From 7e6755866f77024edfc59be1234f58fb265f73d3 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 13 Dec 2011 20:43:36 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7356 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_accelerate.html | 2 +- doc/Section_accelerate.txt | 2 +- doc/Section_howto.html | 14 +++++++------- doc/Section_howto.txt | 14 +++++++------- doc/Section_intro.html | 8 ++++---- doc/Section_intro.txt | 8 ++++---- doc/Section_packages.html | 2 +- doc/Section_packages.txt | 2 +- doc/Section_python.html | 8 ++++---- doc/Section_python.txt | 8 ++++---- doc/Section_start.html | 12 ++++++------ doc/Section_start.txt | 12 ++++++------ doc/compute_ackland_atom.html | 4 ++-- doc/compute_ackland_atom.txt | 4 ++-- doc/compute_centro_atom.html | 4 ++-- doc/compute_centro_atom.txt | 4 ++-- doc/compute_cluster_atom.html | 4 ++-- doc/compute_cluster_atom.txt | 4 ++-- doc/compute_cna_atom.html | 4 ++-- doc/compute_cna_atom.txt | 4 ++-- doc/compute_com_molecule.html | 4 ++-- doc/compute_com_molecule.txt | 4 ++-- doc/compute_coord_atom.html | 4 ++-- doc/compute_coord_atom.txt | 4 ++-- doc/compute_damage_atom.html | 4 ++-- doc/compute_damage_atom.txt | 4 ++-- doc/compute_displace_atom.html | 5 +++-- doc/compute_displace_atom.txt | 5 +++-- doc/compute_erotate_asphere.html | 4 ++-- doc/compute_erotate_asphere.txt | 4 ++-- doc/compute_erotate_sphere.html | 4 ++-- doc/compute_erotate_sphere.txt | 4 ++-- doc/compute_event_displace.html | 4 ++-- doc/compute_event_displace.txt | 4 ++-- doc/compute_gyration.html | 4 ++-- doc/compute_gyration.txt | 4 ++-- doc/compute_ke.html | 4 ++-- doc/compute_ke.txt | 4 ++-- doc/compute_ke_atom.html | 4 ++-- doc/compute_ke_atom.txt | 4 ++-- doc/compute_ke_atom_eff.html | 4 ++-- doc/compute_ke_atom_eff.txt | 4 ++-- doc/compute_ke_eff.html | 4 ++-- doc/compute_ke_eff.txt | 4 ++-- doc/compute_meso_e_atom.html | 4 ++-- doc/compute_meso_e_atom.txt | 4 ++-- doc/compute_meso_rho_atom.html | 4 ++-- doc/compute_meso_rho_atom.txt | 4 ++-- doc/compute_meso_t_atom.html | 4 ++-- doc/compute_meso_t_atom.txt | 4 ++-- doc/compute_pe.html | 5 +++-- doc/compute_pe.txt | 5 +++-- doc/compute_pe_atom.html | 4 ++-- doc/compute_pe_atom.txt | 4 ++-- doc/compute_rdf.html | 4 ++-- doc/compute_rdf.txt | 4 ++-- doc/compute_reduce.html | 4 ++-- doc/compute_reduce.txt | 4 ++-- doc/compute_stress_atom.html | 5 +++-- doc/compute_stress_atom.txt | 5 +++-- doc/compute_ti.html | 5 +++-- doc/compute_ti.txt | 5 +++-- doc/create_box.html | 6 +++--- doc/create_box.txt | 6 +++--- doc/dump.html | 6 +++--- doc/dump.txt | 6 +++--- doc/fix_append_atoms.html | 11 ++++++----- doc/fix_append_atoms.txt | 9 +++++---- doc/fix_meso.html | 6 +++--- doc/fix_meso.txt | 4 ++-- doc/fix_meso_stationary.html | 6 +++--- doc/fix_meso_stationary.txt | 4 ++-- doc/fix_neb.html | 4 ++-- doc/fix_neb.txt | 4 ++-- doc/fix_viscosity.html | 13 +++++++------ doc/fix_viscosity.txt | 13 +++++++------ doc/fix_wall_piston.html | 6 +++--- doc/fix_wall_piston.txt | 4 ++-- doc/if.html | 6 +++--- doc/if.txt | 6 +++--- doc/log.html | 2 +- doc/log.txt | 2 +- doc/neb.html | 10 +++++----- doc/neb.txt | 10 +++++----- doc/partition.html | 2 +- doc/partition.txt | 2 +- doc/prd.html | 14 +++++++------- doc/prd.txt | 14 +++++++------- doc/read_data.html | 6 +++--- doc/read_data.txt | 6 +++--- doc/region.html | 6 +++--- doc/region.txt | 6 +++--- doc/run_style.html | 2 +- doc/run_style.txt | 2 +- doc/tad.html | 5 +++-- doc/tad.txt | 5 +++-- doc/temper.html | 10 +++++----- doc/temper.txt | 10 +++++----- 98 files changed, 274 insertions(+), 260 deletions(-) diff --git a/doc/Section_accelerate.html b/doc/Section_accelerate.html index 838c1713df..88f985bf5e 100644 --- a/doc/Section_accelerate.html +++ b/doc/Section_accelerate.html @@ -69,7 +69,7 @@ The speed-up due to GPU usage depends on a variety of factors, as discussed below.

To see what styles are currently available in each of the accelerated -packages, see this section of the +packages, see Section_commands 5 of the manual. A list of accelerated styles is included in the pair, fix, compute, and kspace sections.

diff --git a/doc/Section_accelerate.txt b/doc/Section_accelerate.txt index 081e6279dd..37a49d5f68 100644 --- a/doc/Section_accelerate.txt +++ b/doc/Section_accelerate.txt @@ -66,7 +66,7 @@ The speed-up due to GPU usage depends on a variety of factors, as discussed below. To see what styles are currently available in each of the accelerated -packages, see "this section"_Section_commands.html#cmd_5 of the +packages, see "Section_commands 5"_Section_commands.html#cmd_5 of the manual. A list of accelerated styles is included in the pair, fix, compute, and kspace sections. diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 540e17bab9..bad450038a 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -674,9 +674,9 @@ of the Python wrapper provided with LAMMPS that operates through the LAMMPS library interface.

The files src/library.cpp and library.h contain the C-style interface -to LAMMPS. See this section of the manual -for a description of the interface and how to extend it for your -needs. +to LAMMPS. See Section_howto 19 of the +manual for a description of the interface and how to extend it for +your needs.

Note that the lammps_open() function that creates an instance of LAMMPS takes an MPI communicator as an argument. This means that @@ -1658,10 +1658,10 @@ converge and requires careful post-processing (Shinoda)

6.19 Library interface to LAMMPS

-

As described in this section, LAMMPS can -be built as a library, so that it can be called by another code, used -in a coupled manner with other codes, or -driven through a Python interface. +

As described in Section_start 4, LAMMPS +can be built as a library, so that it can be called by another code, +used in a coupled manner with other +codes, or driven through a Python interface.

All of these methodologies use a C-style interface to LAMMPS that is provided in the files src/library.cpp and src/library.h. The diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index cc025cfd34..50c24d8b89 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -668,9 +668,9 @@ of the Python wrapper provided with LAMMPS that operates through the LAMMPS library interface. The files src/library.cpp and library.h contain the C-style interface -to LAMMPS. See "this section"_Section_howto.html#howto_19 of the manual -for a description of the interface and how to extend it for your -needs. +to LAMMPS. See "Section_howto 19"_Section_howto.html#howto_19 of the +manual for a description of the interface and how to extend it for +your needs. Note that the lammps_open() function that creates an instance of LAMMPS takes an MPI communicator as an argument. This means that @@ -1645,10 +1645,10 @@ converge and requires careful post-processing "(Shinoda)"_#Shinoda 6.19 Library interface to LAMMPS :link(howto_19),h4 -As described in "this section"_Section_start.html#start_4, LAMMPS can -be built as a library, so that it can be called by another code, used -in a "coupled manner"_Section_howto.html#howto_10 with other codes, or -driven through a "Python interface"_Section_python.html. +As described in "Section_start 4"_Section_start.html#start_4, LAMMPS +can be built as a library, so that it can be called by another code, +used in a "coupled manner"_Section_howto.html#howto_10 with other +codes, or driven through a "Python interface"_Section_python.html. All of these methodologies use a C-style interface to LAMMPS that is provided in the files src/library.cpp and src/library.h. The diff --git a/doc/Section_intro.html b/doc/Section_intro.html index 678f734953..9b278bfc8d 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -51,8 +51,8 @@ LAMMPS performance and scalability, or the Benchmarks section of the

LAMMPS is a freely-available open-source code, distributed under the terms of the GNU Public License, which means you can use or -modify the code however you wish. See this section for a brief -discussion of the open-source philosophy. +modify the code however you wish. See this section for a +brief discussion of the open-source philosophy.

