forked from lijiext/lammps
correct link targets
This commit is contained in:
Axel Kohlmeyer
parent
fb2c18ee88
commit
ff75cf51bb
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@ -1010,7 +1010,7 @@ system. Fix nvt/sllod uses "compute
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temp/deform"_compute_temp_deform.html to compute a thermal temperature
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by subtracting out the streaming velocity of the shearing atoms. The
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velocity profile or other properties of the fluid can be monitored via
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the "fix ave/spatial"_fix_ave_spatial.html command.
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the "fix ave/chunk"_fix_ave_chunk.html command.
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As discussed in the previous section on non-orthogonal simulation
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boxes, the amount of tilt or skew that can be applied is limited by
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@ -1970,7 +1970,7 @@ on each of two regions to add/subtract specified amounts of energy to
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both regions. In both cases, the resulting temperatures of the two
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regions can be monitored with the "compute temp/region" command and
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the temperature profile of the intermediate region can be monitored
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with the "fix ave/spatial"_fix_ave_spatial.html and "compute
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with the "fix ave/chunk"_fix_ave_chunk.html and "compute
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ke/atom"_compute_ke_atom.html commands.
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The third method is to perform a reverse non-equilibrium MD simulation
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@ -1979,7 +1979,7 @@ command which implements the rNEMD algorithm of Muller-Plathe.
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Kinetic energy is swapped between atoms in two different layers of the
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simulation box. This induces a temperature gradient between the two
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layers which can be monitored with the "fix
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ave/spatial"_fix_ave_spatial.html and "compute
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ave/chunk"_fix_ave_chunk.html and "compute
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ke/atom"_compute_ke_atom.html commands. The fix tallies the
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cumulative energy transfer that it performs. See the "fix
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thermal/conductivity"_fix_thermal_conductivity.html command for
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@ -2036,7 +2036,7 @@ velocity to prevent the fluid from heating up.
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In both cases, the velocity profile setup in the fluid by this
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procedure can be monitored by the "fix
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ave/spatial"_fix_ave_spatial.html command, which determines
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ave/chunk"_fix_ave_chunk.html command, which determines
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grad(Vstream) in the equation above. E.g. the derivative in the
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y-direction of the Vx component of fluid motion or grad(Vstream) =
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dVx/dy. The Pxy off-diagonal component of the pressure or stress
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@ -2050,7 +2050,7 @@ using the "fix viscosity"_fix_viscosity.html command which implements
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the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is
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swapped between atoms in two different layers of the simulation box in
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a different dimension. This induces a velocity gradient which can be
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monitored with the "fix ave/spatial"_fix_ave_spatial.html command.
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monitored with the "fix ave/chunk"_fix_ave_chunk.html command.
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The fix tallies the cummulative momentum transfer that it performs.
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See the "fix viscosity"_fix_viscosity.html command for details.
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@ -260,7 +260,7 @@ calculate "virtual diffraction patterns"_compute_xrd.html
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coupled rigid body integration via the "POEMS"_fix_poems.html library
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"QM/MM coupling"_fix_qmmm.html
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"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html
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Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_swap.html
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Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html "atom swapping"_fix_atom_swap.html and "bond swapping"_fix_bond_swap.html
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"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids
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"Peridynamics mesoscale modeling"_pair_peri.html
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"Lattice Boltzmann fluid"_fix_lb_fluid.html
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@ -795,7 +795,7 @@ Supporting info:
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"doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf,
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"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf,
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"doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf, "atom_style
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peri"_atom_style.html, "compute damage"_compute_damage.html,
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peri"_atom_style.html, "compute damage/atom"_compute_damage_atom.html,
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"pair_style peri/pmb"_pair_peri.html, examples/peri
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:line
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@ -846,9 +846,8 @@ PYTHON package :link(PYTHON),h5
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Contents: A "python"_python.html command which allow you to execute
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Python code from a LAMMPS input script. The code can be in a separate
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file or embedded in the input script itself. See "Section python
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11.2"_Section_python.html#py_2" for an overview of using Python from
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LAMMPS and "Section python"_Section_python.html" for other ways to use
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LAMMPS and Python together.
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11.2"_Section_python.html" for an overview of using Python from
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LAMMPS and for other ways to use LAMMPS and Python together.
