Minimize lammps

Minimize lammps

Choose a minimization algorithm to use when a minimize command is performed. Style cg is the Polak-Ribiere version of the conjugate gradient CG algorithm. At each iteration the force gradient is combined with the previous iteration information to compute a new search direction perpendicular conjugate to the previous search direction. The PR variant affects how the direction is chosen and how the CG method is restarted when it ceases to make progress. The PR variant is thought to be the most effective CG choice for most problems.

Style hftn is a Hessian-free truncated Newton algorithm. At each iteration a quadratic model of the energy potential is solved by a conjugate gradient inner iteration. The Hessian second derivatives of the energy is not formed directly, but approximated in each conjugate search direction by a finite difference directional derivative.

minimize lammps

When close to an energy minimum, the algorithm behaves like a Newton method and exhibits a quadratic convergence rate to high accuracy. In most cases the behavior of hftn is similar to cgbut it offers an alternative if cg seems to perform poorly. Style sd is a steepest descent algorithm. At each iteration, the search direction is set to the downhill direction corresponding to the force vector negative gradient of energy.

Typically, steepest descent will not converge as quickly as CG, but may be more robust in some situations. Style quickmin is a damped dynamics method described in Sheppardwhere the damping parameter is related to the projection of the velocity vector along the current force vector for each atom. The velocity of each atom is initialized to 0.

Style fire is a damped dynamics method described in Bitzekwhich is similar to quickmin but adds a variable timestep and alters the projection operation to maintain components of the velocity non-parallel to the current force vector.

This style correspond to an optimized version described in Guenole that include different time integration schemes and defaults parameters. The main differences regarding the current version fire are: time integration by Explicit Euler only, different sequence in maintaining velocity components non-parallel to the current force vector and hard-coded minimization parameters.

The damped dynamic minimizers use whatever timestep you have defined via the timestep command. Often they will converge more quickly if you use a timestep about 10x larger than you would normally use for dynamics simulations. For firethe default timestep is recommended to be equal to the one you would normally use for dynamics simulations.

Styles with a gpuintelkkompor opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the Speed packages doc page.ID, group-ID are documented in fix command.

Apply an external pressure or stress tensor to the simulation box during an energy minimization. This allows the box size and shape to vary during the iterations of the minimizer so that the final configuration will be both an energy minimum for the potential energy of the atoms, and the system pressure tensor will be close to the specified external tensor.

minimize lammps

Conceptually, specifying a positive pressure is like squeezing on the simulation box; a negative pressure typically allows the box to expand. The external pressure tensor is specified using one or more of the isoanisotrixyzxyxzyzand couple keywords.

These keywords give you the ability to specify all 6 components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are varied together during the minimization. Orthogonal simulation boxes have 3 adjustable dimensions x,y,z.

Triclinic non-orthogonal simulation boxes have 6 adjustable dimensions x,y,z,xy,xz,yz.

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The target pressures Ptarget for each of the 6 components of the stress tensor can be specified independently via the xyzxyxzyz keywords, which correspond to the 6 simulation box dimensions. For example, if the y keyword is used, the y-box length will change during the minimization. If the xy keyword is used, the xy tilt factor will change.

A box dimension will not change if that component is not specified. Note that in order to use the xyxzor yz keywords, the simulation box must be triclinic, even if its initial tilt factors are 0.

When the size of the simulation box changes, all atoms are re-scaled to new positions, unless the keyword dilate is specified with a value of partialin which case only the atoms in the fix group are re-scaled. This can be useful for leaving the coordinates of atoms in a solid substrate unchanged and controlling the pressure of a surrounding fluid. The scaleyzscalexzand scalexy keywords control whether or not the corresponding tilt factors are scaled with the associated box dimensions when relaxing triclinic periodic cells.

The default values yes will turn on scaling, which corresponds to adjusting the linear dimensions of the cell while preserving its shape.

Choosing no ensures that the tilt factors are not scaled with the box dimensions. See below for restrictions and default values in different situations. The old behavior can be recovered by setting all three scale keywords to no. The fixedpoint keyword specifies the fixed point for cell relaxation. By default, it is the center of the box.GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Already on GitHub? Sign in to your account. Add Kokkos version of minimize. Closes Skip to content. Dismiss Join GitHub today GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together. Sign up. New issue. Conversation 2 Commits 3 Checks 0 Files changed.

Copy link Quote reply. Summary Add Kokkos version of minimize. Backward Compatibility No issues. Update docs. Fall back to base class function. This comment has been minimized. Sign in to view. Kokkos package regression tests passed. View changes. Hide details View details akohlmey merged commit df63a53 into lammps : master Sep 11, 9 checks passed.GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Already on GitHub? Sign in to your account. Is there something I can look into maybe? Regular minimization requires a specialized "driver" class, similar to VerletKokkos to manage access to the system data.

minimize lammps

Some minimization styles, e. MinQuickMin may be easier to port as they implement some variant of damped dynamics. Right, the biggest issue is the CUDA version. It needs all of the data movement between host and device to work properly. Since I managed to port a fix to Kokkos the other day I can take a look at porting fix viscous.