@@ -421,8 +421,8 @@ Site, or have a suggestion for something to clarify or include, send an email to the developers. -
  • If you find a bug, this section describes -how to report it. +
  • If you find a bug, Section_errors 2 +describes how to report it.
  • If you publish a paper using LAMMPS results, send the citation (and any cool pictures or movies if you like) to add to the Publications, diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index 2a3d77530e..bebab7a731 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -47,8 +47,8 @@ LAMMPS performance and scalability, or the Benchmarks section of the LAMMPS is a freely-available open-source code, distributed under the terms of the "GNU Public License"_gnu, which means you can use or -modify the code however you wish. See "this section"_#intro_4 for a brief -discussion of the open-source philosophy. +modify the code however you wish. See "this section"_#intro_4 for a +brief discussion of the open-source philosophy. :link(gnu,http://www.gnu.org/copyleft/gpl.html) @@ -410,8 +410,8 @@ Site"_lws, or have a suggestion for something to clarify or include, send an email to the "developers"_http://lammps.sandia.gov/authors.html. :l -If you find a bug, "this section"_Section_errors.html#err_2 describes -how to report it. :l +If you find a bug, "Section_errors 2"_Section_errors.html#err_2 +describes how to report it. :l If you publish a paper using LAMMPS results, send the citation (and any cool pictures or movies if you like) to add to the Publications, diff --git a/doc/Section_packages.html b/doc/Section_packages.html index 600f034d3b..af512bd2e4 100644 --- a/doc/Section_packages.html +++ b/doc/Section_packages.html @@ -25,7 +25,7 @@ molecular systems or granular systems are in packages. You can see the list of all packages by typing "make package" from within the src directory of the LAMMPS distribution.

    -

    See this section of the manual for +

    See Section_start 3 of the manual for details on how to include/exclude specific packages as part of the LAMMPS build process, and for more details about the differences between standard packages and user packages in LAMMPS. diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt index 20b016cbcb..425373d7a4 100644 --- a/doc/Section_packages.txt +++ b/doc/Section_packages.txt @@ -22,7 +22,7 @@ molecular systems or granular systems are in packages. You can see the list of all packages by typing "make package" from within the src directory of the LAMMPS distribution. -See "this section"_Section_start.html#start_3 of the manual for +See "Section_start 3"_Section_start.html#start_3 of the manual for details on how to include/exclude specific packages as part of the LAMMPS build process, and for more details about the differences between standard packages and user packages in LAMMPS. diff --git a/doc/Section_python.html b/doc/Section_python.html index a9eb0d34ab..5f09521204 100644 --- a/doc/Section_python.html +++ b/doc/Section_python.html @@ -34,8 +34,8 @@ packages. It can be used to glue multiple pieces of software together, e.g. to run a coupled or multiscale model. See this section of the manual and the couple directory of the distribution for more ideas about coupling LAMMPS to -other codes. See this section about how -to build LAMMPS as a library, and this +other codes. See Section_start 4 about +how to build LAMMPS as a library, and this section for a description of the library interface provided in src/library.cpp and src/library.h and how to extend it for your needs. As described below, that interface is what @@ -502,7 +502,7 @@ subscripting. The one exception is that for a fix that calculates a global vector or array, a single double value from the vector or array is returned, indexed by I (vector) or I and J (array). I,J are zero-based indices. The I,J arguments can be left out if not needed. -See this section of the manual for a +See Section_howto 15 of the manual for a discussion of global, per-atom, and local data, and of scalar, vector, and array data types. See the doc pages for individual computes and fixes for a description of what @@ -582,7 +582,7 @@ following steps: src/library.h.

  • Verify the new function is syntactically correct by building LAMMPS as -a library - see this section of the +a library - see Section_start 4 of the manual.
  • Add a wrapper method in the Python LAMMPS module to python/lammps.py diff --git a/doc/Section_python.txt b/doc/Section_python.txt index 6a80a827b3..44b2a0f014 100644 --- a/doc/Section_python.txt +++ b/doc/Section_python.txt @@ -31,8 +31,8 @@ packages. It can be used to glue multiple pieces of software together, e.g. to run a coupled or multiscale model. See "this section"_Section_howto.html#howto_10 of the manual and the couple directory of the distribution for more ideas about coupling LAMMPS to -other codes. See "this section"_Section_start.html#start_4 about how -to build LAMMPS as a library, and "this +other codes. See "Section_start 4"_Section_start.html#start_4 about +how to build LAMMPS as a library, and "this section"_Section_howto.html#howto_19 for a description of the library interface provided in src/library.cpp and src/library.h and how to extend it for your needs. As described below, that interface is what @@ -497,7 +497,7 @@ subscripting. The one exception is that for a fix that calculates a global vector or array, a single double value from the vector or array is returned, indexed by I (vector) or I and J (array). I,J are zero-based indices. The I,J arguments can be left out if not needed. -See "this section"_Section_howto.html#howto_15 of the manual for a +See "Section_howto 15"_Section_howto.html#howto_15 of the manual for a discussion of global, per-atom, and local data, and of scalar, vector, and array data types. See the doc pages for individual "computes"_compute.html and "fixes"_fix.html for a description of what @@ -577,7 +577,7 @@ Add a new interface function to src/library.cpp and src/library.h. :ulb,l Verify the new function is syntactically correct by building LAMMPS as -a library - see "this section"_Section_start.html#start_4 of the +a library - see "Section_start 4"_Section_start.html#start_4 of the manual. :l Add a wrapper method in the Python LAMMPS module to python/lammps.py diff --git a/doc/Section_start.html b/doc/Section_start.html index a9048e5ee2..29682bcd0b 100644 --- a/doc/Section_start.html +++ b/doc/Section_start.html @@ -717,13 +717,13 @@ src/library.cpp and src/library.h.

    See the sample codes couple/simple/simple.cpp and simple.c as examples of C++ and C codes that invoke LAMMPS thru its library interface. There are other examples as well in the couple directory which are -discussed in this section of the manual. -See Section_python of the manual for a +discussed in Section_howto 10 of the +manual. See Section_python of the manual for a description of the Python wrapper provided with LAMMPS that operates through the LAMMPS library interface.

    The files src/library.cpp and library.h contain the C-style interface -to LAMMPS. See this section of the +to LAMMPS. See Section_howto 19 of the manual for a description of the interface and how to extend it for your needs.

    @@ -938,9 +938,9 @@ installed on a machine (e.g. your desktop), you can run on more (virtual) processors than you have physical processors.

    To run multiple independent simulatoins from one input script, using -multiple partitions, see this section of -the manual. World- and universe-style variables are -useful in this context. +multiple partitions, see Section_howto 4 +of the manual. World- and universe-style variables +are useful in this context. 

