Loading doc/src/Section_howto.txt +5 −5 Original line number Diff line number Diff line Loading @@ -1010,7 +1010,7 @@ system. Fix nvt/sllod uses "compute temp/deform"_compute_temp_deform.html to compute a thermal temperature by subtracting out the streaming velocity of the shearing atoms. The velocity profile or other properties of the fluid can be monitored via the "fix ave/spatial"_fix_ave_spatial.html command. the "fix ave/chunk"_fix_ave_chunk.html command. As discussed in the previous section on non-orthogonal simulation boxes, the amount of tilt or skew that can be applied is limited by Loading Loading @@ -1970,7 +1970,7 @@ on each of two regions to add/subtract specified amounts of energy to both regions. In both cases, the resulting temperatures of the two regions can be monitored with the "compute temp/region" command and the temperature profile of the intermediate region can be monitored with the "fix ave/spatial"_fix_ave_spatial.html and "compute with the "fix ave/chunk"_fix_ave_chunk.html and "compute ke/atom"_compute_ke_atom.html commands. The third method is to perform a reverse non-equilibrium MD simulation Loading @@ -1979,7 +1979,7 @@ command which implements the rNEMD algorithm of Muller-Plathe. Kinetic energy is swapped between atoms in two different layers of the simulation box. This induces a temperature gradient between the two layers which can be monitored with the "fix ave/spatial"_fix_ave_spatial.html and "compute ave/chunk"_fix_ave_chunk.html and "compute ke/atom"_compute_ke_atom.html commands. The fix tallies the cumulative energy transfer that it performs. See the "fix thermal/conductivity"_fix_thermal_conductivity.html command for Loading Loading @@ -2036,7 +2036,7 @@ velocity to prevent the fluid from heating up. In both cases, the velocity profile setup in the fluid by this procedure can be monitored by the "fix ave/spatial"_fix_ave_spatial.html command, which determines ave/chunk"_fix_ave_chunk.html command, which determines grad(Vstream) in the equation above. E.g. the derivative in the y-direction of the Vx component of fluid motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of the pressure or stress Loading @@ -2050,7 +2050,7 @@ using the "fix viscosity"_fix_viscosity.html command which implements the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is swapped between atoms in two different layers of the simulation box in a different dimension. This induces a velocity gradient which can be monitored with the "fix ave/spatial"_fix_ave_spatial.html command. monitored with the "fix ave/chunk"_fix_ave_chunk.html command. The fix tallies the cummulative momentum transfer that it performs. See the "fix viscosity"_fix_viscosity.html command for details. Loading doc/src/Section_intro.txt +1 −1 Original line number Diff line number Diff line Loading @@ -260,7 +260,7 @@ calculate "virtual diffraction patterns"_compute_xrd.html coupled rigid body integration via the "POEMS"_fix_poems.html library "QM/MM coupling"_fix_qmmm.html "path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_swap.html 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 "Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids "Peridynamics mesoscale modeling"_pair_peri.html "Lattice Boltzmann fluid"_fix_lb_fluid.html Loading doc/src/Section_packages.txt +18 −18 Original line number Diff line number Diff line Loading @@ -795,7 +795,7 @@ Supporting info: "doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf, "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf, "doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf, "atom_style peri"_atom_style.html, "compute damage"_compute_damage.html, peri"_atom_style.html, "compute damage/atom"_compute_damage_atom.html, "pair_style peri/pmb"_pair_peri.html, examples/peri :line Loading Loading @@ -846,9 +846,8 @@ PYTHON package :link(PYTHON),h5 Contents: A "python"_python.html command which allow you to execute Python code from a LAMMPS input script. The code can be in a separate file or embedded in the input script itself. See "Section python 11.2"_Section_python.html#py_2" for an overview of using Python from LAMMPS and "Section python"_Section_python.html" for other ways to use LAMMPS and Python together. 