrix.html provides a finite difference
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formulation of the hessian provided by Pair's single_hessian, which is used by
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this compute.
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[Default:] none
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:line
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:link(hma-Moustafa)
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[(Moustafa)] Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, {Very fast averaging of thermal properties of crystals by molecular simulation},
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"Phys. Rev. E \[92\], 043303 (2015)"_https://link.aps.org/doi/10.1103/PhysRevE.92.043303
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@ -47,6 +47,7 @@ Computes :h1
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compute_gyration_shape
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compute_gyration_shape
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compute_heat_flux
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compute_heat_flux
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compute_hexorder_atom
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compute_hexorder_atom
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compute_hma
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compute_improper
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compute_improper
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compute_improper_local
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compute_improper_local
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compute_inertia_chunk
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compute_inertia_chunk
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@ -47,6 +47,9 @@ package"_Build_package.html doc page for more info.
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"fix phonon"_fix_phonon.html
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"fix phonon"_fix_phonon.html
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"compute hma"_compute_hma.html uses an analytic formulation of the hessian
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provided by Pair's single_hessian.
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[Default:]
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[Default:]
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The default settings are file = "dynmat.dyn", binary = no
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The default settings are file = "dynmat.dyn", binary = no
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@ -45,6 +45,7 @@ Aidan
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aij
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aij
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airebo
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airebo
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Aj
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Aj
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ajs
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ajaramil
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ajaramil
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akohlmey
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akohlmey
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Aktulga
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Aktulga
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@ -99,6 +100,7 @@ antisymmetry
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anton
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anton
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Antonelli
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Antonelli
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api
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api
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Apoorva
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Appl
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Appl
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Apu
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Apu
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arccos
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arccos
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@ -523,6 +525,7 @@ Dcut
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de
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de
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dE
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dE
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De
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De
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decorrelation
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debye
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debye
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Debye
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Debye
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Decius
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Decius
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@ -1075,6 +1078,7 @@ Hilger
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histo
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histo
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histogrammed
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histogrammed
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histogramming
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histogramming
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hma
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hmaktulga
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hmaktulga
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hoc
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hoc
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Hochbruck
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Hochbruck
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@ -1331,6 +1335,8 @@ kmax
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Kmax
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Kmax
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Knizhnik
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Knizhnik
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knl
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knl
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Kofke
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kofke
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Kohlmeyer
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Kohlmeyer
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Kohn
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Kohn
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kokkos
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kokkos
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@ -1718,6 +1724,7 @@ Morteza
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Mosayebi
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Mosayebi
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Moseler
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Moseler
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Moskalev
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Moskalev
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Moustafa
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mov
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mov
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mpi
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mpi
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MPI
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MPI
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@ -2217,6 +2224,7 @@ PTM
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ptr
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ptr
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pu
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pu
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purdue
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purdue
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Purohit
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pushstore
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pushstore
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pvar
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pvar
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pw
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pw
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@ -2434,6 +2442,7 @@ Ryckaert
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Rycroft
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Rycroft
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Rydbergs
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Rydbergs
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Rz
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Rz
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Sabry
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saddlebrown
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saddlebrown
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Sadigh
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Sadigh
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saed
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saed
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22
examples/USER/misc/hma/README
Normal file
22
examples/USER/misc/hma/README
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@ -0,0 +1,22 @@
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The example input script sets up a simple FCC crystal using the Lennard-Jones
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potential. The script sets up the HMA compute to calculate the energy, pressure
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and heat capacity. The output columns are:
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1: timestep
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2: measured temperature
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3: potential energy
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4: HMA potential energy
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5: pressure
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6: HMA pressure
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7: HMA heat capacity contribution
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Averages of the potential energy (#3 and #4) agree although #4 (HMA) is more precise.
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Averages of the pressure (#5 and #6) agree once the ideal gas
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contribution is included; #6 (HMA) is more precise.