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Building with the PYTHON package assumes you have a Python shared
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library available on your system, which needs to be a Python 2
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@ -1003,7 +1002,7 @@ make machine :pre
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Make.py -p ^rigid -a machine :pre
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Supporting info: "compute erotate/rigid"_compute_erotate_rigid.html,
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"fix shake"_fix_shake.html, "fix rattle"_fix_rattle.html, "fix
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"fix shake"_fix_shake.html, "fix rattle"_fix_shake.html, "fix
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rigid/*"_fix_rigid.html, examples/ASPHERE, examples/rigid
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:line
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@ -1055,8 +1054,8 @@ make machine :pre
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Make.py -p ^snap -a machine :pre
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Supporting info: "pair snap"_pair_snap.html, "compute
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sna/atom"_compute_sna_atom.html, "compute snad/atom"_compute_sna.html,
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"compute snav/atom"_compute_sna.html, examples/snap
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sna/atom"_compute_sna_atom.html, "compute snad/atom"_compute_sna_atom.html,
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"compute snav/atom"_compute_sna_atom.html, examples/snap
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:line
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@ -1164,8 +1163,8 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
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"USER-SMD"_#USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, -
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"USER-SMTBQ"_#USER-SMTBQ, Second Moment Tight Binding - QEq potential, Salles & Maras & Politano & Tetot (4), "pair_style smtbq"_pair_smtbq.html, USER/smtbq, -, -
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"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
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"USER-TALLY"_#USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute <...>/tally"_compute_tally.html, USER/tally, -, -
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"USER-VTK"_#USER-VTK, VTK-style dumps, Berger and Queteschiner (6), "compute custom/vtk"_compute_custom_vtk.html, -, -, lib/vtk
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"USER-TALLY"_#USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute XXX/tally"_compute_tally.html, USER/tally, -, -
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"USER-VTK"_#USER-VTK, VTK-style dumps, Berger and Queteschiner (6), "compute custom/vtk"_dump_custom_vtk.html, -, -, lib/vtk
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:tb(ea=c)
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:link(atc,http://lammps.sandia.gov/pictures.html#atc)
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@ -1260,7 +1259,7 @@ calculation. See src/USER-AWPMD/README for more details.
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To build LAMMPS with this package ...
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Supporting info: src/USER-AWPMD/README, "fix
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awpmd/cut"_pair_awpmd_cut.html, examples/USER/awpmd
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awpmd/cut"_pair_awpmd.html, examples/USER/awpmd
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Author: Ilya Valuev at the JIHT in Russia (valuev at
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physik.hu-berlin.de). Contact him directly if you have questions.
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@ -1315,7 +1314,7 @@ kinematic diffraction theory. See src/USER-DIFFRACTION/README for
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more details.
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Supporting info: "compute saed"_compute_saed.html, "compute
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xrd"_compute_xrd.html, "fix saed.vtk"_fix_saed_vtk.html,
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xrd"_compute_xrd.html, "fix saed/vtk"_fix_saed_vtk.html,
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examples/USER/diffraction
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Author: Shawn P. Coleman (shawn.p.coleman8.ctr at mail.mil) while at
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@ -1337,10 +1336,11 @@ splitting algorithm. See src/USER-DPD/README for more details.
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Supporting info: /src/USER-DPD/README, "compute dpd"_compute_dpd.html
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"compute dpd/atom"_compute_dpd_atom.html
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"fix eos/cv"_fix_eos_table.html "fix eos/table"_fix_eos_table.html
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"fix shardlow"_fix_shardlow.html
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"pair_dpd/conservative"_pair_dpd_conservative.html
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"pair_dpd/fdt"_pair_dpd_fdt.html
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"pair_dpd/fdt/energy"_pair_dpd_fdt.html, examples/USER/dpd
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"fix eos/table/rx"_fix_eos_table_rx.html "fix shardlow"_fix_shardlow.html
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"fix rx"_fix_rx.html "pair table/rx"_pair_table_rx.html
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"pair dpd/fdt"_pair_dpd_fdt.html "pair dpd/fdt/energy"_pair_dpd_fdt.html
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"pair exp6/rx"_pair_exp6_rx.html "pair multi/lucy"_pair_multi_lucy.html
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"pair multi/lucy/rx"_pair_multi_lucy_rx.html, examples/USER/dpd
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Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil),
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Timothy Mattox (Engility Corp) (Timothy.Mattox at engilitycorp.com)
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@ -1440,7 +1440,7 @@ Phi-enabled styles.
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Supporting info: examples/accelerate, src/USER-INTEL/TEST
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"Section_accelerate"_Section_accelerate.html#acc_9
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"Section_accelerate"_Section_accelerate.html#acc_3
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Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact
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him directly if you have questions.
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@ -1592,7 +1592,7 @@ application itself.
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See this doc page to get started:
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"dump molfile"_dump_molfile.html#acc_5
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"dump molfile"_dump_molfile.html
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The person who created this package is Axel Kohlmeyer at Temple U
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(akohlmey at gmail.com). Contact him directly if you have questions.
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@ -1609,7 +1609,7 @@ styles, and fix styles.
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See this section of the manual to get started:
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"Section_accelerate"_Section_accelerate.html#acc_5
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"Section_accelerate"_Section_accelerate.html#acc_3
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The person who created this package is Axel Kohlmeyer at Temple U
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(akohlmey at gmail.com). Contact him directly if you have questions.
