diff --git a/doc/Developers.pdf b/doc/Developer.pdf similarity index 65% rename from doc/Developers.pdf rename to doc/Developer.pdf index 3e09a11004..55b5015e49 100644 Binary files a/doc/Developers.pdf and b/doc/Developer.pdf differ diff --git a/doc/Manual.txt b/doc/Manual.txt index 2b645ae715..457230649b 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -40,7 +40,7 @@ The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated about once per month. This is because it is large, and we don't want it to be part of very patch. :l -There is also a "Developers.pdf"_Developers.pdf file in the doc +There is also a "Developer.pdf"_Developer.pdf file in the doc directory, which describes the internal structure and algorithms of LAMMPS. :ule,l diff --git a/doc/Section_accelerate.html b/doc/Section_accelerate.html index c314ea830b..bdbc463baa 100644 --- a/doc/Section_accelerate.html +++ b/doc/Section_accelerate.html @@ -58,9 +58,9 @@ 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 manual. -A list of accelerated styles is included in the pair, fix, compute, -and kspace sections. +packages, see this section of the +manual. A list of accelerated styles is included in the pair, fix, +compute, and kspace sections.

The following sections explain:

@@ -73,17 +73,17 @@ and kspace sections.

The final section compares and contrasts the GPU and USER-CUDA packages, since they are both designed to use NVIDIA GPU hardware.

-5.1 OPT package
-5.2 USER-OMP package
-5.3 GPU package
-5.4 USER-CUDA package
-5.5 Comparison of GPU and USER-CUDA packages
+5.1 OPT package
+5.2 USER-OMP package
+5.3 GPU package
+5.4 USER-CUDA package
+5.5 Comparison of GPU and USER-CUDA packages
-

5.1 OPT package +

5.1 OPT package

The OPT package was developed by James Fischer (High Performance Technologies), David Richie, and Vincent Natoli (Stone Ridge @@ -112,7 +112,7 @@ to 20% savings.

-

5.2 USER-OMP package +

5.2 USER-OMP package

This section will be written when the USER-OMP package is released in main LAMMPS. @@ -121,7 +121,7 @@ in main LAMMPS.

-

5.3 GPU package +

5.3 GPU package

The GPU package was developed by Mike Brown at ORNL. It provides GPU versions of several pair styles and for long-range Coulombics via the @@ -263,7 +263,7 @@ requires that your GPU card support double precision.

-

5.4 USER-CUDA package +

5.4 USER-CUDA package

The USER-CUDA package was developed by Christian Trott at U Technology Ilmenau in Germany. It provides NVIDIA GPU versions of many pair @@ -396,7 +396,7 @@ occurs, the faster your simulation will run.

-

5.5 Comparison of GPU and USER-CUDA packages +

5.5 Comparison of GPU and USER-CUDA packages

Both the GPU and USER-CUDA packages accelerate a LAMMPS calculation using NVIDIA hardware, but they do it in different ways. diff --git a/doc/Section_accelerate.txt b/doc/Section_accelerate.txt index 405dc8f6c7..30eefba2f7 100644 --- a/doc/Section_accelerate.txt +++ b/doc/Section_accelerate.txt @@ -55,9 +55,9 @@ 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#3_5 of the manual. -A list of accelerated styles is included in the pair, fix, compute, -and kspace sections. +packages, see "this section"_Section_commands.html#cmd_5 of the +manual. A list of accelerated styles is included in the pair, fix, +compute, and kspace sections. The following sections explain: @@ -70,16 +70,16 @@ speed-ups you can expect :ul The final section compares and contrasts the GPU and USER-CUDA packages, since they are both designed to use NVIDIA GPU hardware. -5.1 "OPT package"_#5_1 -5.2 "USER-OMP package"_#5_2 -5.3 "GPU package"_#5_3 -5.4 "USER-CUDA package"_#5_4 -5.5 "Comparison of GPU and USER-CUDA packages"_#5_4 :all(b) +5.1 "OPT package"_#acc_1 +5.2 "USER-OMP package"_#acc_2 +5.3 "GPU package"_#acc_3 +5.4 "USER-CUDA package"_#acc_4 +5.5 "Comparison of GPU and USER-CUDA packages"_#acc_5 :all(b) :line :line -5.1 OPT package :h4,link(5_1) +5.1 OPT package :h4,link(acc_1) The OPT package was developed by James Fischer (High Performance Technologies), David Richie, and Vincent Natoli (Stone Ridge @@ -107,7 +107,7 @@ to 20% savings. :line :line -5.2 USER-OMP package :h4,link(5_2) +5.2 USER-OMP package :h4,link(acc_2) This section will be written when the USER-OMP package is released in main LAMMPS. @@ -115,7 +115,7 @@ in main LAMMPS. :line :line -5.3 GPU package :h4,link(5_3) +5.3 GPU package :h4,link(acc_3) The GPU package was developed by Mike Brown at ORNL. It provides GPU versions of several pair styles and for long-range Coulombics via the @@ -256,7 +256,7 @@ requires that your GPU card support double precision. :line :line -5.4 USER-CUDA package :h4,link(5_4) +5.4 USER-CUDA package :h4,link(acc_4) The USER-CUDA package was developed by Christian Trott at U Technology Ilmenau in Germany. It provides NVIDIA GPU versions of many pair @@ -388,7 +388,7 @@ occurs, the faster your simulation will run. :line :line -5.5 Comparison of GPU and USER-CUDA packages :h4,link(5_5) +5.5 Comparison of GPU and USER-CUDA packages :h4,link(acc_5) Both the GPU and USER-CUDA packages accelerate a LAMMPS calculation using NVIDIA hardware, but they do it in different ways. diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 69debff39a..eb16907d2e 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -14,15 +14,15 @@

This section describes how a LAMMPS input script is formatted and what commands are used to define a LAMMPS simulation.

-3.1 LAMMPS input script
-3.2 Parsing rules
-3.3 Input script structure
-3.4 Commands listed by category
-3.5 Commands listed alphabetically
+3.1 LAMMPS input script
+3.2 Parsing rules
+3.3 Input script structure
+3.4 Commands listed by category
+3.5 Commands listed alphabetically
-

3.1 LAMMPS input script +

3.1 LAMMPS input script

LAMMPS executes by reading commands from a input script (text file), one line at a time. When the input script ends, LAMMPS exits. Each @@ -75,7 +75,7 @@ command lists restrictions on how the command can be used.

-

3.2 Parsing rules +

3.2 Parsing rules

Each non-blank line in the input script is treated as a command. LAMMPS commands are case sensitive. Command names are lower-case, as @@ -134,7 +134,7 @@ allowed, but that should be sufficient for most use cases.