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The heat capacity can be computed from colume #3 (convential) as
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Cv = Var(#3)/(k T^2)
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With HMA, the heat capacity can be computed from column #4 and #7 as
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Cv = #7 + Var(#4)/(k T^2)
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36
examples/USER/misc/hma/hma.in
Normal file
36
examples/USER/misc/hma/hma.in
Normal file
@ -0,0 +1,36 @@
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# Harmonically mapped average example
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units lj
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dimension 3
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boundary p p p
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atom_style atomic
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atom_modify map array
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# ---------- Create Atoms ----------------------------
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lattice fcc 1.0
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region box block 0 4 0 4 0 4 units lattice
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create_box 1 box
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lattice fcc 1.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
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create_atoms 1 region box
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# ---------- Define Interatomic Potential ---------------------
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pair_style lj/smooth/linear 3
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pair_coeff * * 1.0 1.0
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mass 1 1.0
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atom_modify sort 0 1
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velocity all create 0.1 45678 dist gaussian
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compute u all pe
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compute p all pressure NULL pair
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compute hma all hma settemp u p 9.579586686264458 cv
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timestep 0.005
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fix settemp all nvt temp 1.0 1.0 0.5
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thermo_style custom elapsed temp c_u c_hma[1] c_p c_hma[2] c_hma[3]
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thermo_modify format float '%22.15e'
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thermo 500
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run 20000
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thermo 20
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run 200000
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10159
examples/USER/misc/hma/log.6Nov18.hma.g++.1
Normal file
10159
examples/USER/misc/hma/log.6Nov18.hma.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
10159
examples/USER/misc/hma/log.6Nov18.hma.g++.4
Normal file
10159
examples/USER/misc/hma/log.6Nov18.hma.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -31,6 +31,7 @@ compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013
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compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017
|
compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017
|
||||||
compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018
|
compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018
|
||||||
compute gyration/shape, Evangelos Voyiatzis, evoyiatzis at gmail.com, 25 July 2019
|
compute gyration/shape, Evangelos Voyiatzis, evoyiatzis at gmail.com, 25 July 2019
|
||||||
|
compute hma, Andrew Schultz & David Kofke (UB), ajs42 at buffalo.edu & kofke at buffalo.edu, 1 Jul 2019
|
||||||
compute pressure/cylinder, Cody K. Addington (NCSU), , 2 Oct 2018
|
compute pressure/cylinder, Cody K. Addington (NCSU), , 2 Oct 2018
|
||||||
compute momentum, Rupert Nash (University of Edinburgh), r.nash at epcc.ed.ac.uk, 28 June 2019