    -plog file
    diff --git a/doc/Section_start.txt b/doc/Section_start.txt index a614417f7e..17ad9b6967 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -711,13 +711,13 @@ src/library.cpp and src/library.h. See the sample codes couple/simple/simple.cpp and simple.c as examples of C++ and C codes that invoke LAMMPS thru its library interface. There are other examples as well in the couple directory which are -discussed in "this section"_Section_howto.html#howto_10 of the manual. -See "Section_python"_Section_python.html of the manual for a +discussed in "Section_howto 10"_Section_howto.html#howto_10 of the +manual. See "Section_python"_Section_python.html of the manual for a description of the Python wrapper provided with LAMMPS that operates through the LAMMPS library interface. The files src/library.cpp and library.h contain the C-style interface -to LAMMPS. See "this section"_Section_howto.html#howto_19 of the +to LAMMPS. See "Section_howto 19"_Section_howto.html#howto_19 of the manual for a description of the interface and how to extend it for your needs. @@ -929,9 +929,9 @@ installed on a machine (e.g. your desktop), you can run on more (virtual) processors than you have physical processors. To run multiple independent simulatoins from one input script, using -multiple partitions, see "this section"_Section_howto.html#howto_4 of -the manual. World- and universe-style "variables"_variable.html are -useful in this context. +multiple partitions, see "Section_howto 4"_Section_howto.html#howto_4 +of the manual. World- and universe-style "variables"_variable.html +are useful in this context. -plog file :pre diff --git a/doc/compute_ackland_atom.html b/doc/compute_ackland_atom.html index 16ad975e88..d3445f2f52 100644 --- a/doc/compute_ackland_atom.html +++ b/doc/compute_ackland_atom.html @@ -53,8 +53,8 @@ which computes this quantity.-

    This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    Restrictions:

    diff --git a/doc/compute_ackland_atom.txt b/doc/compute_ackland_atom.txt index 5a9dcebbad..62fa812822 100644 --- a/doc/compute_ackland_atom.txt +++ b/doc/compute_ackland_atom.txt @@ -50,8 +50,8 @@ which computes this quantity.- This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"this section"_Section_howto.html#howto_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. [Restrictions:] diff --git a/doc/compute_centro_atom.html b/doc/compute_centro_atom.html index 63c0c2b95f..6b3c037103 100644 --- a/doc/compute_centro_atom.html +++ b/doc/compute_centro_atom.html @@ -79,8 +79,8 @@ too frequently or to have multiple compute/dump commands, each with a

    This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    The per-atom vector values are unitless values >= 0.0. Their magnitude depends on the lattice style due to the number of diff --git a/doc/compute_centro_atom.txt b/doc/compute_centro_atom.txt index a5a83a0c32..5a9faf9090 100644 --- a/doc/compute_centro_atom.txt +++ b/doc/compute_centro_atom.txt @@ -75,8 +75,8 @@ too frequently or to have multiple compute/dump commands, each with a This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"this section"_Section_howto.html#howto_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. The per-atom vector values are unitless values >= 0.0. Their magnitude depends on the lattice style due to the number of diff --git a/doc/compute_cluster_atom.html b/doc/compute_cluster_atom.html index b2f7b49fdd..f972d2fae0 100644 --- a/doc/compute_cluster_atom.html +++ b/doc/compute_cluster_atom.html @@ -46,8 +46,8 @@ too frequently or to have multiple compute/dump commands, each of a

    This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    The per-atom vector values will be an ID > 0, as explained above.

    diff --git a/doc/compute_cluster_atom.txt b/doc/compute_cluster_atom.txt index 3193331f91..eb4ba32948 100644 --- a/doc/compute_cluster_atom.txt +++ b/doc/compute_cluster_atom.txt @@ -43,8 +43,8 @@ too frequently or to have multiple compute/dump commands, each of a This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"this section"_Section_howto.html#howto_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. The per-atom vector values will be an ID > 0, as explained above. diff --git a/doc/compute_cna_atom.html b/doc/compute_cna_atom.html index 7549fa7c6c..191b8911c8 100644 --- a/doc/compute_cna_atom.html +++ b/doc/compute_cna_atom.html @@ -77,8 +77,8 @@ too frequently or to have multiple compute/dump commands, each with a

    This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    The per-atom vector values will be a number from 0 to 5, as explained above. diff --git a/doc/compute_cna_atom.txt b/doc/compute_cna_atom.txt index 63afcf9a82..7aafcaf807 100644 --- a/doc/compute_cna_atom.txt +++ b/doc/compute_cna_atom.txt @@ -74,8 +74,8 @@ too frequently or to have multiple compute/dump commands, each with a This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"this section"_Section_howto.html#howto_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. The per-atom vector values will be a number from 0 to 5, as explained above. diff --git a/doc/compute_com_molecule.html b/doc/compute_com_molecule.html index 957b3feca8..c5337ec443 100644 --- a/doc/compute_com_molecule.html +++ b/doc/compute_com_molecule.html @@ -64,8 +64,8 @@ file containing coordinates of the atoms in the bodies. Nmolecules and the number of columns = 3 for the x,y,z center-of-mass coordinates of each molecule. These values can be accessed by any command that uses global array values from a compute as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    The array values are "intensive". The array values will be in distance units. diff --git a/doc/compute_com_molecule.txt b/doc/compute_com_molecule.txt index accfd389cf..29ef45413c 100644 --- a/doc/compute_com_molecule.txt +++ b/doc/compute_com_molecule.txt @@ -61,8 +61,8 @@ This compute calculates a global array where the number of rows = Nmolecules and the number of columns = 3 for the x,y,z center-of-mass coordinates of each molecule. These values can be accessed by any command that uses global array values from a compute as input. See -"this section"_Section_howto.html#howto_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. The array values are "intensive". The array values will be in distance "units"_units.html. diff --git a/doc/compute_coord_atom.html b/doc/compute_coord_atom.html index 57738b4f3d..bd4c55d2c5 100644 --- a/doc/compute_coord_atom.html +++ b/doc/compute_coord_atom.html @@ -46,8 +46,8 @@ too frequently or to have multiple compute/dump commands, each of a

    This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    The per-atom vector values will be a number >= 0.0, as explained above. diff --git a/doc/compute_coord_atom.txt b/doc/compute_coord_atom.txt index fc5f2c9000..5fdbd9106e 100644 --- a/doc/compute_coord_atom.txt +++ b/doc/compute_coord_atom.txt @@ -43,8 +43,8 @@ too frequently or to have multiple compute/dump commands, each of a This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"this section"_Section_howto.html#howto_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. The per-atom vector values will be a number >= 0.0, as explained above. diff --git a/doc/compute_damage_atom.html b/doc/compute_damage_atom.html index b5e0d03d89..0d0e378f58 100644 --- a/doc/compute_damage_atom.html +++ b/doc/compute_damage_atom.html @@ -37,8 +37,8 @@ compute group.

    This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    The per-atom vector values will be a number >= 0.0, as explained above. diff --git a/doc/compute_damage_atom.txt b/doc/compute_damage_atom.txt index 104cf22b54..3c640d61ef 100644 --- a/doc/compute_damage_atom.txt +++ b/doc/compute_damage_atom.txt @@ -34,8 +34,8 @@ compute group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"this section"_Section_howto.html#howto_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. The per-atom vector values will be a number >= 0.0, as explained above. diff --git a/doc/compute_displace_atom.html b/doc/compute_displace_atom.html index 79dae15622..2070d896a4 100644 --- a/doc/compute_displace_atom.html +++ b/doc/compute_displace_atom.html @@ -76,8 +76,9 @@ file.

    This compute calculates a per-atom array with 4 columns, which can be accessed by indices 1-4 by any command that uses per-atom values from -a compute as input. See this section -for an overview of LAMMPS output options. +a compute as input. See Section_howto +15 for an overview of LAMMPS output +options.

    The per-atom array values will be in distance units.

    diff --git a/doc/compute_displace_atom.txt b/doc/compute_displace_atom.txt index ecbdf22b38..5b7363db93 100644 --- a/doc/compute_displace_atom.txt +++ b/doc/compute_displace_atom.txt @@ -73,8 +73,9 @@ file. This compute calculates a per-atom array with 4 columns, which can be accessed by indices 1-4 by any command that uses per-atom values from -a compute as input. See "this section"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +a compute as input. See "Section_howto +15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. The per-atom array values will be in distance "units"_units.html. diff --git a/doc/compute_erotate_asphere.html b/doc/compute_erotate_asphere.html index 161aef27c2..8ea9a4e1dc 100644 --- a/doc/compute_erotate_asphere.html +++ b/doc/compute_erotate_asphere.html @@ -43,8 +43,8 @@ inertia will be the same as in 3d.