11.2"_Section_python.html" for an overview of using Python from LAMMPS and for other ways to use LAMMPS and Python together. Building with the PYTHON package assumes you have a Python shared library available on your system, which needs to be a Python 2 Loading Loading @@ -1003,7 +1002,7 @@ make machine :pre Make.py -p ^rigid -a machine :pre Supporting info: "compute erotate/rigid"_compute_erotate_rigid.html, "fix shake"_fix_shake.html, "fix rattle"_fix_rattle.html, "fix "fix shake"_fix_shake.html, "fix rattle"_fix_shake.html, "fix rigid/*"_fix_rigid.html, examples/ASPHERE, examples/rigid :line Loading Loading @@ -1055,8 +1054,8 @@ make machine :pre Make.py -p ^snap -a machine :pre Supporting info: "pair snap"_pair_snap.html, "compute sna/atom"_compute_sna_atom.html, "compute snad/atom"_compute_sna.html, "compute snav/atom"_compute_sna.html, examples/snap sna/atom"_compute_sna_atom.html, "compute snad/atom"_compute_sna_atom.html, "compute snav/atom"_compute_sna_atom.html, examples/snap :line Loading Loading @@ -1164,8 +1163,8 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library "USER-SMD"_#USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, - "USER-SMTBQ"_#USER-SMTBQ, Second Moment Tight Binding - QEq potential, Salles & Maras & Politano & Tetot (4), "pair_style smtbq"_pair_smtbq.html, USER/smtbq, -, - "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, - "USER-TALLY"_#USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute <...>/tally"_compute_tally.html, USER/tally, -, - "USER-VTK"_#USER-VTK, VTK-style dumps, Berger and Queteschiner (6), "compute custom/vtk"_compute_custom_vtk.html, -, -, lib/vtk "USER-TALLY"_#USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute XXX/tally"_compute_tally.html, USER/tally, -, - "USER-VTK"_#USER-VTK, VTK-style dumps, Berger and Queteschiner (6), "compute custom/vtk"_dump_custom_vtk.html, -, -, lib/vtk :tb(ea=c) :link(atc,http://lammps.sandia.gov/pictures.html#atc) Loading Loading @@ -1260,7 +1259,7 @@ calculation. See src/USER-AWPMD/README for more details. To build LAMMPS with this package ... Supporting info: src/USER-AWPMD/README, "fix awpmd/cut"_pair_awpmd_cut.html, examples/USER/awpmd awpmd/cut"_pair_awpmd.html, examples/USER/awpmd Author: Ilya Valuev at the JIHT in Russia (valuev at physik.hu-berlin.de). Contact him directly if you have questions. Loading Loading @@ -1315,7 +1314,7 @@ kinematic diffraction theory. See src/USER-DIFFRACTION/README for more details. Supporting info: "compute saed"_compute_saed.html, "compute xrd"_compute_xrd.html, "fix saed.vtk"_fix_saed_vtk.html, xrd"_compute_xrd.html, "fix saed/vtk"_fix_saed_vtk.html, examples/USER/diffraction Author: Shawn P. Coleman (shawn.p.coleman8.ctr at mail.mil) while at Loading @@ -1337,10 +1336,11 @@ splitting algorithm. See src/USER-DPD/README for more details. Supporting info: /src/USER-DPD/README, "compute dpd"_compute_dpd.html "compute dpd/atom"_compute_dpd_atom.html "fix eos/cv"_fix_eos_table.html "fix eos/table"_fix_eos_table.html "fix shardlow"_fix_shardlow.html "pair_dpd/conservative"_pair_dpd_conservative.html "pair_dpd/fdt"_pair_dpd_fdt.html "pair_dpd/fdt/energy"_pair_dpd_fdt.html, examples/USER/dpd "fix eos/table/rx"_fix_eos_table_rx.html "fix shardlow"_fix_shardlow.html "fix rx"_fix_rx.html "pair table/rx"_pair_table_rx.html "pair dpd/fdt"_pair_dpd_fdt.html "pair dpd/fdt/energy"_pair_dpd_fdt.html "pair exp6/rx"_pair_exp6_rx.html "pair multi/lucy"_pair_multi_lucy.html "pair