|
compute momentum, Rupert Nash (University of Edinburgh), r.nash at epcc.ed.ac.uk, 28 June 2019
|
||||||
compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18
|
compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18
|
||||||
|
|||||||
516
src/USER-MISC/compute_hma.cpp
Normal file
516
src/USER-MISC/compute_hma.cpp
Normal file
@ -0,0 +1,516 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
This compute implements harmonically-mapped averaging for crystalline solids.
|
||||||
|
The current implementation handles atomic crystals.
|
||||||
|
|
||||||
|
Computing the heat capacity relies on being able to compute the second
|
||||||
|
derivative of the energy with respect to atom positions. This capability is
|
||||||
|
provided by the single2 method in Pair, but is currently only implemented for
|
||||||
|
the shifted-force LJ potential (lj/smooth/linear). Pair::single2 takes a single
|
||||||
|
pair and (like Pair::single) returns the energy and sets the force as an out
|
||||||
|
parameter, but also sets the elements of 6-element double array out parameter,
|
||||||
|
which are the unique components of the atomic Hessian tensor for the pair. A
|
||||||
|
helper method exists (Pair::pairTensor), which will compute the tensor from
|
||||||
|
linear derivatives and the vector between the positions. HMA Heat capacity can
|
||||||
|
be computed for other models by implementing single2 in those Pair classes.
|
||||||
|
|
||||||
|
More information about HMA is available in these publications:
|
||||||
|
|
||||||
|
A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy
|
||||||
|
equation of state and coexistence properties for classical Lennard-Jones
|
||||||
|
crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018)
|
||||||
|
https://dx.doi.org/10.1063/1.5053714
|
||||||
|
|
||||||
|
S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for
|
||||||
|
Computing the Free Energy of Classical Crystals by Molecular Simulation: A
|
||||||
|
Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017)
|
||||||
|
https://dx.doi.org/10.1021/acs.jctc.6b01082
|
||||||
|
|
||||||
|
S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal
|
||||||
|
properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015)
|
||||||
|
https://dx.doi.org/10.1103/PhysRevE.92.043303
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include <cmath>
|
||||||
|
#include <cstring>
|
||||||
|
#include <mpi.h>
|
||||||
|
#include "compute_hma.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "update.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "pair.h"
|
||||||
|
#include "bond.h"
|
||||||
|
#include "angle.h"
|
||||||
|
#include "dihedral.h"
|
||||||
|
#include "improper.h"
|
||||||
|
#include "kspace.h"
|
||||||
|
#include "group.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "modify.h"
|
||||||
|
#include "fix.h"
|
||||||
|
#include "fix_store.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "comm.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "neigh_request.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
|
||||||
|
#include <vector>
|
||||||
|
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
ComputeHMA::ComputeHMA(LAMMPS *lmp, int narg, char **arg) :
|
||||||
|
Compute(lmp, narg, arg), id_temp(NULL), deltaR(NULL)
|
||||||
|
{
|
||||||
|
if (narg < 4) error->all(FLERR,"Illegal compute hma command");
|
||||||
|
if (igroup) error->all(FLERR,"Compute hma must use group all");
|
||||||
|
if (strcmp(arg[3],"NULL") == 0) {error->all(FLERR,"fix ID specifying the set temperature of canonical simulation is required");}
|
||||||
|
else {
|
||||||
|
int n = strlen(arg[3]) + 1;
|
||||||
|
id_temp = new char[n];
|
||||||
|
strcpy(id_temp,arg[3]);
|
||||||
|
}
|
||||||
|
|
||||||
|
create_attribute = 1;
|
||||||
|
extscalar = 1;
|
||||||
|
timeflag = 1;
|
||||||
|
|
||||||
|
// (from compute displace/atom) create a new fix STORE style
|
||||||
|
// our new fix's id (id_fix)= compute-ID + COMPUTE_STORE
|
||||||
|
// our new fix's group = same as compute group
|
||||||
|
|
||||||
|
int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
|
||||||
|
id_fix = new char[n];
|
||||||
|
strcpy(id_fix,id);