    This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See this section for an overview -of LAMMPS output options. +input. See Section_howto 15 for an +overview of LAMMPS output options.

    The scalar value calculated by this compute is "extensive". The scalar value will be in energy units. diff --git a/doc/compute_erotate_asphere.txt b/doc/compute_erotate_asphere.txt index 39aded0ed7..a6a14cfa02 100644 --- a/doc/compute_erotate_asphere.txt +++ b/doc/compute_erotate_asphere.txt @@ -40,8 +40,8 @@ inertia will be the same as in 3d. This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See "this section"_Section_howto.html#howto_15 for an overview -of LAMMPS output options. +input. See "Section_howto 15"_Section_howto.html#howto_15 for an +overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The scalar value will be in energy "units"_units.html. diff --git a/doc/compute_erotate_sphere.html b/doc/compute_erotate_sphere.html index d9e328364c..eb6662b13b 100644 --- a/doc/compute_erotate_sphere.html +++ b/doc/compute_erotate_sphere.html @@ -38,8 +38,8 @@ same as in 3d.

    This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See this section for an overview -of LAMMPS output options. +input. See Section_howto 15 for an +overview of LAMMPS output options.

    The scalar value calculated by this compute is "extensive". The scalar value will be in energy units. diff --git a/doc/compute_erotate_sphere.txt b/doc/compute_erotate_sphere.txt index 7e480a2812..eaf2eede16 100644 --- a/doc/compute_erotate_sphere.txt +++ b/doc/compute_erotate_sphere.txt @@ -35,8 +35,8 @@ same as in 3d. This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See "this section"_Section_howto.html#howto_15 for an overview -of LAMMPS output options. +input. See "Section_howto 15"_Section_howto.html#howto_15 for an +overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The scalar value will be in energy "units"_units.html. diff --git a/doc/compute_event_displace.html b/doc/compute_event_displace.html index ae63a96bb9..8efff145ad 100644 --- a/doc/compute_event_displace.html +++ b/doc/compute_event_displace.html @@ -46,8 +46,8 @@ local atom displacements and may generate "false postives."

    This compute calculates a global scalar (the flag). This value can be used by any command that uses a global scalar value from a compute as -input. See this section for an overview -of LAMMPS output options. +input. See Section_howto 15 for an +overview of LAMMPS output options.

    The scalar value calculated by this compute is "intensive". The scalar value will be a 0 or 1 as explained above. diff --git a/doc/compute_event_displace.txt b/doc/compute_event_displace.txt index 7b26d3120e..4d638c74f3 100644 --- a/doc/compute_event_displace.txt +++ b/doc/compute_event_displace.txt @@ -43,8 +43,8 @@ local atom displacements and may generate "false postives." This compute calculates a global scalar (the flag). This value can be used by any command that uses a global scalar value from a compute as -input. See "this section"_Section_howto.html#howto_15 for an overview -of LAMMPS output options. +input. See "Section_howto 15"_Section_howto.html#howto_15 for an +overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The scalar value will be a 0 or 1 as explained above. diff --git a/doc/compute_gyration.html b/doc/compute_gyration.html index 1d8b8389cd..79994c6dfc 100644 --- a/doc/compute_gyration.html +++ b/doc/compute_gyration.html @@ -49,8 +49,8 @@ image command.

    This compute calculates a global scalar (Rg). This value can be used by any command that uses a global scalar value from a compute as -input. See this section for an overview -of LAMMPS output options. +input. See Section_howto 15 for an +overview of LAMMPS output options.

    The scalar value calculated by this compute is "intensive". The scalar value will be in distance units. diff --git a/doc/compute_gyration.txt b/doc/compute_gyration.txt index 867669d0a7..2cc818c5f5 100644 --- a/doc/compute_gyration.txt +++ b/doc/compute_gyration.txt @@ -46,8 +46,8 @@ image"_set.html command. This compute calculates a global scalar (Rg). This value can be used by any command that uses a global scalar value from a compute as -input. See "this section"_Section_howto.html#howto_15 for an overview -of LAMMPS output options. +input. See "Section_howto 15"_Section_howto.html#howto_15 for an +overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The scalar value will be in distance "units"_units.html. diff --git a/doc/compute_ke.html b/doc/compute_ke.html index 12769e0f55..b71d9e3066 100644 --- a/doc/compute_ke.html +++ b/doc/compute_ke.html @@ -47,8 +47,8 @@ include different degrees of freedom (translational, rotational, etc).

    This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See this section for an overview -of LAMMPS output options. +input. See Section_howto 15 for an +overview of LAMMPS output options.

    The scalar value calculated by this compute is "extensive". The scalar value will be in energy units. diff --git a/doc/compute_ke.txt b/doc/compute_ke.txt index 003332c073..cd84381d35 100644 --- a/doc/compute_ke.txt +++ b/doc/compute_ke.txt @@ -44,8 +44,8 @@ include different degrees of freedom (translational, rotational, etc). This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See "this section"_Section_howto.html#howto_15 for an overview -of LAMMPS output options. +input. See "Section_howto 15"_Section_howto.html#howto_15 for an +overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The scalar value will be in energy "units"_units.html. diff --git a/doc/compute_ke_atom.html b/doc/compute_ke_atom.html index 434718e6a6..fdf97f197a 100644 --- a/doc/compute_ke_atom.html +++ b/doc/compute_ke_atom.html @@ -37,8 +37,8 @@ specified compute group.

    This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    The per-atom vector values will be in energy units.

    diff --git a/doc/compute_ke_atom.txt b/doc/compute_ke_atom.txt index fd42651300..66abf81a59 100644 --- a/doc/compute_ke_atom.txt +++ b/doc/compute_ke_atom.txt @@ -34,8 +34,8 @@ specified compute group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"this section"_Section_howto.html#howto_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/compute_ke_atom_eff.html b/doc/compute_ke_atom_eff.html index 19ffb3f77c..d305890bba 100644 --- a/doc/compute_ke_atom_eff.html +++ b/doc/compute_ke_atom_eff.html @@ -62,8 +62,8 @@ electrons) not in the specified compute group.

    This compute calculates a scalar quantity for each atom, which can be accessed by any command that uses per-atom computes as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    The per-atom vector values will be in energy units.

    diff --git a/doc/compute_ke_atom_eff.txt b/doc/compute_ke_atom_eff.txt index 00c32be622..736c386774 100644 --- a/doc/compute_ke_atom_eff.txt +++ b/doc/compute_ke_atom_eff.txt @@ -59,8 +59,8 @@ electrons) not in the specified compute group. This compute calculates a scalar quantity for each atom, which can be accessed by any command that uses per-atom computes as input. See -"this section"_Section_howto.html#howto_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/compute_ke_eff.html b/doc/compute_ke_eff.html index 2fa318f8a6..7c476b9aa6 100644 --- a/doc/compute_ke_eff.html +++ b/doc/compute_ke_eff.html @@ -64,8 +64,8 @@ thermo_modify temp effTemp

    This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See this section for an overview -of LAMMPS output options. +input. See Section_howto 15 for an +overview of LAMMPS output options.

    The scalar value calculated by this compute is "extensive". The scalar value will be in energy units. diff --git a/doc/compute_ke_eff.txt b/doc/compute_ke_eff.txt index 2ebe435dff..61c46d3377 100644 --- a/doc/compute_ke_eff.txt +++ b/doc/compute_ke_eff.txt @@ -61,8 +61,8 @@ See "compute temp/eff"_compute_temp_eff.html. This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See "this section"_Section_howto.html#howto_15 for an overview -of LAMMPS output options. +input. See "Section_howto 15"_Section_howto.html#howto_15 for an +overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The scalar value will be in energy "units"_units.html. diff --git a/doc/compute_meso_e_atom.html b/doc/compute_meso_e_atom.html index 69d903799b..3350eb3000 100644 --- a/doc/compute_meso_e_atom.html +++ b/doc/compute_meso_e_atom.html @@ -41,8 +41,8 @@ specified compute group.