multi/lucy/rx"_pair_multi_lucy_rx.html, examples/USER/dpd Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil), Timothy Mattox (Engility Corp) (Timothy.Mattox at engilitycorp.com) Loading Loading @@ -1440,7 +1440,7 @@ Phi-enabled styles. Supporting info: examples/accelerate, src/USER-INTEL/TEST "Section_accelerate"_Section_accelerate.html#acc_9 "Section_accelerate"_Section_accelerate.html#acc_3 Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact him directly if you have questions. Loading Loading @@ -1592,7 +1592,7 @@ application itself. See this doc page to get started: "dump molfile"_dump_molfile.html#acc_5 "dump molfile"_dump_molfile.html The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions. Loading @@ -1609,7 +1609,7 @@ styles, and fix styles. See this section of the manual to get started: "Section_accelerate"_Section_accelerate.html#acc_5 "Section_accelerate"_Section_accelerate.html#acc_3 The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions. Loading doc/src/Section_start.txt +1 −1 Original line number Diff line number Diff line Loading @@ -1353,7 +1353,7 @@ Note that the keywords do not use a leading minus sign. I.e. the keyword is "t", not "-t". Also note that each of the keywords has a default setting. Example of when to use these options and what settings to use on different platforms is given in "Section 5.8"_Section_accelerate.html#acc_8. 5.8"_Section_accelerate.html#acc_3. d or device g or gpus Loading doc/src/accelerate_kokkos.txt +1 −1 Original line number Diff line number Diff line Loading @@ -246,7 +246,7 @@ used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP provides alternative methods via environment variables for binding threads to hardware cores. More info on binding threads to cores is given in "this section"_Section_accelerate.html#acc_8. given in "this section"_Section_accelerate.html#acc_3. KOKKOS_ARCH=KNC enables compiler switches needed when compling for an Intel Phi processor. Loading Loading
doc/src/Section_howto.txt +5 −5 Original line number Diff line number Diff line Loading @@ -1010,7 +1010,7 @@ system. Fix nvt/sllod uses "compute temp/deform"_compute_temp_deform.html to compute a thermal temperature by subtracting out the streaming velocity of the shearing atoms. The velocity profile or other properties of the fluid can be monitored via the "fix ave/spatial"_fix_ave_spatial.html command. the "fix ave/chunk"_fix_ave_chunk.html command. As discussed in the previous section on non-orthogonal simulation boxes, the amount of tilt or skew that can be applied is limited by Loading Loading @@ -1970,7 +1970,7 @@ on each of two regions to add/subtract specified amounts of energy to both regions. In both cases, the resulting temperatures of the two regions can be monitored with the "compute temp/region" command and the temperature profile of the intermediate region can be monitored with the "fix ave/spatial"_fix_ave_spatial.html and "compute with the "fix ave/chunk"_fix_ave_chunk.html and "compute ke/atom"_compute_ke_atom.html commands. The third method is to perform a reverse non-equilibrium MD simulation Loading @@ -1979,7 +1979,7 @@ command which implements the rNEMD algorithm of Muller-Plathe. Kinetic energy is swapped between atoms in two different layers of the simulation box. This induces a temperature gradient between the two layers which can be monitored with the "fix ave/spatial"_fix_ave_spatial.html and "compute ave/chunk"_fix_ave_chunk.html and "compute ke/atom"_compute_ke_atom.html commands. The fix tallies the cumulative energy transfer that it performs. See the "fix thermal/conductivity"_fix_thermal_conductivity.html command for Loading Loading @@ -2036,7 +2036,7 @@ velocity to prevent the fluid from heating up. In both cases, the velocity profile setup in the fluid by this procedure can be monitored by the "fix ave/spatial"_fix_ave_spatial.html command, which determines