|
||||||
|
strcat(id_fix,"_COMPUTE_STORE");
|
||||||
|
|
||||||
|
char **newarg = new char*[6];
|
||||||
|
newarg[0] = id_fix;
|
||||||
|
newarg[1] = group->names[igroup];
|
||||||
|
newarg[2] = (char *) "STORE";
|
||||||
|
newarg[3] = (char *) "peratom";
|
||||||
|
newarg[4] = (char *) "1";
|
||||||
|
newarg[5] = (char *) "3";
|
||||||
|
modify->add_fix(6,newarg);
|
||||||
|
fix = (FixStore *) modify->fix[modify->nfix-1];
|
||||||
|
|
||||||
|
delete [] newarg;
|
||||||
|
|
||||||
|
// calculate xu,yu,zu for fix store array
|
||||||
|
// skip if reset from restart file
|
||||||
|
|
||||||
|
if (fix->restart_reset) fix->restart_reset = 0;
|
||||||
|
else {
|
||||||
|
double **xoriginal = fix->astore;
|
||||||
|
double **x = atom->x;
|
||||||
|
imageint *image = atom->image;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
|
||||||
|
for (int i = 0; i < nlocal; i++)
|
||||||
|
domain->unmap(x[i],image[i],xoriginal[i]);
|
||||||
|
}
|
||||||
|
|
||||||
|
vector_flag = 1;
|
||||||
|
extvector = -1;
|
||||||
|
comm_forward = 0; // 3 if 2nd derivative needed
|
||||||
|
|
||||||
|
computeU = computeP = computeCv = -1;
|
||||||
|
returnAnharmonic = 0;
|
||||||
|
size_vector = 0;
|
||||||
|
memory->create(extlist, 3, "hma:extlist");
|
||||||
|
for (int iarg=4; iarg<narg; iarg++) {
|
||||||
|
if (!strcmp(arg[iarg], "u")) {
|
||||||
|
if (computeU>-1) continue;
|
||||||
|
computeU = size_vector;
|
||||||
|
extlist[size_vector] = 1;
|
||||||
|
size_vector++;
|
||||||
|
}
|
||||||
|
else if (!strcmp(arg[iarg], "p")) {
|
||||||
|
if (iarg+2 > narg) error->all(FLERR,"Illegal compute hma command");
|
||||||
|
if (computeP>-1) continue;
|
||||||
|
computeP = size_vector;
|
||||||
|
deltaPcap = force->numeric(FLERR, arg[iarg+1]);
|
||||||
|
extlist[size_vector] = 0;
|
||||||
|
size_vector++;
|
||||||
|
iarg++;
|
||||||
|
}
|
||||||
|
else if (!strcmp(arg[iarg], "cv")) {
|
||||||
|
if (computeCv>-1) continue;
|
||||||
|
computeCv = size_vector;
|
||||||
|
comm_forward = 3;
|
||||||
|
extlist[size_vector] = 1;
|
||||||
|
size_vector++;
|
||||||
|
}
|
||||||
|
else if (!strcmp(arg[iarg], "anharmonic")) {
|
||||||
|
// the first time we're called, we'll grab lattice pressure and energy
|
||||||
|
returnAnharmonic = -1;
|
||||||
|
}
|
||||||
|
else {
|
||||||
|
error->all(FLERR,"Illegal compute hma command");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (size_vector == 0) {
|
||||||
|
error->all(FLERR,"Illegal compute hma command");
|
||||||
|
}
|
||||||
|
if (size_vector<3) {
|
||||||
|
memory->grow(extlist, size_vector, "hma:extlist");
|
||||||
|
}
|
||||||
|
memory->create(vector, size_vector, "hma:vector");
|
||||||
|
|
||||||
|
if (computeU>-1 || computeCv>-1) {
|
||||||
|
peflag = 1;
|
||||||
|
}
|
||||||
|
if (computeP>-1) {
|
||||||
|
pressflag = 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
nmax = 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
ComputeHMA::~ComputeHMA()
|
||||||
|
{
|
||||||
|
// check nfix in case all fixes have already been deleted
|
||||||
|
if (modify->nfix) modify->delete_fix(id_fix);
|
||||||
|
|
||||||
|
delete [] id_fix;
|
||||||
|
delete [] id_temp;
|
||||||
|
memory->destroy(extlist);
|
||||||
|
memory->destroy(vector);
|
||||||
|
memory->destroy(deltaR);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeHMA::init() {
|
||||||
|
if (computeCv>-1) {
|
||||||
|
if (force->pair == NULL)
|
||||||
|
error->all(FLERR,"No pair style is defined for compute hma cv");
|
||||||
|
if (force->pair->single_enable == 0)
|
||||||
|
error->all(FLERR,"Pair style does not support compute hma cv");
|
||||||
|
}
|
||||||
|
|
||||||
|
int irequest = neighbor->request(this,instance_me);
|
||||||
|
neighbor->requests[irequest]->pair = 0;
|
||||||
|
neighbor->requests[irequest]->compute = 1;
|
||||||
|
neighbor->requests[irequest]->occasional = 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
void ComputeHMA::init_list(int id, NeighList *ptr)
|
||||||
|
{
|
||||||
|
list = ptr;
|
||||||
|
}
|
||||||
|
|
||||||
|
void ComputeHMA::setup()
|
||||||
|
{
|
||||||
|
int dummy=0;
|
||||||
|
int ifix = modify->find_fix(id_temp);
|
||||||
|
if (ifix < 0) error->all(FLERR,"Could not find compute hma temperature ID");