-

3.3 Input script structure +

3.3 Input script structure

This section describes the structure of a typical LAMMPS input script. The "examples" directory in the LAMMPS distribution contains many @@ -223,11 +223,11 @@ the minimize command. A parallel tempering

-

3.4 Commands listed by category +

3.4 Commands listed by category

This section lists all LAMMPS commands, grouped by category. The -next section lists the same commands alphabetically. Note that -some style options for some commands are part of specific LAMMPS +next section lists the same commands alphabetically. Note +that some style options for some commands are part of specific LAMMPS packages, which means they cannot be used unless the package was included when LAMMPS was built. Not all packages are included in a default LAMMPS build. These dependencies are listed as Restrictions @@ -300,12 +300,12 @@ in the command's documentation.

-

3.5 Individual commands +

3.5 Individual commands

This section lists all LAMMPS commands alphabetically, with a separate -listing below of styles within certain commands. The previous -section lists the same commands, grouped by category. Note that -some style options for some commands are part of specific LAMMPS +listing below of styles within certain commands. The previous +section lists the same commands, grouped by category. Note +that some style options for some commands are part of specific LAMMPS packages, which means they cannot be used unless the package was included when LAMMPS was built. Not all packages are included in a default LAMMPS build. These dependencies are listed as Restrictions diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 8649a561c5..496a5582fa 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -11,15 +11,15 @@ This section describes how a LAMMPS input script is formatted and what commands are used to define a LAMMPS simulation. -3.1 "LAMMPS input script"_#3_1 -3.2 "Parsing rules"_#3_2 -3.3 "Input script structure"_#3_3 -3.4 "Commands listed by category"_#3_4 -3.5 "Commands listed alphabetically"_#3_5 :all(b) +3.1 "LAMMPS input script"_#cmd_1 +3.2 "Parsing rules"_#cmd_2 +3.3 "Input script structure"_#cmd_3 +3.4 "Commands listed by category"_#cmd_4 +3.5 "Commands listed alphabetically"_#cmd_5 :all(b) :line -3.1 LAMMPS input script :link(3_1),h4 +3.1 LAMMPS input script :link(cmd_1),h4 LAMMPS executes by reading commands from a input script (text file), one line at a time. When the input script ends, LAMMPS exits. Each @@ -72,7 +72,7 @@ command lists restrictions on how the command can be used. :line -3.2 Parsing rules :link(3_2),h4 +3.2 Parsing rules :link(cmd_2),h4 Each non-blank line in the input script is treated as a command. LAMMPS commands are case sensitive. Command names are lower-case, as @@ -131,7 +131,7 @@ allowed, but that should be sufficient for most use cases. :line -3.3 Input script structure :h4,link(3_3) +3.3 Input script structure :h4,link(cmd_3) This section describes the structure of a typical LAMMPS input script. The "examples" directory in the LAMMPS distribution contains many @@ -220,11 +220,11 @@ the "minimize"_minimize.html command. A parallel tempering :line -3.4 Commands listed by category :link(3_4),h4 +3.4 Commands listed by category :link(cmd_4),h4 This section lists all LAMMPS commands, grouped by category. The -"next section"_#3_5 lists the same commands alphabetically. Note that -some style options for some commands are part of specific LAMMPS +"next section"_#cmd_5 lists the same commands alphabetically. Note +that some style options for some commands are part of specific LAMMPS packages, which means they cannot be used unless the package was included when LAMMPS was built. Not all packages are included in a default LAMMPS build. These dependencies are listed as Restrictions @@ -297,12 +297,12 @@ Miscellaneous: :line -3.5 Individual commands :h4,link(3_5),link(comm) +3.5 Individual commands :h4,link(cmd_5),link(comm) This section lists all LAMMPS commands alphabetically, with a separate listing below of styles within certain commands. The "previous -section"_#3_4 lists the same commands, grouped by category. Note that -some style options for some commands are part of specific LAMMPS +section"_#cmd_4 lists the same commands, grouped by category. Note +that some style options for some commands are part of specific LAMMPS packages, which means they cannot be used unless the package was included when LAMMPS was built. Not all packages are included in a default LAMMPS build. These dependencies are listed as Restrictions diff --git a/doc/Section_errors.html b/doc/Section_errors.html index 50d20db172..bd7722e923 100644 --- a/doc/Section_errors.html +++ b/doc/Section_errors.html @@ -16,13 +16,13 @@ Section

This section describes the various kinds of errors you can encounter when using LAMMPS.

-12.1 Common problems
-12.2 Reporting bugs
-12.3 Error & warning messages
+12.1 Common problems
+12.2 Reporting bugs
+12.3 Error & warning messages
-

12.1 Common problems +

12.1 Common problems

If two LAMMPS runs do not produce the same answer on different machines or different numbers of processors, this is typically not a @@ -81,7 +81,7 @@ decide if the WARNING is important or not. A WARNING message that is generated in the middle of a run is only printed to the screen, not to the logfile, to avoid cluttering up thermodynamic output. If LAMMPS crashes or hangs without spitting out an error message first then it -could be a bug (see this section) or one of the following +could be a bug (see this section) or one of the following cases:

LAMMPS runs in the available memory a processor allows to be @@ -112,7 +112,7 @@ buffering or boost the sizes of messages that can be buffered.

-

12.2 Reporting bugs +

12.2 Reporting bugs

If you are confident that you have found a bug in LAMMPS, follow these steps. @@ -142,7 +142,7 @@ causing the problem.

-

12.3 Error & warning messages +

12.3 Error & warning messages

These are two alphabetic lists of the ERROR and WARNING messages LAMMPS prints out and the reason why. If the diff --git a/doc/Section_errors.txt b/doc/Section_errors.txt index dc37cb9966..0712fb922f 100644 --- a/doc/Section_errors.txt +++ b/doc/Section_errors.txt @@ -13,13 +13,13 @@ Section"_Section_history.html :c This section describes the various kinds of errors you can encounter when using LAMMPS. -12.1 "Common problems"_#12_1 -12.2 "Reporting bugs"_#12_2 -12.3 "Error & warning messages"_#12_3 :all(b) +12.1 "Common problems"_#err_1 +12.2 "Reporting bugs"_#err_2 +12.3 "Error & warning messages"_#err_3 :all(b) :line -12.1 Common problems :link(12_1),h4 +12.1 Common problems :link(err_1),h4 If two LAMMPS runs do not produce the same answer on different machines or different numbers of processors, this is typically not a @@ -78,7 +78,7 @@ decide if the WARNING is important or not. A WARNING message that is generated in the middle of a run is only printed to the screen, not to the logfile, to avoid cluttering up thermodynamic output. If LAMMPS crashes or hangs without spitting out an error message first then it -could be a bug (see "this section"_#12_2) or one of the following +could be a bug (see "this section"_#err_2) or one of the following cases: LAMMPS runs in the available memory a processor allows to be @@ -109,7 +109,7 @@ buffering or boost the sizes of messages that can be buffered. :line -12.2 Reporting bugs :link(12_2),h4 +12.2 Reporting bugs :link(err_2),h4 If you are confident that you have found a bug in LAMMPS, follow these steps. @@ -139,7 +139,7 @@ As a last resort, you can send an email directly to the :line -12.3 Error & warning messages :h4,link(12_3) +12.3 Error & warning messages :h4,link(err_3) These are two alphabetic lists of the "ERROR"_#error and "WARNING"_#warn messages LAMMPS prints out and the reason why. If the diff --git a/doc/Section_history.html b/doc/Section_history.html index ee854fc829..e84bb721ed 100644 --- a/doc/Section_history.html +++ b/doc/Section_history.html @@ -1,5 +1,7 @@ -