ave/chunk"_fix_ave_chunk.html command, which determines grad(Vstream) in the equation above. E.g. the derivative in the y-direction of the Vx component of fluid motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of the pressure or stress Loading @@ -2050,7 +2050,7 @@ using the "fix viscosity"_fix_viscosity.html command which implements the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is swapped between atoms in two different layers of the simulation box in a different dimension. This induces a velocity gradient which can be monitored with the "fix ave/spatial"_fix_ave_spatial.html command. monitored with the "fix ave/chunk"_fix_ave_chunk.html command. The fix tallies the cummulative momentum transfer that it performs. See the "fix viscosity"_fix_viscosity.html command for details. Loading
doc/src/Section_intro.txt +1 −1 Original line number Diff line number Diff line Loading @@ -260,7 +260,7 @@ calculate "virtual diffraction patterns"_compute_xrd.html coupled rigid body integration via the "POEMS"_fix_poems.html library "QM/MM coupling"_fix_qmmm.html "path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_swap.html 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 "Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids "Peridynamics mesoscale modeling"_pair_peri.html "Lattice Boltzmann fluid"_fix_lb_fluid.html Loading
doc/src/Section_packages.txt +18 −18 Original line number Diff line number Diff line Loading @@ -795,7 +795,7 @@ Supporting info: "doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf, "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf, "doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf, "atom_style peri"_atom_style.html, "compute damage"_compute_damage.html, peri"_atom_style.html, "compute damage/atom"_compute_damage_atom.html, "pair_style peri/pmb"_pair_peri.html, examples/peri :line Loading Loading @@ -846,9 +846,8 @@ PYTHON package :link(PYTHON),h5 Contents: A "python"_python.html command which allow you to execute Python code from a LAMMPS input script. The code can be in a separate file or embedded in the input script itself. See "Section python 11.2"_Section_python.html#py_2" for an overview of using Python from LAMMPS and "Section python"_Section_python.html" for other ways to use LAMMPS and Python together. 11.2"_Section_python.html" for an overview of using Python from LAMMPS and for other ways to use LAMMPS and Python together. Building with the PYTHON package assumes you have a Python shared library available on your system, which needs to be a Python 2 Loading Loading @@ -1003,7 +1002,7 @@ make machine :pre Make.py -p ^rigid -a machine :pre Supporting info: "compute erotate/rigid"_compute_erotate_rigid.html, "fix shake"_fix_shake.html, "fix rattle"_fix_rattle.html, "fix "fix shake"_fix_shake.html, "fix rattle"_fix_shake.html, "fix rigid/*"_fix_rigid.html, examples/ASPHERE, examples/rigid :line Loading Loading @@ -1055,8 +1054,8 @@ make machine :pre Make.py -p ^snap -a machine :pre Supporting info: "pair snap"_pair_snap.html, "compute sna/atom"_compute_sna_atom.html, "compute snad/atom"_compute_sna.html, "compute snav/atom"_compute_sna.html, examples/snap sna/atom"_compute_sna_atom.html, "compute snad/atom"_compute_sna_atom.html, "compute snav/atom"_compute_sna_atom.html, examples/snap :line Loading Loading @@ -1164,8 +1163,8 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library "USER-SMD"_#USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, - "USER-SMTBQ"_#USER-SMTBQ, Second Moment Tight Binding - QEq potential, Salles & Maras & Politano & Tetot (4), "pair_style smtbq"_pair_smtbq.html, USER/smtbq, -, - "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, - "USER-TALLY"_#USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute <...>/tally"_compute_tally.html, USER/tally, -, - "USER-VTK"_#USER-VTK, VTK-style dumps, Berger and Queteschiner (6), "compute custom/vtk"_compute_custom_vtk.html, -, -, lib/vtk "USER-TALLY"_#USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute XXX/tally"_compute_tally.html, USER/tally, -, - "USER-VTK"_#USER-VTK, VTK-style dumps, Berger and Queteschiner (6), "compute custom/vtk"_dump_custom_vtk.html, -, -, lib/vtk :tb(ea=c) :link(atc,http://lammps.sandia.gov/pictures.html#atc) Loading Loading @@ -1260,7 +1259,7 @@ calculation. See src/USER-AWPMD/README for more details. To build LAMMPS with this package ... Supporting info: src/USER-AWPMD/README, "fix awpmd/cut"_pair_awpmd_cut.html, examples/USER/awpmd awpmd/cut"_pair_awpmd.html, examples/USER/awpmd Author: Ilya Valuev at the JIHT in Russia (valuev at physik.hu-berlin.de). Contact him directly if you have questions. Loading Loading @@ -1315,7 +1314,7 @@ kinematic diffraction theory. See src/USER-DIFFRACTION/README for more details. Supporting info: "compute saed"_compute_saed.html, "compute xrd"_compute_xrd.html, "fix saed.vtk"_fix_saed_vtk.html, xrd"_compute_xrd.html, "fix saed/vtk"_fix_saed_vtk.html, examples/USER/diffraction Author: Shawn P. Coleman (shawn.p.coleman8.ctr at mail.mil) while at Loading @@ -1337,10 +1336,11 @@ splitting algorithm. See src/USER-DPD/README for more details. Supporting info: /src/USER-DPD/README, "compute dpd"_compute_dpd.html "compute dpd/atom"_compute_dpd_atom.html "fix eos/cv"_fix_eos_table.html "fix eos/table"_fix_eos_table.html "fix shardlow"_fix_shardlow.html "pair_dpd/conservative"_pair_dpd_conservative.html "pair_dpd/fdt"_pair_dpd_fdt.html "pair_dpd/fdt/energy"_pair_dpd_fdt.html, examples/USER/dpd "fix eos/table/rx"_fix_eos_table_rx.html "fix shardlow"_fix_shardlow.html "fix rx"_fix_rx.html "pair table/rx"_pair_table_rx.html "pair dpd/fdt"_pair_dpd_fdt.html "pair dpd/fdt/energy"_pair_dpd_fdt.html "pair exp6/rx"_pair_exp6_rx.html "pair multi/lucy"_pair_multi_lucy.html "pair multi/lucy/rx"_pair_multi_lucy_rx.html, examples/USER/dpd Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil), Timothy Mattox (Engility Corp) (Timothy.Mattox at engilitycorp.com) Loading Loading @@ -1440,7 +1440,7 @@ Phi-enabled styles. Supporting info: examples/accelerate, src/USER-INTEL/TEST "Section_accelerate"_Section_accelerate.html#acc_9 "Section_accelerate"_Section_accelerate.html#acc_3 Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact him directly if you have questions. Loading Loading @@ -1592,7 +1592,7 @@ application itself. See this doc page to get started: "dump molfile"_dump_molfile.html#acc_5 "dump molfile"_dump_molfile.html The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions. Loading @@ -1609,7 +1609,7 @@ styles, and fix styles. See this section of the manual to get started: "Section_accelerate"_Section_accelerate.html#acc_5 "Section_accelerate"_Section_accelerate.html#acc_3 The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions. Loading
doc/src/Section_start.txt +1 −1 Original line number Diff line number Diff line Loading @@ -1353,7 +1353,7 @@ Note that the keywords do not use a leading minus sign. I.e. the keyword is "t", not "-t". Also note that each of the keywords has a default setting. Example of when to use these options and what settings to use on different platforms is given in "Section 5.8"_Section_accelerate.html#acc_8. 5.8"_Section_accelerate.html#acc_3. d or device g or gpus Loading
doc/src/accelerate_kokkos.txt +1 −1 Original line number Diff line number Diff line Loading @@ -246,7 +246,7 @@ used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP provides alternative methods via environment variables for binding threads to hardware cores. More info on binding threads to cores is given in "this section"_Section_accelerate.html#acc_8. given in "this section"_Section_accelerate.html#acc_3. KOKKOS_ARCH=KNC enables compiler switches needed when compling for an Intel Phi processor. Loading