|
||||||
|
double * temperat = (double *) modify->fix[ifix]->extract("t_target",dummy);
|
||||||
|
if (temperat==NULL) error->all(FLERR,"Could not find compute hma temperature ID");
|
||||||
|
finaltemp = * temperat;
|
||||||
|
|
||||||
|
// set fix which stores original atom coords
|
||||||
|
|
||||||
|
int ifix2 = modify->find_fix(id_fix);
|
||||||
|
if (ifix2 < 0) error->all(FLERR,"Could not find hma store fix ID");
|
||||||
|
fix = (FixStore *) modify->fix[ifix2];
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeHMA::compute_vector()
|
||||||
|
{
|
||||||
|
invoked_vector = update->ntimestep;
|
||||||
|
|
||||||
|
// grow deltaR array if necessary
|
||||||
|
if (comm_forward>0 && atom->nmax > nmax) {
|
||||||
|
memory->destroy(deltaR);
|
||||||
|
nmax = atom->nmax;
|
||||||
|
memory->create(deltaR,nmax,3,"hma:deltaR");
|
||||||
|
}
|
||||||
|
|
||||||
|
double **xoriginal = fix->astore;
|
||||||
|
double fdr = 0.0;
|
||||||
|
double **x = atom->x;
|
||||||
|
double **f = atom->f;
|
||||||
|
|
||||||
|
imageint *image = atom->image;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
|
||||||
|
double *h = domain->h;
|
||||||
|
double xprd = domain->xprd;
|
||||||
|
double yprd = domain->yprd;
|
||||||
|
double zprd = domain->zprd;
|
||||||
|
|
||||||
|
double u = 0.0;
|
||||||
|
if (computeU>-1 || computeCv>-1) {
|
||||||
|
if (force->pair) u += force->pair->eng_vdwl + force->pair->eng_coul;
|
||||||
|
if (force->bond) u += force->bond->energy;
|
||||||
|
if (force->angle) u += force->angle->energy;
|
||||||
|
if (force->dihedral) u += force->dihedral->energy;
|
||||||
|
if (force->improper) u += force->improper->energy;
|
||||||
|
}
|
||||||
|
|
||||||
|
int dimension = domain->dimension;
|
||||||
|
double p = 0, vol = 0;
|
||||||
|
if (computeP>-1) {
|
||||||
|
p = virial_compute(dimension);
|
||||||
|
vol = xprd * yprd;
|
||||||
|
if (dimension == 3) vol *= zprd;
|
||||||
|
p *= force->nktv2p / (dimension*vol);
|
||||||
|
if (returnAnharmonic == -1) {
|
||||||
|
pLat = p;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (domain->triclinic == 0) {
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
int xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||||
|
int ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||||
|
int zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||||
|
double dx = x[i][0] + xbox*xprd - xoriginal[i][0];
|
||||||
|
double dy = x[i][1] + ybox*yprd - xoriginal[i][1];
|
||||||
|
double dz = x[i][2] + zbox*zprd - xoriginal[i][2];
|
||||||
|
if (comm_forward>0) {
|
||||||
|
deltaR[i][0] = dx;
|
||||||
|
deltaR[i][1] = dy;
|
||||||
|
deltaR[i][2] = dz;
|
||||||
|
}
|
||||||
|
fdr += dx*f[i][0] + dy*f[i][1] + dz*f[i][2];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
else {
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
int xbox = (image[i] & IMGMASK) - IMGMAX;
|
||||||
|
int ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||||
|
int zbox = (image[i] >> IMG2BITS) - IMGMAX;
|
||||||
|
double dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xoriginal[i][0];
|
||||||
|
double dy = x[i][1] + h[1]*ybox + h[3]*zbox - xoriginal[i][1];
|
||||||
|
double dz = x[i][2] + h[2]*zbox - xoriginal[i][2];
|
||||||
|
if (comm_forward>0) {
|
||||||
|
deltaR[i][0] = dx;
|
||||||
|
deltaR[i][1] = dy;
|
||||||
|
deltaR[i][2] = dz;
|
||||||
|
}
|
||||||
|
fdr += ((dx*f[i][0])+(dy*f[i][1])+(dz*f[i][2]));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
double phiSum = 0.0;
|
||||||
|
if (computeCv>-1) {
|
||||||
|
comm->forward_comm_compute(this);
|
||||||
|
int *type = atom->type;
|
||||||
|
double** cutsq = force->pair->cutsq;
|
||||||
|
if (force->pair) {
|
||||||
|
double **x = atom->x;
|
||||||
|
double **f = atom->f;
|
||||||
|
int *type = atom->type;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
double *special_lj = force->special_lj;
|
||||||
|
double *special_coul = force->special_coul;
|
||||||
|
int newton_pair = force->newton_pair;
|
||||||
|
|
||||||
|
if (update->firststep == update->ntimestep) neighbor->build_one(list,1);
|
||||||
|
else neighbor->build_one(list);
|
||||||
|
int inum = list->inum;
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