Previous Section - LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands - Next Section +
Previous Section - LAMMPS WWW Site - +LAMMPS Documentation - LAMMPS Commands - Next +Section
@@ -15,12 +17,12 @@ of previous versions of LAMMPS, and features of other parallel molecular dynamics codes I've distributed.

-13.1 Coming attractions
-13.2 Past versions
+13.1 Coming attractions
+13.2 Past versions
-

13.1 Coming attractions +

13.1 Coming attractions

The current version of LAMMPS incorporates nearly all the features from previous parallel MD codes developed at Sandia. These include @@ -49,7 +51,7 @@ page on the LAMMPS WWW site for more details.

-

13.2 Past versions +

13.2 Past versions

LAMMPS development began in the mid 1990s under a cooperative research & development agreement (CRADA) between two DOE labs (Sandia and LLNL) diff --git a/doc/Section_history.txt b/doc/Section_history.txt index ab737285f0..de84ffb2bf 100644 --- a/doc/Section_history.txt +++ b/doc/Section_history.txt @@ -1,4 +1,6 @@ -"Previous Section"_Section_errors.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Manual.html :c +"Previous Section"_Section_errors.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Manual.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -12,12 +14,12 @@ This section lists features we are planning to add to LAMMPS, features of previous versions of LAMMPS, and features of other parallel molecular dynamics codes I've distributed. -13.1 "Coming attractions"_#13_1 -13.2 "Past versions"_#13_2 :all(b) +13.1 "Coming attractions"_#hist_1 +13.2 "Past versions"_#hist_2 :all(b) :line -13.1 Coming attractions :h4,link(13_1) +13.1 Coming attractions :h4,link(hist_1) The current version of LAMMPS incorporates nearly all the features from previous parallel MD codes developed at Sandia. These include @@ -46,7 +48,7 @@ Direct Simulation Monte Carlo - DSMC :ul :line -13.2 Past versions :h4,link(13_2) +13.2 Past versions :h4,link(hist_2) LAMMPS development began in the mid 1990s under a cooperative research & development agreement (CRADA) between two DOE labs (Sandia and LLNL) diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 734ed315c7..7f200f929e 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -14,27 +14,27 @@

The following sections describe how to use various options within LAMMPS.

-6.1 Restarting a simulation
-6.2 2d simulations
-6.3 CHARMM, AMBER, and DREIDING force fields
-6.4 Running multiple simulations from one input script
-6.5 Multi-replica simulations
-6.6 Granular models
-6.7 TIP3P water model
-6.8 TIP4P water model
-6.9 SPC water model
-6.10 Coupling LAMMPS to other codes
-6.11 Visualizing LAMMPS snapshots
-6.12 Triclinic (non-orthogonal) simulation boxes
-6.13 NEMD simulations
-6.14 Extended spherical and aspherical particles
-6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
-6.16 Thermostatting, barostatting and computing temperature
-6.17 Walls
-6.18 Elastic constants
-6.19 Library interface to LAMMPS
-6.20 Calculating thermal conductivity
-6.21 Calculating viscosity
+6.1 Restarting a simulation
+6.2 2d simulations
+6.3 CHARMM, AMBER, and DREIDING force fields
+6.4 Running multiple simulations from one input script
+6.5 Multi-replica simulations
+6.6 Granular models
+6.7 TIP3P water model
+6.8 TIP4P water model
+6.9 SPC water model
+6.10 Coupling LAMMPS to other codes
+6.11 Visualizing LAMMPS snapshots
+6.12 Triclinic (non-orthogonal) simulation boxes
+6.13 NEMD simulations
+6.14 Extended spherical and aspherical particles
+6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
+6.16 Thermostatting, barostatting and computing temperature
+6.17 Walls
+6.18 Elastic constants
+6.19 Library interface to LAMMPS
+6.20 Calculating thermal conductivity
+6.21 Calculating viscosity

The example input scripts included in the LAMMPS distribution and highlighted in this section also show how to @@ -42,7 +42,7 @@ setup and run various kinds of simulations.

-

6.1 Restarting a simulation +

6.1 Restarting a simulation

There are 3 ways to continue a long LAMMPS simulation. Multiple run commands can be used in the same input script. Each @@ -134,7 +134,7 @@ but not in data files.

-

6.2 2d simulations +

6.2 2d simulations

Use the dimension command to specify a 2d simulation.

@@ -169,7 +169,7 @@ the same as in 3d.

-

6.3 CHARMM, AMBER, and DREIDING force fields +

6.3 CHARMM, AMBER, and DREIDING force fields

A force field has 2 parts: the formulas that define it and the coefficients used for a particular system. Here we only discuss @@ -246,7 +246,7 @@ documentation for the formula it computes.

-

6.4 Running multiple simulations from one input script +

6.4 Running multiple simulations from one input script

This can be done in several ways. See the documentation for individual commands for more details on how these examples work. @@ -334,7 +334,7 @@ the 4th simulation, and so forth, until all 8 were completed.

-

6.5 Multi-replica simulations +

6.5 Multi-replica simulations

Several commands in LAMMPS run mutli-replica simulations, meaning that multiple instances (replicas) of your simulation are run @@ -381,7 +381,7 @@ physical processors.

-

6.6 Granular models +

6.6 Granular models

Granular system are composed of spherical particles with a diameter, as opposed to point particles. This means they have an angular @@ -398,7 +398,7 @@ the following commands:

-

calculates rotational kinetic energy which can be output with +

calculates rotational kinetic energy which can be output with thermodynamic info.

Use one of these 3 pair potentials, which compute forces and torques @@ -426,7 +426,7 @@ computations between frozen atoms by using this command:

-

6.7 TIP3P water model +

6.7 TIP3P water model

The TIP3P water model as implemented in CHARMM (MacKerell) specifies a 3-site rigid water molecule with @@ -486,7 +486,7 @@ models.

-

6.8 TIP4P water model +

6.8 TIP4P water model

The four-point TIP4P rigid water model extends the traditional three-point TIP3P model by adding an additional site, usually @@ -545,7 +545,7 @@ models.