    This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    The per-atom vector values will be in energy units.

    diff --git a/doc/compute_meso_e_atom.txt b/doc/compute_meso_e_atom.txt index b85115da49..0cf93ef6ed 100644 --- a/doc/compute_meso_e_atom.txt +++ b/doc/compute_meso_e_atom.txt @@ -38,8 +38,8 @@ specified compute group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"this section"_Section_howto.html#4_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/compute_meso_rho_atom.html b/doc/compute_meso_rho_atom.html index 202be3573c..790e2f9005 100644 --- a/doc/compute_meso_rho_atom.html +++ b/doc/compute_meso_rho_atom.html @@ -41,8 +41,8 @@ specified compute group.

    This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    The per-atom vector values will be in mass/volume units.

    diff --git a/doc/compute_meso_rho_atom.txt b/doc/compute_meso_rho_atom.txt index c09581864d..5ed9ec86dc 100644 --- a/doc/compute_meso_rho_atom.txt +++ b/doc/compute_meso_rho_atom.txt @@ -38,8 +38,8 @@ specified compute group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"this section"_Section_howto.html#4_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. The per-atom vector values will be in mass/volume "units"_units.html. diff --git a/doc/compute_meso_t_atom.html b/doc/compute_meso_t_atom.html index dc41ea8d3b..39b21ccff9 100644 --- a/doc/compute_meso_t_atom.html +++ b/doc/compute_meso_t_atom.html @@ -43,8 +43,8 @@ specified compute group.

    This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    The per-atom vector values will be in temperature units.

    diff --git a/doc/compute_meso_t_atom.txt b/doc/compute_meso_t_atom.txt index 1d1a3a12ae..cfdd787553 100644 --- a/doc/compute_meso_t_atom.txt +++ b/doc/compute_meso_t_atom.txt @@ -40,8 +40,8 @@ specified compute group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"this section"_Section_howto.html#4_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. The per-atom vector values will be in temperature "units"_units.html. diff --git a/doc/compute_pe.html b/doc/compute_pe.html index 97e1fe278a..75f44af57b 100644 --- a/doc/compute_pe.html +++ b/doc/compute_pe.html @@ -83,8 +83,9 @@ more instructions on how to use the accelerated styles effectively.

    This compute calculates a global scalar (the potential energy). This value can be used by any command that uses a global scalar value from -a compute as input. See this section -for an overview of LAMMPS output options. +a compute as input. See Section_howto +15 for an overview of LAMMPS output +options.

    The scalar value calculated by this compute is "extensive". The scalar value will be in energy units. diff --git a/doc/compute_pe.txt b/doc/compute_pe.txt index 5b0e9f29d0..e09ad02b32 100644 --- a/doc/compute_pe.txt +++ b/doc/compute_pe.txt @@ -79,8 +79,9 @@ more instructions on how to use the accelerated styles effectively. This compute calculates a global scalar (the potential energy). This value can be used by any command that uses a global scalar value from -a compute as input. See "this section"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +a compute as input. See "Section_howto +15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. The scalar value calculated by this compute is "extensive". The scalar value will be in energy "units"_units.html. diff --git a/doc/compute_pe_atom.html b/doc/compute_pe_atom.html index af5f158fc7..3e7bc51f48 100644 --- a/doc/compute_pe_atom.html +++ b/doc/compute_pe_atom.html @@ -70,8 +70,8 @@ the system energy.

    This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    The per-atom vector values will be in energy units.

    diff --git a/doc/compute_pe_atom.txt b/doc/compute_pe_atom.txt index c71dceec48..3b3d2a331d 100644 --- a/doc/compute_pe_atom.txt +++ b/doc/compute_pe_atom.txt @@ -67,8 +67,8 @@ the system energy. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"this section"_Section_howto.html#howto_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/compute_rdf.html b/doc/compute_rdf.html index ae66e375bc..50bb94428a 100644 --- a/doc/compute_rdf.html +++ b/doc/compute_rdf.html @@ -104,8 +104,8 @@ coordinate (center of the bin), Each successive set of 2 columns has the g(r) and coord(r) values for a specific set of itypeN versus jtypeN interactions, as described above. These values can be used by any command that uses a global values from a compute as input. See -this section for an overview of LAMMPS -output options. +Section_howto 15 for an overview of +LAMMPS output options.

    The array values calculated by this compute are all "intensive".

    diff --git a/doc/compute_rdf.txt b/doc/compute_rdf.txt index 83e835ff3c..afda1a28b7 100644 --- a/doc/compute_rdf.txt +++ b/doc/compute_rdf.txt @@ -101,8 +101,8 @@ coordinate (center of the bin), Each successive set of 2 columns has the g(r) and coord(r) values for a specific set of {itypeN} versus {jtypeN} interactions, as described above. These values can be used by any command that uses a global values from a compute as input. See -"this section"_Section_howto.html#howto_15 for an overview of LAMMPS -output options. +"Section_howto 15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. The array values calculated by this compute are all "intensive". diff --git a/doc/compute_reduce.html b/doc/compute_reduce.html index f5533307e5..74dbbdd9de 100644 --- a/doc/compute_reduce.html +++ b/doc/compute_reduce.html @@ -173,8 +173,8 @@ divides by the appropriate atom count. specified or a global vector of length N where N is the number of inputs, and which can be accessed by indices 1 to N. These values can be used by any command that uses global scalar or vector values from a -compute as input. See this section for -an overview of LAMMPS output options. +compute as input. See Section_howto 15 +for an overview of LAMMPS output options.

    All the scalar or vector values calculated by this compute are "intensive", except when the sum mode is used on per-atom or local diff --git a/doc/compute_reduce.txt b/doc/compute_reduce.txt index 135f83eefe..be542b8d8b 100644 --- a/doc/compute_reduce.txt +++ b/doc/compute_reduce.txt @@ -160,8 +160,8 @@ This compute calculates a global scalar if a single input value is specified or a global vector of length N where N is the number of inputs, and which can be accessed by indices 1 to N. These values can be used by any command that uses global scalar or vector values from a -compute as input. See "this section"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +compute as input. See "Section_howto 15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. All the scalar or vector values calculated by this compute are "intensive", except when the {sum} mode is used on per-atom or local diff --git a/doc/compute_stress_atom.html b/doc/compute_stress_atom.html index f39d75300f..fb9a8634bd 100644 --- a/doc/compute_stress_atom.html +++ b/doc/compute_stress_atom.html @@ -102,8 +102,9 @@ contribution can easily be computed.

    This compute calculates a per-atom array with 6 columns, which can be accessed by indices 1-6 by any command that uses per-atom values from -a compute as input. See this section -for an overview of LAMMPS output options. +a compute as input. See Section_howto +15 for an overview of LAMMPS output +options.

    The per-atom array values will be in pressure*volume units as discussed above. diff --git a/doc/compute_stress_atom.txt b/doc/compute_stress_atom.txt index f8d073397f..6cdd4b0289 100644 --- a/doc/compute_stress_atom.txt +++ b/doc/compute_stress_atom.txt @@ -99,8 +99,9 @@ contribution can easily be computed. This compute calculates a per-atom array with 6 columns, which can be accessed by indices 1-6 by any command that uses per-atom values from -a compute as input. See "this section"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +a compute as input. See "Section_howto +15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. The per-atom array values will be in pressure*volume "units"_units.html as discussed above. diff --git a/doc/compute_ti.html b/doc/compute_ti.html index 4e997fb1c5..b3e7c63581 100644 --- a/doc/compute_ti.html +++ b/doc/compute_ti.html @@ -102,8 +102,9 @@ du/dl can be found in the paper by Eike.

    This compute calculates a global scalar, namely dUs/dlambda. This value can be used by any command that uses a global scalar value from -a compute as input. See this section -for an overview of LAMMPS output options. +a compute as input. See Section_howto +15 for an overview of LAMMPS output +options.