|
||||||
|
for (int ii = 0; ii < inum; ii++) {
|
||||||
|
int i = ilist[ii];
|
||||||
|
double fac = (newton_pair || i < nlocal) ? 1.0 : 0.5;
|
||||||
|
double* ix = x[i];
|
||||||
|
int itype = type[i];
|
||||||
|
int *jlist = firstneigh[i];
|
||||||
|
int jnum = numneigh[i];
|
||||||
|
double *idr = deltaR[i];
|
||||||
|
for (int jj = 0; jj < jnum; jj++) {
|
||||||
|
int j = jlist[jj];
|
||||||
|
if (!newton_pair && j>=nlocal) fac -= 0.5;
|
||||||
|
double factor_lj = special_lj[sbmask(j)];
|
||||||
|
double factor_coul = special_coul[sbmask(j)];
|
||||||
|
j &= NEIGHMASK;
|
||||||
|
double* jx = x[j];
|
||||||
|
double delr[3];
|
||||||
|
delr[0] = ix[0] - jx[0];
|
||||||
|
delr[1] = ix[1] - jx[1];
|
||||||
|
delr[2] = ix[2] - jx[2];
|
||||||
|
double rsq = delr[0]*delr[0] + delr[1]*delr[1] + delr[2]*delr[2];
|
||||||
|
int jtype = type[j];
|
||||||
|
if (rsq < cutsq[itype][jtype]) {
|
||||||
|
double* jdr = deltaR[j];
|
||||||
|
double fforce, d2u[6];
|
||||||
|
force->pair->single_hessian(i, j, itype, jtype, rsq, delr, factor_coul, factor_lj, fforce, d2u);
|
||||||
|
int m = 0;
|
||||||
|
for (int k=0; k<3; k++) {
|
||||||
|
double a = fac;
|
||||||
|
for (int l=k; l<3; l++) {
|
||||||
|
phiSum += a*(idr[k]*jdr[l]+jdr[k]*idr[l])*d2u[m];
|
||||||
|
phiSum -= a*(idr[k]*idr[l]*d2u[m] + jdr[k]*jdr[l]*d2u[m]);
|
||||||
|
m++;
|
||||||
|
if (k==l) a *= 2;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// compute and sum up properties across processors
|
||||||
|
|
||||||
|
double fdrTotal;
|
||||||
|
MPI_Allreduce(&fdr,&fdrTotal,1,MPI_DOUBLE,MPI_SUM,world);
|
||||||
|
double uTotal;
|
||||||
|
if (computeU>-1 || computeCv>-1) {
|
||||||
|
MPI_Allreduce(&u,&uTotal,1,MPI_DOUBLE,MPI_SUM,world);
|
||||||
|
if (returnAnharmonic == -1) {
|
||||||
|
uLat = uTotal;
|
||||||
|
}
|
||||||
|
if (computeU>-1) {
|
||||||
|
if (returnAnharmonic) {
|
||||||
|
vector[computeU] = uTotal - uLat + 0.5*fdrTotal;
|
||||||
|
}
|
||||||
|
else {
|
||||||
|
vector[computeU] = uTotal + 0.5*fdrTotal + 0.5*dimension*(atom->natoms - 1)*force->boltz*finaltemp;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (computeP>-1) {
|
||||||
|
double fv = ((deltaPcap)-(force->boltz*finaltemp*force->nktv2p*atom->natoms/vol))/(force->boltz*finaltemp*dimension*(atom->natoms - 1));
|
||||||
|
if (returnAnharmonic) {
|
||||||
|
vector[computeP] = p - pLat + (fv*fdrTotal);
|
||||||
|
}
|
||||||
|
else {
|
||||||
|
vector[computeP] = p + (fv*fdrTotal) + deltaPcap;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (computeCv>-1) {
|
||||||
|
if (computeU==-1) MPI_Allreduce(&u,&uTotal,1,MPI_DOUBLE,MPI_SUM,world);
|
||||||
|
double buTot;
|
||||||
|
if (returnAnharmonic) {
|
||||||
|
buTot = (uTotal - uLat + 0.5*fdrTotal)/finaltemp;
|
||||||
|
}
|
||||||
|
else {
|
||||||
|
buTot = (uTotal + 0.5*fdrTotal)/finaltemp + 0.5*dimension*(atom->natoms - 1)*force->boltz;
|
||||||
|
}
|
||||||
|
double one = -0.25*(fdr + phiSum)/finaltemp;
|
||||||
|
double Cv;
|
||||||
|
MPI_Allreduce(&one,&Cv,1,MPI_DOUBLE,MPI_SUM,world);
|
||||||
|
vector[computeCv] = Cv + buTot*buTot;
|
||||||
|
if (!returnAnharmonic) {
|
||||||
|
vector[computeCv] += 0.5*dimension*(atom->natoms-1);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (returnAnharmonic == -1) {
|
||||||
|
// we have our lattice properties
|
||||||
|
returnAnharmonic = 1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
double ComputeHMA::virial_compute(int n)
|
||||||
|
{
|
||||||
|
double v = 0;
|
||||||
|
|
||||||
|
// sum contributions to virial from forces and fixes
|
||||||
|
|
||||||
|
if (force->pair) v += sumVirial(n, force->pair->virial);
|
||||||
|
if (force->bond) v += sumVirial(n, force->bond->virial);
|
||||||
|
if (force->angle) v += sumVirial(n, force->angle->virial);
|
||||||
|
if (force->dihedral) v += sumVirial(n, force->dihedral->virial);
|
||||||
|
if (force->improper) v += sumVirial(n, force->improper->virial);
|
||||||
|
for (int i = 0; i < modify->nfix; i++)
|
||||||
|
if (modify->fix[i]->thermo_virial) v += sumVirial(n, modify->fix[i]->virial);
|
||||||
|
|
||||||
|
// sum virial across procs
|
||||||
|
|
||||||
|
double virial;
|
||||||
|
MPI_Allreduce(&v,&virial,1,MPI_DOUBLE,MPI_SUM,world);