-

6.9 SPC water model +

6.9 SPC water model

The SPC water model specifies a 3-site rigid water molecule with charges and Lennard-Jones parameters assigned to each of the 3 atoms. @@ -590,7 +590,7 @@ models.

-

6.10 Coupling LAMMPS to other codes +

6.10 Coupling LAMMPS to other codes

LAMMPS is designed to allow it to be coupled to other codes. For example, a quantum mechanics code might compute forces on a subset of @@ -673,7 +673,7 @@ 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 +to LAMMPS. See this section of the manual for a description of the interface and how to extend it for your needs.

@@ -690,7 +690,7 @@ instances of LAMMPS to perform different calculations.

-

6.11 Visualizing LAMMPS snapshots +

6.11 Visualizing LAMMPS snapshots

LAMMPS itself does not do visualization, but snapshots from LAMMPS simulations can be visualized (and analyzed) in a variety of ways. @@ -749,7 +749,7 @@ See the dump command for more information on XTC files

-

6.12 Triclinic (non-orthogonal) simulation boxes +

6.12 Triclinic (non-orthogonal) simulation boxes

By default, LAMMPS uses an orthogonal simulation box to encompass the particles. The boundary command sets the boundary @@ -882,7 +882,7 @@ on non-equilibrium MD (NEMD) simulations.

-

6.13 NEMD simulations +

6.13 NEMD simulations

Non-equilibrium molecular dynamics or NEMD simulations are typically used to measure a fluid's rheological properties such as viscosity. @@ -920,7 +920,7 @@ profile consistent with the applied shear strain rate.

-

6.14 Extended spherical and aspherical particles +

6.14 Extended spherical and aspherical particles

Typical MD models treat atoms or particles as point masses. Sometimes, however, it is desirable to have a model with finite-size @@ -1100,7 +1100,7 @@ particles are point masses.

-

6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) +

6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)

There are four basic kinds of LAMMPS output:

@@ -1394,7 +1394,7 @@ vector input could be a column of an array.
-

6.16 Thermostatting, barostatting, and computing temperature +

6.16 Thermostatting, barostatting, and computing temperature

Thermostatting means controlling the temperature of particles in an MD simulation. Barostatting means controlling the pressure. Since the @@ -1455,7 +1455,7 @@ thermostatting can be invoked via the dpd/tstat pair style:

Fix nvt only thermostats the translational velocity of particles. Fix nvt/sllod also does this, except that it subtracts out a velocity bias due to a deforming box and -integrates the SLLOD equations of motion. See the NEMD +integrates the SLLOD equations of motion. See the NEMD simulations section of this page for further details. Fix nvt/sphere and fix nvt/asphere thermostat not only translation @@ -1545,7 +1545,7 @@ thermodynamic output.

-

6.17 Walls +

6.17 Walls

Walls in an MD simulation are typically used to bound particle motion, i.e. to serve as a boundary condition. @@ -1619,7 +1619,7 @@ frictional walls, as well as triangulated surfaces.

-

6.18 Elastic constants +

6.18 Elastic constants

Elastic constants characterize the stiffness of a material. The formal definition is provided by the linear relation that holds between the @@ -1655,11 +1655,11 @@ converge and requires careful post-processing (Shinoda)

-

6.19 Library interface to LAMMPS +

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 +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 @@ -1736,10 +1736,10 @@ grab data from LAMMPS, change it, and put it back into LAMMPS.

-

6.20 Calculating thermal conductivity +

6.20 Calculating thermal conductivity

The thermal conductivity kappa of a material can be measured in at -least 3 ways using various options in LAMMPS. (See this +least 3 ways using various options in LAMMPS. (See this section of the manual for an analogous discussion for viscosity). The thermal conducitivity tensor kappa is a measure of the propensity of a material to transmit heat energy in a @@ -1756,7 +1756,7 @@ scalar.

The first method is to setup two thermostatted regions at opposite ends of a simulation box, or one in the middle and one at the end of a periodic box. By holding the two regions at different temperatures -with a thermostatting fix, the energy added +with a thermostatting fix, the energy added to the hot region should equal the energy subtracted from the cold region and be proportional to the heat flux moving between the regions. See the paper by Ikeshoji and Hafskjold for @@ -1801,10 +1801,10 @@ formalism.

-

6.21 Calculating viscosity +

6.21 Calculating viscosity

The shear viscosity eta of a fluid can be measured in at least 3 ways -using various options in LAMMPS. (See this +using various options in LAMMPS. (See this section of the manual for an analogous discussion for thermal conductivity). Eta is a measure of the propensity of a fluid to transmit momentum in a direction @@ -1830,7 +1830,7 @@ y-direction of the Vx component of fluid motion or grad(Vstream) = dVx/dy. In this case, the Pxy off-diagonal component of the pressure or stress tensor, as calculated by the compute pressure command, can also be monitored, which -is the J term in the equation above. See this +is the J term in the equation above. See this section of the manual for details on NEMD simulations.

diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index da1de76d78..65131975fb 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -11,27 +11,27 @@ The following sections describe how to use various options within LAMMPS. -6.1 "Restarting a simulation"_#6_1 -6.2 "2d simulations"_#6_2 -6.3 "CHARMM, AMBER, and DREIDING force fields"_#6_3 -6.4 "Running multiple simulations from one input script"_#6_4 -6.5 "Multi-replica simulations"_#6_5 -6.6 "Granular models"_#6_6 -6.7 "TIP3P water model"_#6_7 -6.8 "TIP4P water model"_#6_8 -6.9 "SPC water model"_#6_9 -6.10 "Coupling LAMMPS to other codes"_#6_10 -6.11 "Visualizing LAMMPS snapshots"_#6_11 -6.12 "Triclinic (non-orthogonal) simulation boxes"_#6_12 -6.13 "NEMD simulations"_#6_13 -6.14 "Extended spherical and aspherical particles"_#6_14 -6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#6_15 -6.16 "Thermostatting, barostatting and computing temperature"_#6_16 -6.17 "Walls"_#6_17 -6.18 "Elastic constants"_#6_18 -6.19 "Library interface to LAMMPS"_#6_19 -6.20 "Calculating thermal conductivity"_#6_20 -6.21 "Calculating viscosity"_#6_21 :all(b) +6.1 "Restarting a simulation"_#howto_1 +6.2 "2d simulations"_#howto_2 +6.3 "CHARMM, AMBER, and DREIDING force fields"_#howto_3 +6.4 "Running multiple simulations from one input script"_#howto_4 +6.5 "Multi-replica simulations"_#howto_5 +6.6 "Granular models"_#howto_6 +6.7 "TIP3P water model"_#howto_7 +6.8 "TIP4P water model"_#howto_8 +6.9 "SPC water model"_#howto_9 +6.10 "Coupling LAMMPS to other codes"_#howto_10 +6.11 "Visualizing LAMMPS snapshots"_#howto_11 +6.12 "Triclinic (non-orthogonal) simulation boxes"_#howto_12 +6.13 "NEMD simulations"_#howto_13 +6.14 "Extended spherical and aspherical particles"_#howto_14 +6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#howto_15 +6.16 "Thermostatting, barostatting and computing temperature"_#howto_16 +6.17 "Walls"_#howto_17 +6.18 "Elastic constants"_#howto_18 +6.19 "Library interface to LAMMPS"_#howto_19 +6.20 "Calculating thermal conductivity"_#howto_20 +6.21 "Calculating viscosity"_#howto_21 :all(b) The example input scripts included in the LAMMPS distribution and highlighted in "this section"_Section_example.html also show how to @@ -39,7 +39,7 @@ setup and run various kinds of simulations. :line -6.1 Restarting a simulation :link(6_1),h4 +6.1 Restarting a simulation :link(howto_1),h4 There are 3 ways to continue a long LAMMPS simulation. Multiple "run"_run.html commands can be used in the same input script. Each @@ -131,7 +131,7 @@ but not in data files. :line -6.2 2d simulations :link(6_2),h4 +6.2 2d simulations :link(howto_2),h4 Use the "dimension"_dimension.html command to specify a 2d simulation. @@ -166,7 +166,7 @@ the same as in 3d. :line -6.3 CHARMM, AMBER, and DREIDING force fields :link(6_3),h4 +6.3 CHARMM, AMBER, and DREIDING force fields :link(howto_3),h4 A force field has 2 parts: the formulas that define it and the coefficients used for a particular system. Here we only discuss @@ -242,7 +242,7 @@ documentation for the formula it computes. :line -6.4 Running multiple simulations from one input script :link(6_4),h4 +6.4 Running multiple simulations from one input script :link(howto_4),h4 This can be done in several ways. See the documentation for individual commands for more details on how these examples work. @@ -330,7 +330,7 @@ the 4th simulation, and so forth, until all 8 were completed. :line -6.5 Multi-replica simulations :link(6_5),h4 +6.5 Multi-replica simulations :link(howto_5),h4 Several commands in LAMMPS run mutli-replica simulations, meaning that multiple instances (replicas) of your simulation are run @@ -377,7 +377,7 @@ physical processors. :line -6.6 Granular models :link(6_6),h4 +6.6 Granular models :link(howto_6),h4 Granular system are composed of spherical particles with a diameter, as opposed to point particles. This means they have an angular @@ -395,7 +395,7 @@ This compute "compute erotate/sphere"_compute_erotate_sphere.html :ul calculates rotational kinetic energy which can be "output with -thermodynamic info"_Section_howto.html#6_15. +thermodynamic info"_Section_howto.html#howto_15. Use one of these 3 pair potentials, which compute forces and torques between interacting pairs of particles: @@ -422,7 +422,7 @@ computations between frozen atoms by using this command: :line -6.7 TIP3P water model :link(6_7),h4 +6.7 TIP3P water model :link(howto_7),h4 The TIP3P water model as implemented in CHARMM "(MacKerell)"_#MacKerell specifies a 3-site rigid water molecule with @@ -482,7 +482,7 @@ models"_http://en.wikipedia.org/wiki/Water_model. :line -6.8 TIP4P water model :link(6_8),h4 +6.8 TIP4P water model :link(howto_8),h4 The four-point TIP4P rigid water model extends the traditional three-point TIP3P model by adding an additional site, usually @@ -541,7 +541,7 @@ models"_http://en.wikipedia.org/wiki/Water_model. :line -6.9 SPC water model :link(6_9),h4 +6.9 SPC water model :link(howto_9),h4 The SPC water model specifies a 3-site rigid water molecule with charges and Lennard-Jones parameters assigned to each of the 3 atoms. @@ -586,7 +586,7 @@ models"_http://en.wikipedia.org/wiki/Water_model. :line -6.10 Coupling LAMMPS to other codes :link(6_10),h4 +6.10 Coupling LAMMPS to other codes :link(howto_10),h4 LAMMPS is designed to allow it to be coupled to other codes. For example, a quantum mechanics code might compute forces on a subset of @@ -668,7 +668,7 @@ 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#6_19 of the manual +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. @@ -685,7 +685,7 @@ instances of LAMMPS to perform different calculations. :line -6.11 Visualizing LAMMPS snapshots :link(6_11),h4 +6.11 Visualizing LAMMPS snapshots :link(howto_11),h4 LAMMPS itself does not do visualization, but snapshots from LAMMPS simulations can be visualized (and analyzed) in a variety of ways. @@ -741,7 +741,7 @@ See the "dump"_dump.html command for more information on XTC files. :line -6.12 Triclinic (non-orthogonal) simulation boxes :link(6_12),h4 +6.12 Triclinic (non-orthogonal) simulation boxes :link(howto_12),h4 By default, LAMMPS uses an orthogonal simulation box to encompass the particles. The "boundary"_boundary.html command sets the boundary @@ -874,7 +874,7 @@ on non-equilibrium MD (NEMD) simulations. :line -6.13 NEMD simulations :link(6_13),h4 +6.13 NEMD simulations :link(howto_13),h4 Non-equilibrium molecular dynamics or NEMD simulations are typically used to measure a fluid's rheological properties such as viscosity. @@ -912,7 +912,7 @@ An alternative method for calculating viscosities is provided via the :line -6.14 Extended spherical and aspherical particles :link(6_14),h4 +6.14 Extended spherical and aspherical particles :link(howto_14),h4 Typical MD models treat atoms or particles as point masses. Sometimes, however, it is desirable to have a model with finite-size @@ -1092,7 +1092,7 @@ particles are point masses. :line -6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) :link(6_15),h4 +6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) :link(howto_15),h4 There are four basic kinds of LAMMPS output: @@ -1382,7 +1382,7 @@ Command: Input: Output: :line -6.16 Thermostatting, barostatting, and computing temperature :link(6_16),h4 +6.16 Thermostatting, barostatting, and computing temperature :link(howto_16),h4 Thermostatting means controlling the temperature of particles in an MD simulation. Barostatting means controlling the pressure. Since the @@ -1444,7 +1444,7 @@ thermostatting can be invoked via the {dpd/tstat} pair style: particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except that it subtracts out a velocity bias due to a deforming box and integrates the SLLOD equations of motion. See the "NEMD -simulations"_#6_13 section of this page for further details. "Fix +simulations"_#howto_13 section of this page for further details. "Fix nvt/sphere"_fix_nvt_sphere.html and "fix nvt/asphere"_fix_nvt_asphere.html thermostat not only translation velocities but also rotational velocities for spherical and aspherical @@ -1533,7 +1533,7 @@ thermodynamic output. :line -6.17 Walls :link(6_17),h4 +6.17 Walls :link(howto_17),h4 Walls in an MD simulation are typically used to bound particle motion, i.e. to serve as a boundary condition. @@ -1607,7 +1607,7 @@ frictional walls, as well as triangulated surfaces. :line -6.18 Elastic constants :link(6_18),h4 +6.18 Elastic constants :link(howto_18),h4 Elastic constants characterize the stiffness of a material. The formal definition is provided by the linear relation that holds between the @@ -1643,11 +1643,11 @@ converge and requires careful post-processing "(Shinoda)"_#Shinoda :line -6.19 Library interface to LAMMPS :link(6_19),h4 +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#6_10 with other codes, or +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 @@ -1724,11 +1724,11 @@ grab data from LAMMPS, change it, and put it back into LAMMPS. :line -6.20 Calculating thermal conductivity :link(6_20),h4 +6.20 Calculating thermal conductivity :link(howto_20),h4 The thermal conductivity kappa of a material can be measured in at least 3 ways using various options in LAMMPS. (See "this -section"_Section_howto.html#6_21 of the manual for an analogous +section"_Section_howto.html#howto_21 of the manual for an analogous discussion for viscosity). The thermal conducitivity tensor kappa is a measure of the propensity of a material to transmit heat energy in a diffusive manner as given by Fourier's law @@ -1744,7 +1744,7 @@ scalar. The first method is to setup two thermostatted regions at opposite ends of a simulation box, or one in the middle and one at the end of a periodic box. By holding the two regions at different temperatures -with a "thermostatting fix"_Section_howto.html#6_13, the energy added +with a "thermostatting fix"_Section_howto.html#howto_13, the energy added to the hot region should equal the energy subtracted from the cold region and be proportional to the heat flux moving between the regions. See the paper by "Ikeshoji and Hafskjold"_#Ikeshoji for @@ -1789,11 +1789,11 @@ formalism. :line -6.21 Calculating viscosity :link(6_21),h4 +6.21 Calculating viscosity :link(howto_21),h4 The shear viscosity eta of a fluid can be measured in at least 3 ways using various options in LAMMPS. (See "this -section"_Section_howto.html#6_20 of the manual for an analogous +section"_Section_howto.html#howto_20 of the manual for an analogous discussion for thermal conductivity). Eta is a measure of the propensity of a fluid to transmit momentum in a direction perpendicular to the direction of velocity or momentum flow. @@ -1819,7 +1819,7 @@ dVx/dy. In this case, the Pxy off-diagonal component of the pressure or stress tensor, as calculated by the "compute pressure"_compute_pressure.html command, can also be monitored, which is the J term in the equation above. See "this -section"_Section_howto.html#6_13 of the manual for details on NEMD +section"_Section_howto.html#howto_13 of the manual for details on NEMD simulations. The second method is to perform a reverse non-equilibrium MD diff --git a/doc/Section_intro.html b/doc/Section_intro.html index 91fcf813a0..1e7001a9d9 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -417,7 +417,7 @@ 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 +
  • If you find a bug, this section describes how to report it.
  • If you publish a paper using LAMMPS results, send the citation (and diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index 91b1f4deb8..4c3a6be8a9 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -407,7 +407,7 @@ 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#10_2 describes +If you find a bug, "this section"_Section_errors.html#err_2 describes how to report it. :l If you publish a paper using LAMMPS results, send the citation (and diff --git a/doc/Section_modify.html b/doc/Section_modify.html index fef55c93e6..765f7440ba 100644 --- a/doc/Section_modify.html +++ b/doc/Section_modify.html @@ -121,26 +121,26 @@ details on this at the bottom of this page.

