From ff75cf51bb5fd043b3414c54da8cd687eabd2477 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Sep 2016 00:01:26 -0400 Subject: [PATCH] correct link targets --- doc/src/Section_howto.txt | 10 ++++---- doc/src/Section_intro.txt | 2 +- doc/src/Section_packages.txt | 36 ++++++++++++++--------------- doc/src/Section_start.txt | 2 +- doc/src/accelerate_kokkos.txt | 2 +- doc/src/compute_damage_atom.txt | 4 ++-- doc/src/compute_dilatation_atom.txt | 4 ++-- doc/src/compute_erotate_rigid.txt | 2 +- doc/src/compute_plasticity_atom.txt | 4 ++-- doc/src/compute_reduce.txt | 2 +- doc/src/compute_temp_deform_eff.txt | 9 ++++---- doc/src/compute_temp_eff.txt | 2 +- doc/src/dihedral_table.txt | 2 +- doc/src/dump.txt | 2 +- doc/src/dump_custom_vtk.txt | 26 ++++++++++----------- doc/src/fix_ave_chunk.txt | 4 ++-- doc/src/fix_bond_create.txt | 2 +- doc/src/fix_deform.txt | 2 +- doc/src/fix_deposit.txt | 2 +- doc/src/fix_ehex.txt | 4 ++-- doc/src/fix_eos_table.txt | 4 ++-- doc/src/fix_eos_table_rx.txt | 2 +- doc/src/fix_lb_momentum.txt | 2 +- doc/src/fix_lb_pc.txt | 2 +- doc/src/fix_nh_eff.txt | 2 +- doc/src/fix_phonon.txt | 2 +- doc/src/fix_pour.txt | 2 +- doc/src/fix_reax_bonds.txt | 2 +- doc/src/fix_rx.txt | 2 +- doc/src/fix_shardlow.txt | 2 +- doc/src/fix_smd.txt | 10 ++++---- doc/src/fix_wall_piston.txt | 2 +- doc/src/kspace_style.txt | 2 +- doc/src/molecule.txt | 2 +- doc/src/neighbor.txt | 2 +- doc/src/pair_brownian.txt | 2 +- doc/src/pair_dipole.txt | 18 +++++++-------- doc/src/pair_dpd_fdt.txt | 2 +- doc/src/pair_gayberne.txt | 2 +- doc/src/pair_line_lj.txt | 2 +- doc/src/pair_thole.txt | 2 +- doc/src/pair_tri_lj.txt | 2 +- doc/src/python.txt | 2 +- doc/src/rerun.txt | 2 +- doc/src/variable.txt | 2 +- 45 files changed, 99 insertions(+), 100 deletions(-) diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index a680b24529..d54d0b2c3f 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -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 @@ -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 @@ -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 @@ -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 @@ -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. diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt index aa31153386..99751a13ff 100644 --- a/doc/src/Section_intro.txt +++ b/doc/src/Section_intro.txt @@ -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 diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index 6be763cb70..5282eaa4bb 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -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 @@ -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 @@ -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 @@ -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 @@ -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) @@ -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. @@ -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 @@ -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) @@ -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. @@ -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. @@ -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. diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index c1b0e796b6..0231fb3357 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -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 diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt index b69bf8a3d9..a3d1c9efbd 100644 --- a/doc/src/accelerate_kokkos.txt +++ b/doc/src/accelerate_kokkos.txt @@ -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. diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt index 22be26b573..ab76cf82de 100644 --- a/doc/src/compute_damage_atom.txt +++ b/doc/src/compute_damage_atom.txt @@ -57,7 +57,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] -"compute dilatation"_compute_dilatation.html, "compute -plasticity"_compute_plasticity.html +"compute dilatation/atom"_compute_dilatation_atom.html, +"compute plasticity/atom"_compute_plasticity_atom.html [Default:] none diff --git a/doc/src/compute_dilatation_atom.txt b/doc/src/compute_dilatation_atom.txt index 7d550e48f1..0bd27184e3 100644 --- a/doc/src/compute_dilatation_atom.txt +++ b/doc/src/compute_dilatation_atom.txt @@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] -"compute damage"_compute_damage.html, "compute -plasticity"_compute_plasticity.html +"compute damage/atom"_compute_damage_atom.html, +"compute plasticity/atom"_compute_plasticity_atom.html [Default:] none diff --git a/doc/src/compute_erotate_rigid.txt b/doc/src/compute_erotate_rigid.txt index 3044449faf..58f511a624 100644 --- a/doc/src/compute_erotate_rigid.txt +++ b/doc/src/compute_erotate_rigid.txt @@ -56,6 +56,6 @@ LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] -"compute ke/rigid"_compute_erotate_ke_rigid.html +"compute ke/rigid"_compute_ke_rigid.html [Default:] none diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt index ebea299b26..5e6b86641f 100644 --- a/doc/src/compute_plasticity_atom.txt +++ b/doc/src/compute_plasticity_atom.txt @@ -54,8 +54,8 @@ LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] -"compute damage"_compute_damage.html, "compute -dilatation"_compute_dilatation.html +"compute damage/atom"_compute_damage_atom.html, +"compute dilatation/atom"_compute_dilatation_atom.html [Default:] none diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt index 09ab48b12f..b28f94d969 100644 --- a/doc/src/compute_reduce.txt +++ b/doc/src/compute_reduce.txt @@ -93,7 +93,7 @@ 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 compute reduce commands are -equivalent, since the "compute stress/atom"_compute_stress/atom.html +equivalent, since the "compute stress/atom"_compute_stress_atom.html command creates a per-atom array with 6 columns: compute myPress all stress/atom NULL diff --git a/doc/src/compute_temp_deform_eff.txt b/doc/src/compute_temp_deform_eff.txt index 199fa5fdc4..d09a0ace2f 100644 --- a/doc/src/compute_temp_deform_eff.txt +++ b/doc/src/compute_temp_deform_eff.txt @@ -26,12 +26,12 @@ nuclei and electrons in the "electron force field"_pair_eff.html model, after subtracting out a streaming velocity induced by the simulation box changing size and/or shape, for example in a non-equilibrium MD (NEMD) simulation. The size/shape change is -induced by use of the "fix deform/eff"_fix_deform_eff.html command. A +induced by use of the "fix deform"_fix_deform.html command. A compute of this style is created by the "fix nvt/sllod/eff"_fix_nvt_sllod_eff.html command to compute the thermal temperature of atoms for thermostatting purposes. A compute of this style can also be used by any command that computes a temperature, -e.g. "thermo_modify"_thermo_modify.html, "fix npt/eff"_fix_nh.html, +e.g. "thermo_modify"_thermo_modify.html, "fix npt/eff"_fix_nh_eff.html, etc. The calculation performed by this compute is exactly like that @@ -66,8 +66,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] -"compute temp/ramp"_compute_temp_ramp.html, "fix -deform/eff"_fix_deform_eff.html, "fix -nvt/sllod/eff"_fix_nvt_sllod_eff.html +"compute temp/ramp"_compute_temp_ramp.html, "fix deform"_fix_deform.html, +"fix nvt/sllod/eff"_fix_nvt_sllod_eff.html [Default:] none diff --git a/doc/src/compute_temp_eff.txt b/doc/src/compute_temp_eff.txt index a3629fef87..905369fbfd 100644 --- a/doc/src/compute_temp_eff.txt +++ b/doc/src/compute_temp_eff.txt @@ -26,7 +26,7 @@ Define a computation that calculates the temperature of a group of nuclei and electrons in the "electron force field"_pair_eff.html model. A compute of this style can be used by commands that compute a temperature, e.g. "thermo_modify"_thermo_modify.html, "fix -npt/eff"_fix_npt_eff.html, etc. +npt/eff"_fix_nh_eff.html, etc. The temperature is calculated by the formula KE = dim/2 N k T, where KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt index 2df3ad0b47..bad6ad2c0d 100644 --- a/doc/src/dihedral_table.txt +++ b/doc/src/dihedral_table.txt @@ -195,7 +195,7 @@ more instructions on how to use the accelerated styles effectively. [Restrictions:] This dihedral style can only be used if LAMMPS was built with the -USER-MISC package. See the "Making LAMMPS"_Section_start.html#2_3 +USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] diff --git a/doc/src/dump.txt b/doc/src/dump.txt index 5b3508ed69..ffeef1b0f6 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -441,7 +441,7 @@ 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 dump commands are -equivalent, since the "compute stress/atom"_compute_stress/atom.html +equivalent, since the "compute stress/atom"_compute_stress_atom.html command creates a per-atom array with 6 columns: compute