|
||||||
|
|
||||||
|
// KSpace virial contribution is already summed across procs
|
||||||
|
|
||||||
|
if (force->kspace)
|
||||||
|
for (int i = 0; i < n; i++) virial += force->kspace->virial[i];
|
||||||
|
return virial;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
int ComputeHMA::pack_forward_comm(int n, int *list, double *buf,
|
||||||
|
int pbc_flag, int *pbc)
|
||||||
|
{
|
||||||
|
double **xoriginal = fix->astore;
|
||||||
|
imageint *image = atom->image;
|
||||||
|
double **x = atom->x;
|
||||||
|
double *h = domain->h;
|
||||||
|
double xprd = domain->xprd;
|
||||||
|
double yprd = domain->yprd;
|
||||||
|
double zprd = domain->zprd;
|
||||||
|
|
||||||
|
int m = 0;
|
||||||
|
for (int ii = 0; ii < n; ii++) {
|
||||||
|
int i = list[ii];
|
||||||
|
buf[m++] = deltaR[i][0];
|
||||||
|
buf[m++] = deltaR[i][1];
|
||||||
|
buf[m++] = deltaR[i][2];
|
||||||
|
}
|
||||||
|
return m;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeHMA::unpack_forward_comm(int n, int first, double *buf)
|
||||||
|
{
|
||||||
|
double **xoriginal = fix->astore;
|
||||||
|
int i,m,last;
|
||||||
|
|
||||||
|
m = 0;
|
||||||
|
last = first + n;
|
||||||
|
for (i = first; i < last; i++) {
|
||||||
|
deltaR[i][0] = buf[m++];
|
||||||
|
deltaR[i][1] = buf[m++];
|
||||||
|
deltaR[i][2] = buf[m++];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
initialize one atom's storage values, called when atom is created
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeHMA::set_arrays(int i)
|
||||||
|
{
|
||||||
|
double **xoriginal = fix->astore;
|
||||||
|
double **x = atom->x;
|
||||||
|
xoriginal[i][0] = x[i][0];
|
||||||
|
xoriginal[i][1] = x[i][1];
|
||||||
|
xoriginal[i][2] = x[i][2];
|
||||||
|
}
|
||||||
|
|
||||||
|
double ComputeHMA::memory_usage()
|
||||||
|
{
|
||||||
|
double bytes = nmax * 3 * sizeof(double);
|
||||||
|
return bytes;
|
||||||
|
}
|
||||||
67
src/USER-MISC/compute_hma.h
Normal file
67
src/USER-MISC/compute_hma.h
Normal file
@ -0,0 +1,67 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef COMPUTE_CLASS
|
||||||
|
|
||||||
|
ComputeStyle(hma,ComputeHMA)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_COMPUTE_HMA_H
|
||||||
|
#define LMP_COMPUTE_HMA_H
|
||||||
|
|
||||||
|
#include "compute.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class ComputeHMA : public Compute {
|
||||||
|
public:
|
||||||
|
ComputeHMA(class LAMMPS *, int, char **);
|
||||||
|
~ComputeHMA();
|
||||||
|
void setup();
|
||||||
|
void init();
|
||||||
|
void init_list(int, class NeighList *);
|
||||||
|
void compute_vector();
|
||||||
|
void set_arrays(int);
|
||||||
|
int pack_forward_comm(int, int *, double *, int, int *);
|
||||||
|
void unpack_forward_comm(int, int, double *);
|
||||||
|
double memory_usage();
|
||||||
|
|
||||||
|
private:
|
||||||
|
int nmax;
|
||||||
|
int atomsingroup;
|
||||||
|
char *id_fix;
|
||||||
|
char *id_temp;
|
||||||
|
double finaltemp;
|
||||||
|
class FixStore *fix;
|
||||||
|
double boltz, nktv2p, inv_volume;
|
||||||
|
double deltaPcap;
|
||||||
|
double virial_compute(int);
|
||||||
|
static double sumVirial(int n, double* v) {
|
||||||
|
double x = 0;
|
||||||
|
for (int i=0; i<n; i++) x += v[i];
|
||||||
|
return x;
|
||||||
|
}
|
||||||
|
int computeU, computeP, computeCv;
|
||||||
|
class NeighList *list; // half neighbor list
|
||||||
|
double **deltaR;
|
||||||
|
int returnAnharmonic;
|
||||||
|
double uLat, pLat;
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
|
||||||
13
src/pair.cpp
13
src/pair.cpp
@ -54,6 +54,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
|
|||||||
comm_forward = comm_reverse = comm_reverse_off = 0;
|
comm_forward = comm_reverse = comm_reverse_off = 0;
|
||||||
|
|
||||||
single_enable = 1;
|
single_enable = 1;
|
||||||
|
single_hessian_enable = 0;
|
||||||
restartinfo = 1;
|
restartinfo = 1;
|
||||||
respa_enable = 0;
|
respa_enable = 0;
|
||||||
one_coeff = 0;
|
one_coeff = 0;
|
||||||
@ -1743,6 +1744,18 @@ void Pair::init_bitmap(double inner, double outer, int ntablebits,
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void Pair::hessian_twobody(double fforce, double dfac, double delr[3], double phiTensor[6]) {
|
||||||
|