    Here are the subsequent topics discussed below, most of which are new features that can be added in the manner just described:

    -10.1 Atom styles
    -10.2 Bond, angle, dihedral, improper potentials
    -10.3 Compute styles
    -10.4 Dump styles
    -10.5 Dump custom output options
    -10.6 Fix styles which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc
    -10.7 Input script commands
    -10.8 Kspace computations
    -10.9 Minimization styles
    -10.10 Pairwise potentials
    -10.11 Region styles
    -10.12 Thermodynamic output options
    -10.13 Variable options
    -10.14 Submitting new features for inclusion in LAMMPS
    +10.1 Atom styles
    +10.2 Bond, angle, dihedral, improper potentials
    +10.3 Compute styles
    +10.4 Dump styles
    +10.5 Dump custom output options
    +10.6 Fix styles which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc
    +10.7 Input script commands
    +10.8 Kspace computations
    +10.9 Minimization styles
    +10.10 Pairwise potentials
    +10.11 Region styles
    +10.12 Thermodynamic output options
    +10.13 Variable options
    +10.14 Submitting new features for inclusion in LAMMPS
    -

    10.1 Atom styles +

    10.1 Atom styles

    Classes that define an atom style are derived from the Atom class. The atom style determines what quantities are associated with an atom. @@ -190,7 +190,7 @@ modify.

    -

    10.2 Bond, angle, dihedral, improper potentials +

    10.2 Bond, angle, dihedral, improper potentials

    Classes that compute molecular interactions are derived from the Bond, Angle, Dihedral, and Improper classes. New styles can be created to @@ -214,7 +214,7 @@ details.

    -

    10.3 Compute styles +

    10.3 Compute styles

    Classes that compute scalar and vector quantities like temperature and the pressure tensor, as well as classes that compute per-atom @@ -242,9 +242,9 @@ class. See compute.h for details.

    -

    10.4 Dump styles +

    10.4 Dump styles

    -

    10.5 Dump custom output options +

    10.5 Dump custom output options

    Classes that dump per-atom info to files are derived from the Dump class. To dump new quantities or in a new format, a new derived dump @@ -275,7 +275,7 @@ half-dozen or so locations where code will need to be added.

    -

    10.6 Fix styles +

    10.6 Fix styles

    In LAMMPS, a "fix" is any operation that is computed during timestepping that alters some property of the system. Essentially @@ -353,7 +353,7 @@ quantities and/or to be summed to the potential energy of the system.

    -

    10.7 Input script commands +

    10.7 Input script commands

    New commands can be added to LAMMPS input scripts by adding new classes that have a "command" method. For example, the create_atoms, @@ -375,7 +375,7 @@ needed.

    -

    10.8 Kspace computations +

    10.8 Kspace computations

    Classes that compute long-range Coulombic interactions via K-space representations (Ewald, PPPM) are derived from the KSpace class. New @@ -395,7 +395,7 @@ class. See kspace.h for details.

    -

    10.9 Minimization styles +

    10.9 Minimization styles

    Classes that perform energy minimization derived from the Min class. New styles can be created to add new minimization algorithms to @@ -414,7 +414,7 @@ class. See min.h for details.