myPress all stress/atom NULL diff --git a/doc/src/dump_custom_vtk.txt b/doc/src/dump_custom_vtk.txt index 7db9390200..c2408bab90 100644 --- a/doc/src/dump_custom_vtk.txt +++ b/doc/src/dump_custom_vtk.txt @@ -34,7 +34,7 @@ args = list of arguments for a particular style :l proc = ID of processor that owns atom procp1 = ID+1 of processor that owns atom type = atom type - element = name of atom element, as defined by "dump_modify"_dump_modify_vtk.html command + element = name of atom element, as defined by "dump_modify"_dump_modify.html command mass = atom mass x,y,z = unscaled atom coordinates xs,ys,zs = scaled atom coordinates @@ -71,7 +71,7 @@ for the XML format; see the "VTK homepage"_http://www.vtk.org/VTK/img/file-formats.pdf for a detailed description of these formats. Since this naming convention conflicts with the way binary output is usually specified (see below), -"dump_modify binary"_dump_modify_vtk.html allows to set the binary +"dump_modify binary"_dump_modify.html allows to set the binary flag for this dump style explicitly. [Description:] @@ -81,10 +81,10 @@ timesteps in a format readable by the "VTK visualization toolkit"_http://www.vtk.org or other visualization tools that use it, e.g. "ParaView"_http://www.paraview.org. The timesteps on which dump output is written can also be controlled by a variable; see the -"dump_modify every"_dump_modify_vtk.html command for details. +"dump_modify every"_dump_modify.html command for details. Only information for atoms in the specified group is dumped. The -"dump_modify thresh and region"_dump_modify_vtk.html commands can also +"dump_modify thresh and region"_dump_modify.html commands can also alter what atoms are included; see details below. As described below, special characters ("*", "%") in the filename @@ -95,7 +95,7 @@ on timesteps when neighbor lists are rebuilt, the coordinates of an atom written to a dump file may be slightly outside the simulation box. -IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify_vtk.html +IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify.html option is invoked, the lines of atom information written to dump files will be in an indeterminate order for each snapshot. This is even true when running on a single processor, if the "atom_modify @@ -106,7 +106,7 @@ data for a single snapshot is collected from multiple processors, each of which owns a subset of the atoms. 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 diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index 796cf5e331..d02fa17e10 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -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 diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt index dac50154d0..85cef5071a 100755 --- a/doc/src/fix_bond_create.txt +++ b/doc/src/fix_bond_create.txt @@ -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 diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index 2f86440664..6b3118b74f 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -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 diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt index ab8674c90e..ea9c5643dd 100644 --- a/doc/src/fix_deposit.txt +++ b/doc/src/fix_deposit.txt @@ -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 diff --git a/doc/src/fix_ehex.txt b/doc/src/fix_ehex.txt index f726bd984b..df3ab4c687 100644 --- a/doc/src/fix_ehex.txt +++ b/doc/src/fix_ehex.txt @@ -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. diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt index b6b7daacad..e606f58a86 100644 --- a/doc/src/fix_eos_table.txt +++ b/doc/src/fix_eos_table.txt @@ -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 diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt index 9c97151202..d87449c4c7 100644 --- a/doc/src/fix_eos_table_rx.txt +++ b/doc/src/fix_eos_table_rx.txt @@ -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 diff --git a/doc/src/fix_lb_momentum.txt b/doc/src/fix_lb_momentum.txt index 9e31bea784..be2f77543f 100755 --- a/doc/src/fix_lb_momentum.txt +++ b/doc/src/fix_lb_momentum.txt @@ -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. diff --git a/doc/src/fix_lb_pc.txt b/doc/src/fix_lb_pc.txt index fe8f03af80..81b2c4a284 100755 --- a/doc/src/fix_lb_pc.txt +++ b/doc/src/fix_lb_pc.txt @@ -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. diff --git