QuickMin could probably be implemented as a simple fix, which I could try to do afterwards probably low priority if fix viscous does the job just fine. See Skip to content. Code Issues 63 Pull requests 30 Security Pulse. Dismiss Join GitHub today GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together. Sign up. New issue. Jump to bottom. Copy link Quote reply. This comment has been minimized.

Sign in to view. I started working on this. Add Kokkos version of minimize Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment. Linked pull requests.You seem to have CSS turned off. Please don't fill out this field. Please provide the ad click URL, if possible:. Help Create Join Login. Operations Management. IT Management. Project Management. Services Business VoIP. Resources Blog Articles Deals. Menu Help Create Join Login. Re: [lammps-users] minimize command Re: [lammps-users] minimize command.

Re: [lammps-users] minimize command. Oh no! Some styles failed to load. Sign Up No, Thank you. Thanks for helping keep SourceForge clean. X You seem to have CSS turned off. Briefly describe the problem required :. Upload screenshot of ad required :. I apologize. Unfortunately the rerun script I posted requires a DATA file because it extract the coordinates from the dump file and merges them with the other information from your original DATA file.

If you had a data file, you would run rerun. Here are several ways to make them: 1 restart2data: You can run the simulation for 0 timesteps, create a restart file, and convert it to a data file using restart2data. Then I am assuming you could use the dump2data. This is not the same "dump2data.

Sorry again for the confusion. Your mail is really helpful for me. Should this file look like normal lammps input file? I'm attaching rerun. It can't be a DCD file. If so, post it! This is just a quick script which I use. Alas I just realized that the "dump2data.Please contact me if you have any questions or comments about this tutorial. I'll try to add questions and answers to the bottom of the tutorial pages as they arise.

Email: Mark Tschopp, mark. This example shows how to build a periodic stack of Al-Ni nanoscale laminates and to run an atomistic simulation to obtain the relaxed structure. Both Al and Ni are fcc metals. Corresponding Author: Mark A. This molecular dynamics simulation first generates a bi-layered simulation cell. The [], [], and [] crystal directions in both layers are aligned with the x, y, z- directions of the simulation box.

For this example, the simulation box size is 54 lattice units for nickel and 47 lattice units for aluminum in the x and y direction and 7 lattice unit for nickel and 6 lattice unit for aluminum in the z direction. The keyword origin in the lattice command was used to eliminate gap at interface causing lattice to be shifted by a fraction preventing upper region from overlapping with atoms from lower region.

The potential used here is the Mishin-Al-Ni The upper region is made of nickel while the lower region is made of aluminum. The custom dump file includes the x, y, and z coordinates the centrosymmetry parameter values, the potential energy, and the stress tensor per atom. This can directly be visualized using Ovito [3]. For this example, the use of lattice units rather than box units is more convenient. In box units the geometry is defined in simulation box units ex.

Angstrom, based on command unit. In units lattice which is the defaultthe geometry is define in terms of units each representing the lattice parameter, ao, of the specific materials used. A lattice consists of a unit cell, a set of basis atoms within that cell, and a set of transformation parameters scale, origin, orient that map the unit cell into the simulation box.

Because the lattice parameters of Al and Ni are different, this example uses different number of the lattice units to minimize the accumulated mismatch over the size of the simulation box. The choice of 47 units and 54 units for Al and Ni, respectively, is based on this approach better matches with larger number of units cells is possible but then the computational effort become high; a compromise should be made based on the specific circumstances and accuracy required by the user.

If the match is poor, then non physical artifacts are introduced in the model in the form of higher energy and stresses at the edges of box making atoms have higher energy. This input script was run using the December version of Lammps. Changes in some commands in more recent versions may require revision of the input script. To run this script, store it in "relaxed. Go to the next tutorial.

Claudia Rankins, Award No. The corresponding author author would like to acknowledge funding for the overarching EVOWiki project through the Department of Energy. Jump to: navigationsearch. Personal tools Log in.

minimize lammps

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Government retains certain rights in this software. Check the input script syntax and compare to the documentation for the command. E: Too many iterations You must use a number of iterations that fit in a bit integer for minimization. You signed in with another tab or window.

Reload to refresh your session. You signed out in another tab or window. Steve Plimpton, sjplimp sandia. Copyright Sandia Corporation. Under the terms of Contract. Government retains. This software is distributed under. CommandStyle minimize,Minimize. E: Illegal Check the input script syntax and compare to the. You can use -echo screen as a. E: Minimize command before simulation box is defined. E: Too many iterations. You must use a number of iterations that fit in a bit integer.

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