    -

    10.10 Pairwise potentials +

    10.10 Pairwise potentials

    Classes that compute pairwise interactions are derived from the Pair class. In LAMMPS, pairwise calculation include manybody potentials @@ -443,7 +443,7 @@ includes some optional methods to enable its use with rRESPA.

    -

    10.11 Region styles +

    10.11 Region styles

    Classes that define geometric regions are derived from the Region class. Regions are used elsewhere in LAMMPS to group atoms, delete @@ -461,7 +461,7 @@ class. See region.h for details.

    -

    10.12 Thermodynamic output options +

    10.12 Thermodynamic output options

    There is one class that computes and prints thermodynamic information to the screen and log file; see the file thermo.cpp. @@ -490,7 +490,7 @@ by adding a new keyword to the thermo command.

    -

    10.13 Variable options +

    10.13 Variable options

    There is one class that computes and stores variable information in LAMMPS; see the file variable.cpp. The value @@ -532,7 +532,7 @@ then be accessed by variables) was discussed

    -

    10.14 Submitting new features for inclusion in LAMMPS +

    10.14 Submitting new features for inclusion in LAMMPS

    We encourage users to submit new features that they add to LAMMPS to the developers, especially if diff --git a/doc/Section_modify.txt b/doc/Section_modify.txt index d91ad10f8b..933520a04c 100644 --- a/doc/Section_modify.txt +++ b/doc/Section_modify.txt @@ -118,27 +118,27 @@ details on this at the bottom of this page. :l,ule Here are the subsequent topics discussed below, most of which are new features that can be added in the manner just described: -10.1 "Atom styles"_#10_1 -10.2 "Bond, angle, dihedral, improper potentials"_#10_2 -10.3 "Compute styles"_#10_3 -10.4 "Dump styles"_#10_4 -10.5 "Dump custom output options"_#10_5 -10.6 "Fix styles"_#10_6 which include integrators, \ +10.1 "Atom styles"_#mod_1 +10.2 "Bond, angle, dihedral, improper potentials"_#mod_2 +10.3 "Compute styles"_#mod_3 +10.4 "Dump styles"_#mod_4 +10.5 "Dump custom output options"_#mod_5 +10.6 "Fix styles"_#mod_6 which include integrators, \ temperature and pressure control, force constraints, \ boundary conditions, diagnostic output, etc -10.7 "Input script commands"_10_7 -10.8 "Kspace computations"_#10_8 -10.9 "Minimization styles"_#10_9 -10.10 "Pairwise potentials"_#10_10 -10.11 "Region styles"_#10_11 -10.12 "Thermodynamic output options"_#10_12 -10.13 "Variable options"_#10_13 -10.14 "Submitting new features for inclusion in LAMMPS"_#10_14 :all(b) +10.7 "Input script commands"_mod_7 +10.8 "Kspace computations"_#mod_8 +10.9 "Minimization styles"_#mod_9 +10.10 "Pairwise potentials"_#mod_10 +10.11 "Region styles"_#mod_11 +10.12 "Thermodynamic output options"_#mod_12 +10.13 "Variable options"_#mod_13 +10.14 "Submitting new features for inclusion in LAMMPS"_#mod_14 :all(b) :line :line -10.1 Atom styles :link(10_1),h4 +10.1 Atom styles :link(mod_1),h4 Classes that define an atom style are derived from the Atom class. The atom style determines what quantities are associated with an atom. @@ -186,7 +186,7 @@ modify. :line -10.2 Bond, angle, dihedral, improper potentials :link(10_2),h4 +10.2 Bond, angle, dihedral, improper potentials :link(mod_2),h4 Classes that compute molecular interactions are derived from the Bond, Angle, Dihedral, and Improper classes. New styles can be created to @@ -208,7 +208,7 @@ single: force and energy of a single bond :tb(s=:) :line -10.3 Compute styles :link(10_3),h4 +10.3 Compute styles :link(mod_3),h4 Classes that compute scalar and vector quantities like temperature and the pressure tensor, as well as classes that compute per-atom @@ -234,8 +234,8 @@ memory_usage: tally memory usage :tb(s=:) :line -10.4 Dump styles :link(10_4),h4 -10.5 Dump custom output options :link(10_5),h4 +10.4 Dump styles :link(mod_4),h4 +10.5 Dump custom output options :link(mod_5),h4 Classes that dump per-atom info to files are derived from the Dump class. To dump new quantities or in a new format, a new derived dump @@ -264,7 +264,7 @@ half-dozen or so locations where code will need to be added. :line -10.6 Fix styles :link(10_6),h4 +10.6 Fix styles :link(mod_6),h4 In LAMMPS, a "fix" is any operation that is computed during timestepping that alters some property of the system. Essentially @@ -340,7 +340,7 @@ quantities and/or to be summed to the potential energy of the system. :line -10.7 Input script commands :link(10_7),h4 +10.7 Input script commands :link(mod_7),h4 New commands can be added to LAMMPS input scripts by adding new classes that have a "command" method. For example, the create_atoms, @@ -360,7 +360,7 @@ needed. :line -10.8 Kspace computations :link(10_8),h4 +10.8 Kspace computations :link(mod_8),h4 Classes that compute long-range Coulombic interactions via K-space representations (Ewald, PPPM) are derived from the KSpace class. New @@ -378,7 +378,7 @@ memory_usage: tally of memory usage :tb(s=:) :line -10.9 Minimization styles :link(10_9),h4 +10.9 Minimization styles :link(mod_9),h4 Classes that perform energy minimization derived from the Min class. New styles can be created to add new minimization algorithms to @@ -395,7 +395,7 @@ memory_usage: tally of memory usage :tb(s=:) :line -10.10 Pairwise potentials :link(10_10),h4 +10.10 Pairwise potentials :link(mod_10),h4 Classes that compute pairwise interactions are derived from the Pair class. In LAMMPS, pairwise calculation include manybody potentials @@ -422,7 +422,7 @@ The inner/middle/outer routines are optional. :line -10.11 Region styles :link(10_11),h4 +10.11 Region styles :link(mod_11),h4 Classes that define geometric regions are derived from the Region class. Regions are used elsewhere in LAMMPS to group atoms, delete @@ -438,7 +438,7 @@ match: determine whether a point is in the region :tb(s=:) :line -10.12 Thermodynamic output options :link(10_12),h4 +10.12 Thermodynamic output options :link(mod_12),h4 There is one class that computes and prints thermodynamic information to the screen and log file; see the file thermo.cpp. @@ -467,7 +467,7 @@ by adding a new keyword to the thermo command. :line -10.13 Variable options :link(10_13),h4 +10.13 Variable options :link(mod_13),h4 There is one class that computes and stores "variable"_variable.html information in LAMMPS; see the file variable.cpp. The value @@ -508,7 +508,7 @@ then be accessed by variables) was discussed :line :line -10.14 Submitting new features for inclusion in LAMMPS :link(10_14),h4 +10.14 Submitting new features for inclusion in LAMMPS :link(mod_14),h4 We encourage users to submit new features that they add to LAMMPS to "the developers"_http://lammps.sandia.gov/authors.html, especially if diff --git a/doc/Section_python.html b/doc/Section_python.html index 0847d73173..92de682b05 100644 --- a/doc/Section_python.html +++ b/doc/Section_python.html @@ -20,11 +20,11 @@ either from a Python script or interactively from a Python prompt.