a/doc/src/fix_nh_eff.txt b/doc/src/fix_nh_eff.txt index 817d5786e8..d90ce52caa 100644 --- a/doc/src/fix_nh_eff.txt +++ b/doc/src/fix_nh_eff.txt @@ -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 diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt index 2d3baacb58..46f8f57c33 100644 --- a/doc/src/fix_phonon.txt +++ b/doc/src/fix_phonon.txt @@ -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 diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt index cd1b1d6853..6d5ed3ac06 100644 --- a/doc/src/fix_pour.txt +++ b/doc/src/fix_pour.txt @@ -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 diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt index cc8966db6f..a0396ce210 100644 --- a/doc/src/fix_reax_bonds.txt +++ b/doc/src/fix_reax_bonds.txt @@ -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. diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt index 8180294a91..97ffd89c65 100644 --- a/doc/src/fix_rx.txt +++ b/doc/src/fix_rx.txt @@ -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 diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt index 485f0a4b6f..21de9a9e0b 100644 --- a/doc/src/fix_shardlow.txt +++ b/doc/src/fix_shardlow.txt @@ -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 diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt index 01ec79e71e..aa23cc3fc3 100644 --- a/doc/src/fix_smd.txt +++ b/doc/src/fix_smd.txt @@ -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) diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt index 347d1edc58..5595c0195f 100644 --- a/doc/src/fix_wall_piston.txt +++ b/doc/src/fix_wall_piston.txt @@ -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. diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index ac713ba297..f9f27f6e9c 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -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: diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt index 05971b5ddc..7b8c14fdad 100644 --- a/doc/src/molecule.txt +++ b/doc/src/molecule.txt @@ -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 diff --git a/doc/src/neighbor.txt b/doc/src/neighbor.txt index b73b893cb2..7b8f499ba8 100644 --- a/doc/src/neighbor.txt +++ b/doc/src/neighbor.txt @@ -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:] diff --git a/doc/src/pair_brownian.txt b/doc/src/pair_brownian.txt index 2bbff42b9b..33eed77629 100644 --- a/doc/src/pair_brownian.txt +++ b/doc/src/pair_brownian.txt @@ -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. diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt index f8f5dbf87f..be6608d57b 100755 --- a/doc/src/pair_dipole.txt +++ b/doc/src/pair_dipole.txt @@ -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 diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt index 07d5f3d5bb..ca1baeabe2 100644 --- a/doc/src/pair_dpd_fdt.txt +++ b/doc/src/pair_dpd_fdt.txt @@ -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 diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt index 109f578549..037e5c47e5 100755 --- a/doc/src/pair_gayberne.txt +++ b/doc/src/pair_gayberne.txt @@ -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 diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt index 3e91e97c2d..85bb3664fa 100644 --- a/doc/src/pair_line_lj.txt +++ b/doc/src/pair_line_lj.txt @@ -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 diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt index af1dffc1a6..ab3b832ad6 100644 --- a/doc/src/pair_thole.txt +++ b/doc/src/pair_thole.txt @@ -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 diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt index cfc64c52fd..e4eed927f5 100644 --- a/doc/src/pair_tri_lj.txt +++ b/doc/src/pair_tri_lj.txt @@ -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 diff --git a/doc/src/python.txt b/doc/src/python.txt index 2c1e6c0b30..2ec2fdcfca 100644 --- a/doc/src/python.txt +++ b/doc/src/python.txt @@ -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 diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt index bd331f2d7e..c623d4bebc 100644 --- a/doc/src/rerun.txt +++ b/doc/src/rerun.txt @@ -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 diff --git a/doc/src/variable.txt b/doc/src/variable.txt index b928160d57..9f40beacb4 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -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