    The scalar value calculated by this compute is "extensive".

    diff --git a/doc/compute_ti.txt b/doc/compute_ti.txt index 1d8041ae97..11888ddb18 100644 --- a/doc/compute_ti.txt +++ b/doc/compute_ti.txt @@ -94,8 +94,9 @@ du/dl can be found in the paper by "Eike"_#Eike. This compute calculates a global scalar, namely dUs/dlambda. This value can be used by any command that uses a global scalar value from -a compute as input. See "this section"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +a compute as input. See "Section_howto +15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. The scalar value calculated by this compute is "extensive". diff --git a/doc/create_box.html b/doc/create_box.html index 974af9ee35..235e2bc3ff 100644 --- a/doc/create_box.html +++ b/doc/create_box.html @@ -55,9 +55,9 @@ since if the maximum tilt factor is 5 (as in this example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all geometrically equivalent.

    -

    See this section of the doc pages for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used +

    See Section_howto 12 of the doc pages +for a geometric description of triclinic boxes, as defined by LAMMPS, +and how to transform these parameters to and from other commonly used triclinic representations.

    When a prism region is used, the simulation domain must be periodic in diff --git a/doc/create_box.txt b/doc/create_box.txt index 247486503a..08fce9e6b0 100644 --- a/doc/create_box.txt +++ b/doc/create_box.txt @@ -52,9 +52,9 @@ since if the maximum tilt factor is 5 (as in this example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all geometrically equivalent. -See "this section"_Section_howto.html#howto_12 of the doc pages for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used +See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages +for a geometric description of triclinic boxes, as defined by LAMMPS, +and how to transform these parameters to and from other commonly used triclinic representations. When a prism region is used, the simulation domain must be periodic in diff --git a/doc/dump.html b/doc/dump.html index 9b3d6264a1..8e8c903499 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -283,9 +283,9 @@ coordinate format that many codes can read.

    Note that DCD, XTC, and XYZ formatted files can be read directly by VMD (a popular molecular viewing -program). See this section of the manual and -the tools/lmp2vmd/README.txt file for more information about support -in VMD for reading and visualizing LAMMPS dump files. +program). See Section tools of the manual +and the tools/lmp2vmd/README.txt file for more information about +support in VMD for reading and visualizing LAMMPS dump files.

    diff --git a/doc/dump.txt b/doc/dump.txt index 8f4e6c5698..be599aafb6 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -272,9 +272,9 @@ coordinate format that many codes can read. Note that DCD, XTC, and XYZ formatted files can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd (a popular molecular viewing -program). See "this section"_Section_tools.html#vmd of the manual and -the tools/lmp2vmd/README.txt file for more information about support -in VMD for reading and visualizing LAMMPS dump files. +program). See "Section tools"_Section_tools.html#vmd of the manual +and the tools/lmp2vmd/README.txt file for more information about +support in VMD for reading and visualizing LAMMPS dump files. :line diff --git a/doc/fix_append_atoms.html b/doc/fix_append_atoms.html index 1523661ced..f9a0d6e606 100644 --- a/doc/fix_append_atoms.html +++ b/doc/fix_append_atoms.html @@ -87,9 +87,9 @@ define the lattice spacings.

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can be -used with the start/stop keywords of the run command. +by this fix for access by various output +commands. No parameter of this fix can +be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

    Restrictions: @@ -98,8 +98,9 @@ This fix is not invoked during energy minimization LAMMPS was built with that package. See the Making LAMMPS section for more info.

    -

    The zhi boundary on which atoms are added with append_atoms must be shrink-wrapped. -The zlo boundary may be any boundary type other than periodic. +

    The zhi boundary on which atoms are added with append_atoms must be +shrink-wrapped. The zlo boundary may be any boundary type other than +periodic.

    Related commands:

    diff --git a/doc/fix_append_atoms.txt b/doc/fix_append_atoms.txt index a98c9734d6..a698ae6a54 100644 --- a/doc/fix_append_atoms.txt +++ b/doc/fix_append_atoms.txt @@ -78,8 +78,8 @@ 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 -used with the {start/stop} keywords of the "run"_run.html command. +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. [Restrictions:] @@ -88,8 +88,9 @@ This fix style is part of the SHOCK package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -The zhi boundary on which atoms are added with append_atoms must be shrink-wrapped. -The zlo boundary may be any boundary type other than periodic. +The zhi boundary on which atoms are added with append_atoms must be +shrink-wrapped. The zlo boundary may be any boundary type other than +periodic. [Related commands:] diff --git a/doc/fix_meso.html b/doc/fix_meso.html index b3684d8720..81bb833347 100644 --- a/doc/fix_meso.html +++ b/doc/fix_meso.html @@ -37,9 +37,9 @@ LAMMPS.

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can be -used with the start/stop keywords of the run command. +by this fix for access by various output +commands. No parameter of this fix can +be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

    Restrictions: diff --git a/doc/fix_meso.txt b/doc/fix_meso.txt index 7c6a5cfc43..85f5838dd2 100644 --- a/doc/fix_meso.txt +++ b/doc/fix_meso.txt @@ -35,8 +35,8 @@ 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 -used with the {start/stop} keywords of the "run"_run.html command. +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. [Restrictions:] diff --git a/doc/fix_meso_stationary.html b/doc/fix_meso_stationary.html index 67a9a6a207..cf339c2560 100644 --- a/doc/fix_meso_stationary.html +++ b/doc/fix_meso_stationary.html @@ -38,9 +38,9 @@ LAMMPS.

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can be -used with the start/stop keywords of the run command. +by this fix for access by various output +commands. No parameter of this fix can +be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

    Restrictions: diff --git a/doc/fix_meso_stationary.txt b/doc/fix_meso_stationary.txt index 31bdb4b1f3..5b83573bc8 100644 --- a/doc/fix_meso_stationary.txt +++ b/doc/fix_meso_stationary.txt @@ -36,8 +36,8 @@ 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 -used with the {start/stop} keywords of the "run"_run.html command. +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. [Restrictions:] diff --git a/doc/fix_neb.html b/doc/fix_neb.html index 79390f9b38..23a8b894d3 100644 --- a/doc/fix_neb.html +++ b/doc/fix_neb.html @@ -29,8 +29,8 @@ simulation run via the neb command to perform a nudged elastic band (NEB) calculation for transition state finding. Hi-level explanations of NEB are given with the neb command and in -this section of the manual. The fix neb -command must be used with the "neb" command to define how +Section_howto 5 of the manual. The fix +neb command must be used with the "neb" command to define how inter-replica forces are computed.

    Only the N atoms in the fix group experience inter-replica forces. diff --git a/doc/fix_neb.txt b/doc/fix_neb.txt index 397a259c4f..c84b46a422 100644 --- a/doc/fix_neb.txt +++ b/doc/fix_neb.txt @@ -26,8 +26,8 @@ Add inter-replica forces to atoms in the group for a multi-replica simulation run via the "neb"_neb.html command to perform a nudged elastic band (NEB) calculation for transition state finding. Hi-level explanations of NEB are given with the "neb"_neb.html command and in -"this section"_Section_howto.html#howto_5 of the manual. The fix neb -command must be used with the "neb" command to define how +"Section_howto 5"_Section_howto.html#howto_5 of the manual. The fix +neb command must be used with the "neb" command to define how inter-replica forces are computed. Only the N atoms in the fix group experience inter-replica forces. diff --git a/doc/fix_viscosity.html b/doc/fix_viscosity.html index 51eee268f6..57e0502b30 100644 --- a/doc/fix_viscosity.html +++ b/doc/fix_viscosity.html @@ -103,12 +103,13 @@ you cannot accurately infer a viscosity and should try increasing the Nevery parameter.