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@ -1353,7 +1353,7 @@ Note that the keywords do not use a leading minus sign. I.e. the
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keyword is "t", not "-t". Also note that each of the keywords has a
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default setting. Example of when to use these options and what
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settings to use on different platforms is given in "Section
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5.8"_Section_accelerate.html#acc_8.
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5.8"_Section_accelerate.html#acc_3.
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d or device
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g or gpus
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@ -246,7 +246,7 @@ used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
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necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
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provides alternative methods via environment variables for binding
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threads to hardware cores. More info on binding threads to cores is
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given in "this section"_Section_accelerate.html#acc_8.
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given in "this section"_Section_accelerate.html#acc_3.
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KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
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Intel Phi processor.
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@ -57,7 +57,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"compute dilatation"_compute_dilatation.html, "compute
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plasticity"_compute_plasticity.html
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"compute dilatation/atom"_compute_dilatation_atom.html,
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"compute plasticity/atom"_compute_plasticity_atom.html
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[Default:] none
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@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"compute damage"_compute_damage.html, "compute
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plasticity"_compute_plasticity.html
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"compute damage/atom"_compute_damage_atom.html,
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"compute plasticity/atom"_compute_plasticity_atom.html
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[Default:] none
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@ -56,6 +56,6 @@ LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"compute ke/rigid"_compute_erotate_ke_rigid.html
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"compute ke/rigid"_compute_ke_rigid.html
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[Default:] none
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@ -54,8 +54,8 @@ LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"compute damage"_compute_damage.html, "compute
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dilatation"_compute_dilatation.html
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"compute damage/atom"_compute_damage_atom.html,
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"compute dilatation/atom"_compute_dilatation_atom.html
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[Default:] none
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@ -93,7 +93,7 @@ means all indices from m to n (inclusive).
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Using a wildcard is the same as if the individual columns of the array
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had been listed one by one. E.g. these 2 compute reduce commands are
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equivalent, since the "compute stress/atom"_compute_stress/atom.html
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equivalent, since the "compute stress/atom"_compute_stress_atom.html
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command creates a per-atom array with 6 columns:
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compute myPress all stress/atom NULL
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@ -26,12 +26,12 @@ nuclei and electrons in the "electron force field"_pair_eff.html
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model, after subtracting out a streaming velocity induced by the
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simulation box changing size and/or shape, for example in a
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non-equilibrium MD (NEMD) simulation. The size/shape change is
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induced by use of the "fix deform/eff"_fix_deform_eff.html command. A
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induced by use of the "fix deform"_fix_deform.html command. A
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compute of this style is created by the "fix
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nvt/sllod/eff"_fix_nvt_sllod_eff.html command to compute the thermal
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temperature of atoms for thermostatting purposes. A compute of this
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style can also be used by any command that computes a temperature,
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e.g. "thermo_modify"_thermo_modify.html, "fix npt/eff"_fix_nh.html,
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e.g. "thermo_modify"_thermo_modify.html, "fix npt/eff"_fix_nh_eff.html,
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etc.
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The calculation performed by this compute is exactly like that
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@ -66,8 +66,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"compute temp/ramp"_compute_temp_ramp.html, "fix
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deform/eff"_fix_deform_eff.html, "fix
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nvt/sllod/eff"_fix_nvt_sllod_eff.html
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"compute temp/ramp"_compute_temp_ramp.html, "fix deform"_fix_deform.html,
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"fix nvt/sllod/eff"_fix_nvt_sllod_eff.html
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[Default:] none
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@ -26,7 +26,7 @@ Define a computation that calculates the temperature of a group of
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nuclei and electrons in the "electron force field"_pair_eff.html
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model. A compute of this style can be used by commands that compute a
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temperature, e.g. "thermo_modify"_thermo_modify.html, "fix
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npt/eff"_fix_npt_eff.html, etc.
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npt/eff"_fix_nh_eff.html, etc.
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The temperature is calculated by the formula KE = dim/2 N k T, where
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KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for
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@ -195,7 +195,7 @@ more instructions on how to use the accelerated styles effectively.
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[Restrictions:]
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This dihedral style can only be used if LAMMPS was built with the
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USER-MISC package. See the "Making LAMMPS"_Section_start.html#2_3
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USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
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section for more info on packages.
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[Related commands:]
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|
|
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@ -441,7 +441,7 @@ from m to n (inclusive).