int m = 0;
|
||||||
|
for (int k=0; k<3; k++) {
|
||||||
|
phiTensor[m] = fforce;
|
||||||
|
for (int l=k; l<3; l++) {
|
||||||
|
if (l>k) phiTensor[m] = 0;
|
||||||
|
phiTensor[m++] += delr[k]*delr[l] * dfac;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
double Pair::memory_usage()
|
double Pair::memory_usage()
|
||||||
{
|
{
|
||||||
double bytes = comm->nthreads*maxeatom * sizeof(double);
|
double bytes = comm->nthreads*maxeatom * sizeof(double);
|
||||||
|
|||||||
11
src/pair.h
11
src/pair.h
@ -46,6 +46,7 @@ class Pair : protected Pointers {
|
|||||||
int comm_reverse_off; // size of reverse comm even if newton off
|
int comm_reverse_off; // size of reverse comm even if newton off
|
||||||
|
|
||||||
int single_enable; // 1 if single() routine exists
|
int single_enable; // 1 if single() routine exists
|
||||||
|
int single_hessian_enable; // 1 if single_hessian() routine exists
|
||||||
int restartinfo; // 1 if pair style writes restart info
|
int restartinfo; // 1 if pair style writes restart info
|
||||||
int respa_enable; // 1 if inner/middle/outer rRESPA routines
|
int respa_enable; // 1 if inner/middle/outer rRESPA routines
|
||||||
int one_coeff; // 1 if allows only one coeff * * call
|
int one_coeff; // 1 if allows only one coeff * * call
|
||||||
@ -148,6 +149,16 @@ class Pair : protected Pointers {
|
|||||||
return 0.0;
|
return 0.0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
void hessian_twobody(double fforce, double dfac, double delr[3], double phiTensor[6]);
|
||||||
|
|
||||||
|
virtual double single_hessian(int, int, int, int,
|
||||||
|
double, double[3], double, double,
|
||||||
|
double& fforce, double d2u[6]) {
|
||||||
|
fforce = 0.0;
|
||||||
|
for (int i=0; i<6; i++) d2u[i] = 0;
|
||||||
|
return 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
virtual void settings(int, char **) = 0;
|
virtual void settings(int, char **) = 0;
|
||||||
virtual void coeff(int, char **) = 0;
|
virtual void coeff(int, char **) = 0;
|
||||||
|
|
||||||
|
|||||||
@ -29,7 +29,9 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
PairLJSmoothLinear::PairLJSmoothLinear(LAMMPS *lmp) : Pair(lmp) {}
|
PairLJSmoothLinear::PairLJSmoothLinear(LAMMPS *lmp) : Pair(lmp) {
|
||||||
|
single_hessian_enable = 1;
|
||||||
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
@ -345,3 +347,26 @@ double PairLJSmoothLinear::single(int /*i*/, int /*j*/, int itype, int jtype,
|
|||||||
|
|
||||||
return factor_lj*philj;
|
return factor_lj*philj;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
double PairLJSmoothLinear::single_hessian(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
|
||||||
|
double delr[3], double /*factor_coul*/, double factor_lj,
|
||||||
|
double &fforce, double d2u[6])
|
||||||
|
{
|
||||||
|
double r2inv,r6inv,forcelj,philj,r,rinv;
|
||||||
|
|
||||||
|
r2inv = 1.0/rsq;
|
||||||
|
r6inv = r2inv*r2inv*r2inv;
|
||||||
|
rinv = sqrt(r2inv);
|
||||||
|
r = sqrt(rsq);
|
||||||
|
forcelj = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype]);
|
||||||
|
forcelj = rinv*forcelj - dljcut[itype][jtype];
|
||||||
|
fforce = factor_lj*forcelj*rinv;
|
||||||
|
|
||||||
|
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
|
||||||
|
philj = philj - ljcut[itype][jtype]
|
||||||
|
+ (r-cut[itype][jtype])*dljcut[itype][jtype];
|
||||||
|
|
||||||
|
double d2r = factor_lj * r6inv * (13.0*lj1[itype][jtype]*r6inv - 7.0*lj2[itype][jtype])/rsq;
|
||||||
|
hessian_twobody(fforce, -(fforce + d2r) / rsq, delr, d2u);
|
||||||
|
return factor_lj*philj;
|
||||||
|
}
|
||||||
|
|||||||
@ -38,6 +38,7 @@ class PairLJSmoothLinear : public Pair {
|
|||||||
void write_restart_settings(FILE *);
|
void write_restart_settings(FILE *);
|
||||||
void read_restart_settings(FILE *);
|
void read_restart_settings(FILE *);
|
||||||
double single(int, int, int, int, double, double, double, double &);
|
double single(int, int, int, int, double, double, double, double &);
|
||||||
|
double single_hessian(int, int, int, int, double, double[3], double, double, double&, double[6]);
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
double cut_global;
|
double cut_global;
|
||||||
|
|||||||
Reference in New Issue
Block a user