    An alternative method for calculating a viscosity is to run a NEMD -simulation, as described in this section -of the manual. NEMD simulations deform the simmulation box via the -fix deform command. Thus they cannot be run on a -charged system using a PPPM solver since PPPM does -not currently support non-orthogonal boxes. Using fix viscosity keeps -the box orthogonal; thus it does not suffer from this limitation. +simulation, as described in Section_howto +13 of the manual. NEMD simulations +deform the simmulation box via the fix deform +command. Thus they cannot be run on a charged system using a PPPM +solver since PPPM does not currently support +non-orthogonal boxes. Using fix viscosity keeps the box orthogonal; +thus it does not suffer from this limitation.

    Restart, fix_modify, output, run start/stop, minimize info:

    diff --git a/doc/fix_viscosity.txt b/doc/fix_viscosity.txt index 3e39526876..511c194bbb 100644 --- a/doc/fix_viscosity.txt +++ b/doc/fix_viscosity.txt @@ -92,12 +92,13 @@ you cannot accurately infer a viscosity and should try increasing the Nevery parameter. An alternative method for calculating a viscosity is to run a NEMD -simulation, as described in "this section"_Section_howto.html#howto_13 -of the manual. NEMD simulations deform the simmulation box via the -"fix deform"_fix_deform.html command. Thus they cannot be run on a -charged system using a "PPPM solver"_kspace_style.html since PPPM does -not currently support non-orthogonal boxes. Using fix viscosity keeps -the box orthogonal; thus it does not suffer from this limitation. +simulation, as described in "Section_howto +13"_Section_howto.html#howto_13 of the manual. NEMD simulations +deform the simmulation box via the "fix deform"_fix_deform.html +command. Thus they cannot be run on a charged system using a "PPPM +solver"_kspace_style.html since PPPM does not currently support +non-orthogonal boxes. Using fix viscosity keeps the box orthogonal; +thus it does not suffer from this limitation. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/fix_wall_piston.html b/doc/fix_wall_piston.html index 17b3262da2..12b25dc307 100644 --- a/doc/fix_wall_piston.html +++ b/doc/fix_wall_piston.html @@ -101,9 +101,9 @@ define the lattice spacings.

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various output -commands. No parameter of this fix can be -used with the start/stop keywords of the run command. +by this fix for access by various output +commands. No parameter of this fix can +be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

    Restrictions: diff --git a/doc/fix_wall_piston.txt b/doc/fix_wall_piston.txt index 5194733c75..f4c3a5dd42 100644 --- a/doc/fix_wall_piston.txt +++ b/doc/fix_wall_piston.txt @@ -92,8 +92,8 @@ 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 -used with the {start/stop} keywords of the "run"_run.html command. +commands"_Section_howto.html#howoto_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. [Restrictions:] diff --git a/doc/if.html b/doc/if.html index 3baffda0fc..a0014191f5 100644 --- a/doc/if.html +++ b/doc/if.html @@ -66,9 +66,9 @@ above.

    IMPORTANT NOTE: If a command itself requires a quoted argument (e.g. a print command), then double and single quotes can be used and nested in the usual manner, as in the examples above and below. -See this section of the manual for more -details on using quotes in arguments. Only one of level of nesting is -allowed, but that should be sufficient for most use cases. +See Section_commands 2 of the manual for +more details on using quotes in arguments. Only one of level of +nesting is allowed, but that should be sufficient for most use cases.

    Note that by using the line continuation character "&", the if command can be spread across many lines, though it is still a single command: diff --git a/doc/if.txt b/doc/if.txt index a92b9213b9..494021e4aa 100644 --- a/doc/if.txt +++ b/doc/if.txt @@ -63,9 +63,9 @@ above. IMPORTANT NOTE: If a command itself requires a quoted argument (e.g. a "print"_print.html command), then double and single quotes can be used and nested in the usual manner, as in the examples above and below. -See "this section"_Section_commands.html#cmd_2 of the manual for more -details on using quotes in arguments. Only one of level of nesting is -allowed, but that should be sufficient for most use cases. +See "Section_commands 2"_Section_commands.html#cmd_2 of the manual for +more details on using quotes in arguments. Only one of level of +nesting is allowed, but that should be sufficient for most use cases. Note that by using the line continuation character "&", the if command can be spread across many lines, though it is still a single command: diff --git a/doc/log.html b/doc/log.html index 2edfe3fcd6..10db3c0b4c 100644 --- a/doc/log.html +++ b/doc/log.html @@ -33,7 +33,7 @@ the same log file.

    The file "log.lammps" is the default log file for a LAMMPS run. The name of the initial log file can also be set by the command-line -switch -log. See this section for +switch -log. See Section_start 6 for details.

    Restrictions: none diff --git a/doc/log.txt b/doc/log.txt index dc56bfcb60..bfd4462c47 100644 --- a/doc/log.txt +++ b/doc/log.txt @@ -30,7 +30,7 @@ the same log file. The file "log.lammps" is the default log file for a LAMMPS run. The name of the initial log file can also be set by the command-line -switch -log. See "this section"_Section_start.html#start_6 for +switch -log. See "Section_start 6"_Section_start.html#start_6 for details. [Restrictions:] none diff --git a/doc/neb.html b/doc/neb.html index 25cc68b644..6549538085 100644 --- a/doc/neb.html +++ b/doc/neb.html @@ -42,11 +42,11 @@ follows the discussion in these 3 papers: (Henkelman1)

    Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line -switch; see this section of the manual. -Note that if you have MPI installed, you can run a multi-replica -simulation with more replicas (partitions) than you have physical -processors, e.g you can run a 10-replica simulation on one or two -processors. You will simply not get the performance speed-up you +switch; see Section_start 6 of the +manual. Note that if you have MPI installed, you can run a +multi-replica simulation with more replicas (partitions) than you have +physical processors, e.g you can run a 10-replica simulation on one or +two processors. You will simply not get the performance speed-up you would see with one or more physical processors per replica. See this section of the manual for further discussion. diff --git a/doc/neb.txt b/doc/neb.txt index 1965f23348..78c3a927ba 100644 --- a/doc/neb.txt +++ b/doc/neb.txt @@ -39,11 +39,11 @@ follows the discussion in these 3 papers: "(Henkelman1)"_#Henkelman1, Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line -switch; see "this section"_Section_start.html#start_6 of the manual. -Note that if you have MPI installed, you can run a multi-replica -simulation with more replicas (partitions) than you have physical -processors, e.g you can run a 10-replica simulation on one or two -processors. You will simply not get the performance speed-up you +switch; see "Section_start 6"_Section_start.html#start_6 of the +manual. Note that if you have MPI installed, you can run a +multi-replica simulation with more replicas (partitions) than you have +physical processors, e.g you can run a 10-replica simulation on one or +two processors. You will simply not get the performance speed-up you would see with one or more physical processors per replica. See "this section"_Section_howto.html#howto_5 of the manual for further discussion. diff --git a/doc/partition.html b/doc/partition.html index 6bd24564ab..6435653681 100644 --- a/doc/partition.html +++ b/doc/partition.html @@ -30,7 +30,7 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1

    This command invokes the specified command on a subset of the partitions of processors you have defined via the -partition -command-line switch. See this section +command-line switch. See Section_start 6 for an explanation of the switch.

    Normally, every input script command in your script is invoked by diff --git a/doc/partition.txt b/doc/partition.txt index 6fb8c54d90..65f98b545f 100644 --- a/doc/partition.txt +++ b/doc/partition.txt @@ -27,7 +27,7 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1 :pre This command invokes the specified command on a subset of the partitions of processors you have defined via the -partition -command-line switch. See "this section"_Section_start.html#start_6 +command-line switch. See "Section_start 6"_Section_start.html#start_6 for an explanation of the switch. Normally, every input script command in your script is invoked by diff --git a/doc/prd.html b/doc/prd.html index 270a48c0a6..baad8b3dfb 100644 --- a/doc/prd.html +++ b/doc/prd.html @@ -71,13 +71,13 @@ event to occur.

    Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line -switch; see this section of the manual. -Note that if you have MPI installed, you can run a multi-replica -simulation with more replicas (partitions) than you have physical -processors, e.g you can run a 10-replica simulation on one or two -processors. For PRD, this makes little sense, since this offers no -effective parallel speed-up in searching for infrequent events. See -this section of the manual for further +switch; see Section_start 6 of the +manual. Note that if you have MPI installed, you can run a +multi-replica simulation with more replicas (partitions) than you have +physical processors, e.g you can run a 10-replica simulation on one or +two processors. For PRD, this makes little sense, since this offers +no effective parallel speed-up in searching for infrequent events. See +Section_howto 5 of the manual for further discussion.

    When a PRD simulation is performed, it is assumed that each replica is diff --git a/doc/prd.txt b/doc/prd.txt index 33130c17b6..52c5406eee 100644 --- a/doc/prd.txt +++ b/doc/prd.txt @@ -58,13 +58,13 @@ event to occur. Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line -switch; see "this section"_Section_start.html#start_6 of the manual. -Note that if you have MPI installed, you can run a multi-replica -simulation with more replicas (partitions) than you have physical -processors, e.g you can run a 10-replica simulation on one or two -processors. For PRD, this makes little sense, since this offers no -effective parallel speed-up in searching for infrequent events. See -"this section"_Section_howto.html#howto_5 of the manual for further +switch; see "Section_start 6"_Section_start.html#start_6 of the +manual. Note that if you have MPI installed, you can run a +multi-replica simulation with more replicas (partitions) than you have +physical processors, e.g you can run a 10-replica simulation on one or +two processors. For PRD, this makes little sense, since this offers +no effective parallel speed-up in searching for infrequent events. See +"Section_howto 5"_Section_howto.html#howto_5 of the manual for further discussion. When a PRD simulation is performed, it is assumed that each replica is diff --git a/doc/read_data.html b/doc/read_data.html index fcf68f4680..bf57ec18e0 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -111,9 +111,9 @@ limitation, since if the maximum tilt factor is 5 (as in this example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all geometrically equivalent.

    -

    See this section of the doc pages for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used +

    See Section_howto 12 of the doc pages +for a geometric description of triclinic boxes, as defined by LAMMPS, +and how to transform these parameters to and from other commonly used triclinic representations.

    When a triclinic system is used, the simulation domain must be diff --git a/doc/read_data.txt b/doc/read_data.txt index b9fcccd0f6..fd28395df2 100644 --- a/doc/read_data.txt +++ b/doc/read_data.txt @@ -108,9 +108,9 @@ limitation, since if the maximum tilt factor is 5 (as in this example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all geometrically equivalent. -See "this section"_Section_howto.html#howto_12 of the doc pages for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used +See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages +for a geometric description of triclinic boxes, as defined by LAMMPS, +and how to transform these parameters to and from other commonly used triclinic representations. When a triclinic system is used, the simulation domain must be diff --git a/doc/region.html b/doc/region.html index a9b089de7c..58832093d3 100644 --- a/doc/region.html +++ b/doc/region.html @@ -175,9 +175,9 @@ since if the maximum tilt factor is 5 (as in this example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all geometrically equivalent.

    -

    See this section of the doc pages for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used +

    See Section_howto 12 of the doc pages +for a geometric description of triclinic boxes, as defined by LAMMPS, +and how to transform these parameters to and from other commonly used triclinic representations.

    The union style creates a region consisting of the volume of all the diff --git a/doc/region.txt b/doc/region.txt index c8da7594f3..74744ab501 100644 --- a/doc/region.txt +++ b/doc/region.txt @@ -166,9 +166,9 @@ since if the maximum tilt factor is 5 (as in this example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all geometrically equivalent. -See "this section"_Section_howto.html#howto_12 of the doc pages for a -geometric description of triclinic boxes, as defined by LAMMPS, and -how to transform these parameters to and from other commonly used +See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages +for a geometric description of triclinic boxes, as defined by LAMMPS, +and how to transform these parameters to and from other commonly used triclinic representations. The {union} style creates a region consisting of the volume of all the diff --git a/doc/run_style.html b/doc/run_style.html index a1defb9e1c..abe21ecdd7 100644 --- a/doc/run_style.html +++ b/doc/run_style.html @@ -69,7 +69,7 @@ simulations performed by LAMMPS.

    The verlet/split style is also a velocity-Verlet integrator, but it splits the force calculation within each timestep over 2 partitions of -processors. See this section for an +processors. See Section_start 6 for an explanation of the -partition command-line switch.

    Specifically, this style performs all computation except the diff --git a/doc/run_style.txt b/doc/run_style.txt index 6f98479091..2484fc4dfa 100644 --- a/doc/run_style.txt +++ b/doc/run_style.txt @@ -64,7 +64,7 @@ The {verlet} style is a standard velocity-Verlet integrator. The {verlet/split} style is also a velocity-Verlet integrator, but it splits the force calculation within each timestep over 2 partitions of -processors. See "this section"_Section_start.html#start_6 for an +processors. See "Section_start 6"_Section_start.html#start_6 for an explanation of the -partition command-line switch. Specifically, this style performs all computation except the diff --git a/doc/tad.html b/doc/tad.html index 08a87fc8bf..459bdb1c1d 100644 --- a/doc/tad.html +++ b/doc/tad.html @@ -102,8 +102,9 @@ restricts you to having exactly one processor per replica. For more information, see the documentation for the neb command. In the current LAMMPS implementation of TAD, all the non-NEB TAD operations are performed on the first partition, while the other -partitions remain idle. See this section -of the manual for further discussion of multi-replica simulations. +partitions remain idle. See Section_howto +5 of the manual for further discussion of +multi-replica simulations.

    A TAD run has several stages, which are repeated each time an event is performed. The logic for a TAD run is as follows: diff --git a/doc/tad.txt b/doc/tad.txt index adb10fcc3a..e62e92a664 100644 --- a/doc/tad.txt +++ b/doc/tad.txt @@ -91,8 +91,9 @@ restricts you to having exactly one processor per replica. For more information, see the documentation for the "neb"_neb.html command. In the current LAMMPS implementation of TAD, all the non-NEB TAD operations are performed on the first partition, while the other -partitions remain idle. See "this section"_Section_howto.html#howto_5 -of the manual for further discussion of multi-replica simulations. +partitions remain idle. See "Section_howto +5"_Section_howto.html#howto_5 of the manual for further discussion of +multi-replica simulations. A TAD run has several stages, which are repeated each time an event is diff --git a/doc/temper.html b/doc/temper.html index 514db78868..01157902aa 100644 --- a/doc/temper.html +++ b/doc/temper.html @@ -35,11 +35,11 @@ replicas (ensembles) of a system. Two or more replicas must be used.

    Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line -switch; see this section of the manual. -Note that if you have MPI installed, you can run a multi-replica -simulation with more replicas (partitions) than you have physical -processors, e.g you can run a 10-replica simulation on one or two -processors. You will simply not get the performance speed-up you +switch; see Section_start 6 of the +manual. Note that if you have MPI installed, you can run a +multi-replica simulation with more replicas (partitions) than you have +physical processors, e.g you can run a 10-replica simulation on one or +two processors. You will simply not get the performance speed-up you would see with one or more physical processors per replica. See this section of the manual for further discussion. diff --git a/doc/temper.txt b/doc/temper.txt index 70f1e2f0d9..803c505cd5 100644 --- a/doc/temper.txt +++ b/doc/temper.txt @@ -32,11 +32,11 @@ replicas (ensembles) of a system. Two or more replicas must be used. Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line -switch; see "this section"_Section_start.html#start_6 of the manual. -Note that if you have MPI installed, you can run a multi-replica -simulation with more replicas (partitions) than you have physical -processors, e.g you can run a 10-replica simulation on one or two -processors. You will simply not get the performance speed-up you +switch; see "Section_start 6"_Section_start.html#start_6 of the +manual. Note that if you have MPI installed, you can run a +multi-replica simulation with more replicas (partitions) than you have +physical processors, e.g you can run a 10-replica simulation on one or +two processors. You will simply not get the performance speed-up you would see with one or more physical processors per replica. See "this section"_Section_howto.html#howto_5 of the manual for further discussion.