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Using a wildcard is the same as if the individual columns of the array
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had been listed one by one. E.g. these 2 dump commands are
|
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equivalent, since the "compute stress/atom"_compute_stress/atom.html
|
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equivalent, since the "compute stress/atom"_compute_stress_atom.html
|
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command creates a per-atom array with 6 columns:
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compute myPress all stress/atom NULL
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@ -34,7 +34,7 @@ args = list of arguments for a particular style :l
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proc = ID of processor that owns atom
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procp1 = ID+1 of processor that owns atom
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type = atom type
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element = name of atom element, as defined by "dump_modify"_dump_modify_vtk.html command
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element = name of atom element, as defined by "dump_modify"_dump_modify.html command
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mass = atom mass
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x,y,z = unscaled atom coordinates
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xs,ys,zs = scaled atom coordinates
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@ -71,7 +71,7 @@ for the XML format; see the "VTK
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homepage"_http://www.vtk.org/VTK/img/file-formats.pdf for a detailed
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description of these formats. Since this naming convention conflicts
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with the way binary output is usually specified (see below),
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"dump_modify binary"_dump_modify_vtk.html allows to set the binary
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"dump_modify binary"_dump_modify.html allows to set the binary
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flag for this dump style explicitly.
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[Description:]
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@ -81,10 +81,10 @@ timesteps in a format readable by the "VTK visualization
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toolkit"_http://www.vtk.org or other visualization tools that use it,
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e.g. "ParaView"_http://www.paraview.org. The timesteps on which dump
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output is written can also be controlled by a variable; see the
|
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"dump_modify every"_dump_modify_vtk.html command for details.
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"dump_modify every"_dump_modify.html command for details.
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Only information for atoms in the specified group is dumped. The
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"dump_modify thresh and region"_dump_modify_vtk.html commands can also
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"dump_modify thresh and region"_dump_modify.html commands can also
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alter what atoms are included; see details below.
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As described below, special characters ("*", "%") in the filename
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@ -95,7 +95,7 @@ on timesteps when neighbor lists are rebuilt, the coordinates of an
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atom written to a dump file may be slightly outside the simulation
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box.
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IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify_vtk.html
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IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify.html
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option is invoked, the lines of atom information written to dump files
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will be in an indeterminate order for each snapshot. This is even
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true when running on a single processor, if the "atom_modify
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@ -106,7 +106,7 @@ data for a single snapshot is collected from multiple processors, each
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of which owns a subset of the atoms.
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For the {custom/vtk} style, sorting is off by default. See the
|
||||
"dump_modify"_dump_modify_vtk.html doc page for details.
|
||||
"dump_modify"_dump_modify.html doc page for details.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -148,21 +148,21 @@ timestep 0) and on the last timestep of a minimization if the
|
|||
minimization converges. Note that this means a dump will not be
|
||||
performed on the initial timestep after the dump command is invoked,
|
||||
if the current timestep is not a multiple of N. This behavior can be
|
||||
changed via the "dump_modify first"_dump_modify_vtk.html command, which
|
||||
changed via the "dump_modify first"_dump_modify.html command, which
|
||||
can also be useful if the dump command is invoked after a minimization
|
||||
ended on an arbitrary timestep. N can be changed between runs by
|
||||
using the "dump_modify every"_dump_modify_vtk.html command.
|
||||
The "dump_modify every"_dump_modify_vtk.html command
|
||||
using the "dump_modify every"_dump_modify.html command.
|
||||
The "dump_modify every"_dump_modify.html command
|
||||
also allows a variable to be used to determine the sequence of
|
||||
timesteps on which dump files are written. In this mode a dump on the
|
||||
first timestep of a run will also not be written unless the
|
||||
"dump_modify first"_dump_modify_vtk.html command is used.
|
||||
"dump_modify first"_dump_modify.html command is used.
|
||||
|
||||
Dump filenames can contain two wildcard characters. If a "*"
|
||||
character appears in the filename, then one file per snapshot is
|
||||
written and the "*" character is replaced with the timestep value.
|
||||
For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
|
||||
tmp.dump20000.vtk, etc. Note that the "dump_modify pad"_dump_modify_vtk.html
|
||||
tmp.dump20000.vtk, etc. Note that the "dump_modify pad"_dump_modify.html
|
||||
command can be used to insure all timestep numbers are the same length
|
||||
(e.g. 00010), which can make it easier to read a series of dump files
|
||||
in order with some post-processing tools.
|
||||
|
|
@ -176,7 +176,7 @@ mode of output on parallel machines that support parallel I/O for output.
|
|||
|
||||
By default, P = the number of processors meaning one file per
|
||||
processor, but P can be set to a smaller value via the {nfile} or
|
||||
{fileper} keywords of the "dump_modify"_dump_modify_vtk.html command.
|
||||
{fileper} keywords of the "dump_modify"_dump_modify.html command.
|
||||
These options can be the most efficient way of writing out dump files
|
||||
when running on large numbers of processors.
|
||||
|
||||
|
|
@ -202,7 +202,7 @@ The {id}, {mol}, {proc}, {procp1}, {type}, {element}, {mass}, {vx},
|
|||
{id} is the atom ID. {mol} is the molecule ID, included in the data
|
||||
file for molecular systems. {type} is the atom type. {element} is
|
||||
typically the chemical name of an element, which you must assign to
|
||||
each type via the "dump_modify element"_dump_modify_vtk.html command.
|
||||
each type via the "dump_modify element"_dump_modify.html command.
|
||||
More generally, it can be any string you wish to associate with an
|
||||
atom type. {mass} is the atom mass. {vx}, {vy}, {vz}, {fx}, {fy},
|
||||
{fz}, and {q} are components of atom velocity and force and atomic
|
||||
|
|
|
|||
|
|
@ -141,7 +141,7 @@ means all indices from m to n (inclusive).
|
|||
Using a wildcard is the same as if the individual columns of the array
|
||||
had been listed one by one. E.g. these 2 fix ave/chunk commands are
|
||||
equivalent, since the "compute
|
||||
property/atom"_compute_property/atom.html command creates, in this
|
||||
property/atom"_compute_property_atom.html command creates, in this
|
||||
case, a per-atom array with 3 columns:
|
||||
|
||||
compute myAng all property/atom angmomx angmomy angmomz
|
||||
|
|
@ -150,7 +150,7 @@ fix 2 all ave/chunk 100 1 100 cc1 c_myAng\[1\] c_myAng\[2\] c_myAng\[3\] file tm
|
|||
|
||||
NOTE: This fix works by creating an array of size {Nchunk} by Nvalues
|
||||
on each processor. {Nchunk} is the number of chunks which is defined
|
||||
by the "compute chunk/atom"_doc/compute_chunk_atom.html command.
|
||||
by the "compute chunk/atom"_compute_chunk_atom.html command.
|
||||
Nvalues is the number of input values specified. Each processor loops
|
||||
over its atoms, tallying its values to the appropriate chunk. Then
|
||||
the entire array is summed across all processors. This means that
|
||||
|
|
|
|||
|
|
@ -122,7 +122,7 @@ become one moleclue due to the created bond, all atoms in the new
|
|||
moleclue retain their original molecule IDs.
|
||||
|
||||
If the {atype} keyword is used and if an angle potential is defined
|
||||
via the "angle_style"_angle.html command, then any new 3-body
|
||||
via the "angle_style"_angle_style.html command, then any new 3-body
|
||||
interactions inferred by the creation of a bond will create new angles
|
||||
of type {angletype}, with parameters assigned by the corresponding
|
||||
"angle_coeff"_angle_coeff.html command. Likewise, the {dtype} and
|
||||
|
|
|
|||
|
|
@ -487,7 +487,7 @@ NOTE: For non-equilibrium MD (NEMD) simulations using "remap v" it is
|
|||
usually desirable that the fluid (or flowing material, e.g. granular
|
||||
particles) stream with a velocity profile consistent with the
|
||||
deforming box. As mentioned above, using a thermostat such as "fix
|
||||
nvt/sllod"_fix_nvt_sllod.html or "fix lavgevin"_doc/fix_langevin.html
|
||||
nvt/sllod"_fix_nvt_sllod.html or "fix lavgevin"_fix_langevin.html
|
||||
(with a bias provided by "compute
|
||||
temp/deform"_compute_temp_deform.html), will typically accomplish
|
||||
that. If you do not use a thermostat, then there is no driving force
|
||||
|
|
|
|||
|
|
@ -147,7 +147,7 @@ the list of relative probabilities. The N values must sum to 1.0.
|
|||
|
||||
If you wish to insert molecules via the {mol} keyword, that will be
|
||||
treated as rigid bodies, use the {rigid} keyword, specifying as its
|
||||
value the ID of a separate "fix rigid/small"_fix_rigid_small.html
|
||||
value the ID of a separate "fix rigid/small"_fix_rigid.html
|
||||
command which also appears in your input script.
|
||||
|
||||
If you wish to insert molecules via the {mol} keyword, that will have
|
||||
|
|
|
|||
|
|
@ -111,7 +111,7 @@ the keyword {hex} is specified.
|
|||
[Compatibility with SHAKE and RATTLE (rigid molecules)]:
|
||||
|
||||
This fix is compatible with "fix shake"_fix_shake.html and "fix
|
||||
rattle"_fix_rattle.html. If either of these constraining algorithms is
|
||||
rattle"_fix_shake.html. If either of these constraining algorithms is
|
||||
specified in the input script and the keyword {constrain} is set, the
|
||||
bond distances will be corrected a second time at the end of the
|
||||
integration step. It is recommended to specify the keyword {com} in
|
||||
|
|
@ -124,7 +124,7 @@ rescaling takes place if the centre of mass lies outside the region.
|
|||
NOTE: You can only use the keyword {com} along with {constrain}.
|
||||
|
||||
To achieve the highest accuracy it is recommended to use "fix
|
||||
rattle"_fix_rattle.html with the keywords {constrain} and {com} as
|
||||
rattle"_fix_shake.html with the keywords {constrain} and {com} as
|
||||
shown in the second example. Only if RATTLE is employed, the velocity
|
||||
constraints will be satisfied.
|
||||
|
||||
|
|
|
|||
|
|
@ -71,7 +71,7 @@ initial text must match the argument specified in the fix command.
|
|||
The next line lists the number of table entries. The parameter "N" is
|
||||
required and its value is the number of table entries that follow.
|
||||
Note that this may be different than the {N} specified in the "fix
|
||||
eos/table"_fix_style.html command. Let Ntable = {N} in the fix
|
||||
eos/table"_fix_eos_table.html command. Let Ntable = {N} in the fix
|
||||
command, and Nfile = "N" in the tabulated file. What LAMMPS does is a
|
||||
preliminary interpolation by creating splines using the Nfile
|
||||
tabulated values as nodal points. It uses these to interpolate as
|
||||
|
|
@ -112,6 +112,6 @@ are not within the table cutoffs.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"fix shardlow"_fix_shardlow.html, "pair dpd/fdt"_dpd_fdt.html
|
||||
"fix shardlow"_fix_shardlow.html, "pair dpd/fdt"_pair_dpd_fdt.html
|
||||
|
||||
[Default:] none
|
||||
|
|
|
|||
|
|
@ -135,7 +135,7 @@ are not within the table cutoffs.
|
|||
[Related commands:]
|
||||
|
||||
"fix rx"_fix_rx.html,
|
||||
"pair dpd/fdt"_dpd_fdt.html
|
||||
"pair dpd/fdt"_pair_dpd_fdt.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -50,7 +50,7 @@ No information about this fix is written to "binary restart
|
|||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various "output
|
||||
commands"_Section_howto.html#4_15. No parameter of this fix can be
|
||||
commands"_Section_howto.html#howto_15. No parameter of this fix can be
|
||||
used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
|
|
|
|||
|
|
@ -35,7 +35,7 @@ No information about this fix is written to "binary restart
|
|||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various "output
|
||||
commands"_Section_howto.html#4_15. No parameter of this fix can be
|
||||
commands"_Section_howto.html#howto_15. No parameter of this fix can be
|
||||
used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
|
|
|
|||
|
|
@ -75,7 +75,7 @@ doc page), are performed with computes that include the eFF contribution
|
|||
to the temperature or kinetic energy from the electron radial velocity.
|
||||
|
||||
NOTE: there are two different pressures that can be reported for eFF
|
||||
when defining the pair_style (see "pair eff/cut"_pair_eff_cut.html to
|
||||
when defining the pair_style (see "pair eff/cut"_pair_eff.html to
|
||||
understand these settings), one (default) that considers electrons do
|
||||
not contribute radial virial components (i.e. electrons treated as
|
||||
incompressible 'rigid' spheres) and one that does. The radial
|
||||
|
|
|
|||
|
|
@ -148,7 +148,7 @@ fix. You can use it to change the temperature compute from thermo_temp
|
|||
to the one that reflects the true temperature of atoms in the group.
|
||||
|
||||
No global scalar or vector or per-atom quantities are stored by this
|
||||
fix for access by various "output commands"_Section_howto.html#4_15.
|
||||
fix for access by various "output commands"_Section_howto.html#howto_15.
|
||||
|
||||
Instead, this fix outputs its initialization information (including
|
||||
mapping information) and the calculated dynamical matrices to the file
|
||||
|
|
|
|||
|
|
@ -114,7 +114,7 @@ the list of relative probabilities. The N values must sum to 1.0.
|
|||
|
||||
If you wish to insert molecules via the {mol} keyword, that will be
|
||||
treated as rigid bodies, use the {rigid} keyword, specifying as its
|
||||
value the ID of a separate "fix rigid/small"_fix_rigid_small.html
|
||||
value the ID of a separate "fix rigid/small"_fix_rigid.html
|
||||
command which also appears in your input script.
|
||||
|
||||
If you wish to insert molecules via the {mol} keyword, that will have
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ reax/c"_pair_reax_c.html in the exact same format as the original
|
|||
stand-alone ReaxFF code of Adri van Duin. The bond information is
|
||||
written to {filename} on timesteps that are multiples of {Nevery},
|
||||
including timestep 0. For time-averaged chemical species analysis,
|
||||
please see the "fix species"_fix_species.html command.
|
||||
please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
|
||||
|
||||
The format of the output file should be self-explantory.
|
||||
|
||||
|
|
|
|||
|
|
@ -198,6 +198,6 @@ enthalpy DPD simulation.
|
|||
|
||||
"fix eos/table/rx"_fix_eos_table_rx.html,
|
||||
"fix shardlow"_fix_shardlow.html,
|
||||
"pair dpd/fdt/energy"_dpd_fdt_energy.html
|
||||
"pair dpd/fdt/energy"_pair_dpd_fdt.html
|
||||
|
||||
[Default:] none
|
||||
|
|
|
|||
|
|
@ -26,7 +26,7 @@ integrate the DPD equations of motion. The SSA splits the integration
|
|||
into a stochastic and deterministic integration step. The fix
|
||||
{shardlow} performs the stochastic integration step and must be used
|
||||
in conjunction with a deterministic integrator (e.g. "fix
|
||||
nve"_fix_nve.html or "fix nph"_fix_nph.html). The stochastic
|
||||
nve"_fix_nve.html or "fix nph"_fix_nh.html). The stochastic
|
||||
integration of the dissipative and random forces is performed prior to
|
||||
the deterministic integration of the conservative force. Further
|
||||
details regarding the method are provided in "(Lisal)"_#Lisal and
|
||||
|
|
|
|||
|
|
@ -138,14 +138,14 @@ LAMMPS"_Section_start.html#start_3 section for more info.
|
|||
|
||||
:line
|
||||
|
||||
:link(Israilev)
|
||||
:link(Izrailev)
|
||||
[(Izrailev)] Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
|
||||
Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
|
||||
Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
|
||||
Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
|
||||
|
||||
[(Park)]
|
||||
Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
|
||||
:link(Park)
|
||||
[(Park)] Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
|
||||
|
||||
[(Jarzynski)]
|
||||
Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
|
||||
:link(Jarzynski)
|
||||
[(Jarzynski)] Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
|
||||
|
|
|
|||
|
|
@ -92,7 +92,7 @@ No information about this fix is written to "binary restart
|
|||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various "output
|
||||
commands"_Section_howto.html#howoto_15. No parameter of this fix can
|
||||
commands"_Section_howto.html#howto_15. No parameter of this fix can
|
||||
be used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
|
|
|
|||
|
|
@ -74,7 +74,7 @@ interacts with charges in an infinite array of periodic images of the
|
|||
simulation domain.
|
||||
|
||||
Note that using a long-range solver requires use of a matching "pair
|
||||
style"_pair.html to perform consistent short-range pairwise
|
||||
style"_pair_style.html to perform consistent short-range pairwise
|
||||
calculations. This means that the name of the pair style contains a
|
||||
matching keyword to the name of the KSpace style, as in this table:
|
||||
|
||||
|
|
|
|||
|
|
@ -184,7 +184,7 @@ NOTE: Whether a section is required depends on how the molecule
|
|||
template is used by other LAMMPS commands. For example, to add a
|
||||
molecule via the "fix deposit"_fix_deposit.html command, the Coords
|
||||
and Types sections are required. To add a rigid body via the "fix
|
||||
pour"_fix_pout.html command, the Bonds (Angles, etc) sections are not
|
||||
pour"_fix_pour.html command, the Bonds (Angles, etc) sections are not
|
||||
required, since the molecule will be treated as a rigid body. Some
|
||||
sections are optional. For example, the "fix pour"_fix_pour.html
|
||||
command can be used to add "molecules" which are clusters of
|
||||
|
|
|
|||
|
|
@ -73,7 +73,7 @@ section"_Section_start.html#start_8 for details.
|
|||
[Related commands:]
|
||||
|
||||
"neigh_modify"_neigh_modify.html, "units"_units.html,
|
||||
"comm_modify"_cmom_modify.html
|
||||
"comm_modify"_comm_modify.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
|
|
|||
|
|
@ -123,7 +123,7 @@ This pair style can only be used via the {pair} keyword of the
|
|||
|
||||
These styles are part of the COLLOID package. They are only enabled
|
||||
if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
Only spherical monodisperse particles are allowed for pair_style
|
||||
brownian.
|
||||
|
|
|
|||
|
|
@ -138,19 +138,18 @@ dipole interactions. The long-range portion is calculated by using
|
|||
computed at all.
|
||||
|
||||
Atoms with dipole moments should be integrated using the "fix
|
||||
nve/sphere update dipole"_fix_nve_sphere.html command to rotate the
|
||||
nve/sphere update dipole"_fix_nve_sphere.html or the "fix
|
||||
nvt/sphere update dipole"_fix_nvt_sphere.html command to rotate the
|
||||
dipole moments. The {omega} option on the "fix
|
||||
langevin"_fix_langevin.html command can be used to thermostat the
|
||||
rotational motion. The "compute temp/sphere"_compute_temp_sphere.html
|
||||
command can be used to monitor the temperature, since it includes
|
||||
rotational degrees of freedom. The "atom_style
|
||||
dipole"_atom_style.html command should be used since it defines the
|
||||
point dipoles and their rotational state. The magnitude of the dipole
|
||||
moment for each type of particle can be defined by the
|
||||
"dipole"_dipole.html command or in the "Dipoles" section of the data
|
||||
file read in by the "read_data"_read_data.html command. Their initial
|
||||
orientation can be defined by the "set dipole"_set.html command or in
|
||||
the "Atoms" section of the data file.
|
||||
hybrid dipole sphere"_atom_style.html command should be used since
|
||||
it defines the point dipoles and their rotational state.
|
||||
The magnitude and orientation of the dipole moment for each particle
|
||||
can be defined by the "set"_set.html command or in the "Atoms" section
|
||||
of the data file read in by the "read_data"_read_data.html command.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
||||
|
|
@ -242,7 +241,8 @@ currently supported.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
"pair_coeff"_pair_coeff.html, "set"_set.html, "read_data"_read_data.html,
|
||||
"fix nve/sphere"_fix_nve_sphere.html, "fix nvt/sphere"_fix_nvt_sphere.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -115,7 +115,7 @@ enabled if LAMMPS was built with that package. See the "Making
|
|||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the
|
||||
"communicate vel yes"_communicate.html option so that velocites are
|
||||
"comm_modify vel yes"_comm_modify.html option so that velocites are
|
||||
stored by ghost atoms.
|
||||
|
||||
Pair style {dpd/fdt/energy} requires "atom_style dpd"_atom_style.html
|
||||
|
|
|
|||
|
|
@ -191,7 +191,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
|
|||
These pair style require that atoms store torque and a quaternion to
|
||||
represent their orientation, as defined by the
|
||||
"atom_style"_atom_style.html. It also require they store a per-type
|
||||
"shape"_shape.html. The particles cannot store a per-particle
|
||||
"shape"_set.html. The particles cannot store a per-particle
|
||||
diameter.
|
||||
|
||||
This pair style requires that atoms be ellipsoids as defined by the
|
||||
|
|
|
|||
|
|
@ -131,7 +131,7 @@ This pair style can only be used via the {pair} keyword of the
|
|||
|
||||
This style is part of the ASPHERE package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
Defining particles to be line segments so they participate in
|
||||
line/line or line/particle interactions requires the use the
|
||||
|
|
|
|||
|
|
@ -60,7 +60,7 @@ it also allows for mixing pair coefficients instead of listing them all.
|
|||
The {lj/cut/thole/long} pair style is also a bit faster because it avoids an
|
||||
overlay and can benefit from OMP acceleration. Moreover, it uses a more
|
||||
precise approximation of the direct Coulomb interaction at short range similar
|
||||
to "coul/long/cs"_pair_coul_long_cs.html, which stabilizes the temperature of
|
||||
to "coul/long/cs"_pair_cs.html, which stabilizes the temperature of
|
||||
Drude particles.
|
||||
|
||||
The {thole} pair styles compute the Coulomb interaction damped at
|
||||
|
|
|
|||
|
|
@ -102,7 +102,7 @@ This pair style can only be used via the {pair} keyword of the
|
|||
|
||||
This style is part of the ASPHERE package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#2_3 section for more info.
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
Defining particles to be triangles so they participate in tri/tri or
|
||||
tri/particle interactions requires the use the "atom_style
|
||||
|
|
|
|||
|
|
@ -460,7 +460,7 @@ your Python function must be able to to load the Python module in
|
|||
python/lammps.py that wraps the LAMMPS library interface. These are
|
||||
the same steps required to use Python by itself to wrap LAMMPS.
|
||||
Details on these steps are explained in "Section
|
||||
python"_Section.python.html. Note that it is important that the
|
||||
python"_Section_python.html. Note that it is important that the
|
||||
stand-alone LAMMPS executable and the LAMMPS shared library be
|
||||
consistent (built from the same source code files) in order for this
|
||||
to work. If the two have been built at different times using
|
||||
|
|
|
|||
|
|
@ -53,7 +53,7 @@ Compute the energy and forces of snaphots using a different potential.
|
|||
Calculate one or more diagnostic quantities on the snapshots that
|
||||
weren't computed in the initial run. These can also be computed with
|
||||
settings not used in the initial run, e.g. computing an RDF via the
|
||||
"compute rdf"_compute.rdf.html command with a longer cutoff than was
|
||||
"compute rdf"_compute_rdf.html command with a longer cutoff than was
|
||||
used initially. :l
|
||||
|
||||
Calculate the portion of per-atom forces resulting from a subset of
|
||||
|
|
|
|||
|
|
@ -1108,7 +1108,7 @@ with a leading $ sign (e.g. $x or $\{abc\}) versus with a leading "v_"
|
|||
command, including a variable command. The input script parser
|
||||
evaluates the reference variable immediately and substitutes its value
|
||||
into the command. As explained in "Section commands
|
||||
3.2"_Section_commands.html#3_2 for "Parsing rules", you can also use
|
||||
3.2"_Section_commands.html#cmd_2 for "Parsing rules", you can also use
|
||||
un-named "immediate" variables for this purpose. For example, a
|
||||
string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script
|
||||
command evaluates the string between the parenthesis as an equal-style
|
||||
|
|
|
|||
Loading…
Reference in New Issue