    Python is a powerful scripting and programming language which can be used to wrap software like LAMMPS and other packages. It can be used to glue multiple pieces of software -together, e.g. to run a coupled or multiscale model. See this +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 +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 @@ -89,13 +89,13 @@ setup discussion. The next to last sub-section describes the Python syntax used to invoke LAMMPS. The last sub-section describes example Python scripts included in the python directory.

    -

    There are also additional angle styles submitted by users which are included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the angle section of this +the individual styles are given in the angle section of this page.

    diff --git a/doc/angle_coeff.txt b/doc/angle_coeff.txt index 08ed66db24..091ebb4e4e 100644 --- a/doc/angle_coeff.txt +++ b/doc/angle_coeff.txt @@ -79,7 +79,7 @@ specified by the associated "angle_coeff"_angle_coeff.html command: There are also additional angle styles submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the angle section of "this -page"_Section_commands.html#3_5. +page"_Section_commands.html#cmd_5. :line diff --git a/doc/angle_cosine_periodic.html b/doc/angle_cosine_periodic.html index a3ad373b4c..b5d316fc2b 100644 --- a/doc/angle_cosine_periodic.html +++ b/doc/angle_cosine_periodic.html @@ -23,10 +23,10 @@ angle_coeff * 75.0 1 6

    Description:

    The cosine/periodic angle style uses the following potential, which -is commonly used in the DREIDING force field, -particularly for organometallic systems where n = 4 might be used -for an octahedral complex and n = 3 might be used for a trigonal -center: +is commonly used in the DREIDING force +field, particularly for organometallic systems where n = 4 might be +used for an octahedral complex and n = 3 might be used for a +trigonal center:

    diff --git a/doc/angle_cosine_periodic.txt b/doc/angle_cosine_periodic.txt index 9e36537440..024c914ad1 100644 --- a/doc/angle_cosine_periodic.txt +++ b/doc/angle_cosine_periodic.txt @@ -20,10 +20,10 @@ angle_coeff * 75.0 1 6 :pre [Description:] The {cosine/periodic} angle style uses the following potential, which -is commonly used in the "DREIDING"_Section_howto.html#4_4 force field, -particularly for organometallic systems where {n} = 4 might be used -for an octahedral complex and {n} = 3 might be used for a trigonal -center: +is commonly used in the "DREIDING"_Section_howto.html#howto_4 force +field, particularly for organometallic systems where {n} = 4 might be +used for an octahedral complex and {n} = 3 might be used for a +trigonal center: :c,image(Eqs/angle_cosine_periodic.jpg) diff --git a/doc/angle_style.html b/doc/angle_style.html index 24b520bd1d..3edbe63e26 100644 --- a/doc/angle_style.html +++ b/doc/angle_style.html @@ -73,7 +73,7 @@ specified by the associated angle_coeff command

    There are also additional angle styles submitted by users which are included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the angle section of this +the individual styles are given in the angle section of this page.

    diff --git a/doc/angle_style.txt b/doc/angle_style.txt index afeec60631..e5faffa666 100644 --- a/doc/angle_style.txt +++ b/doc/angle_style.txt @@ -72,7 +72,7 @@ specified by the associated "angle_coeff"_angle_coeff.html command: There are also additional angle styles submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the angle section of "this -page"_Section_commands.html#3_5. +page"_Section_commands.html#cmd_5. :line diff --git a/doc/bond_coeff.html b/doc/bond_coeff.html index 434f0fb3d4..58ce6406a0 100644 --- a/doc/bond_coeff.html +++ b/doc/bond_coeff.html @@ -77,7 +77,7 @@ specified by the associated bond_coeff command:

    There are also additional bond styles submitted by users which are included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the bond section of this +the individual styles are given in the bond section of this page.

    diff --git a/doc/bond_coeff.txt b/doc/bond_coeff.txt index 737d5e2abe..25110e9166 100644 --- a/doc/bond_coeff.txt +++ b/doc/bond_coeff.txt @@ -75,7 +75,7 @@ specified by the associated "bond_coeff"_bond_coeff.html command: There are also additional bond styles submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the bond section of "this -page"_Section_commands.html#3_5. +page"_Section_commands.html#cmd_5. :line diff --git a/doc/bond_style.html b/doc/bond_style.html index 2010c22e0a..5be22aa834 100644 --- a/doc/bond_style.html +++ b/doc/bond_style.html @@ -82,7 +82,7 @@ specified by the associated bond_coeff command:

    There are also additional bond styles submitted by users which are included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the bond section of this +the individual styles are given in the bond section of this page.

    diff --git a/doc/bond_style.txt b/doc/bond_style.txt index 3ba68c3e35..953a764cea 100644 --- a/doc/bond_style.txt +++ b/doc/bond_style.txt @@ -80,7 +80,7 @@ specified by the associated "bond_coeff"_bond_coeff.html command: There are also additional bond styles submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the bond section of "this -page"_Section_commands.html#3_5. +page"_Section_commands.html#cmd_5. :line diff --git a/doc/change_box.html b/doc/change_box.html index 0cc459a9f4..e258ec2337 100644 --- a/doc/change_box.html +++ b/doc/change_box.html @@ -28,7 +28,7 @@ change_box triclinic

    Description:

    By default LAMMPS runs a simulation in an orthogonal, axis-aligned -simulation box. LAMMPS can also run simulations in non-orthogonal +simulation box. LAMMPS can also run simulations in non-orthogonal (triclinic) simulation boxes. A box is defined as either orthogonal or non-orthogonal when it is created via the create_box, read_data, or @@ -37,9 +37,9 @@ the create_box, read_

    This command allows you to toggle the existing simulation box from orthogonal to non-orthogonal and vice versa. For example, an initial equilibration simulation can be run in an orthogonal box, the box can -be toggled to non-orthogonal, and then a non-equilibrium MD (NEMD) -simulation can be run with deformation via -the fix deform command. +be toggled to non-orthogonal, and then a non-equilibrium MD (NEMD) +simulation can be run with deformation +via the fix deform command.

    Note that if the simulation box is currently non-orthogonal and has non-zero tilt in xy, yz, or xz, then it cannot be converted to an diff --git a/doc/change_box.txt b/doc/change_box.txt index fc0ff37b2c..78c2c757d9 100644 --- a/doc/change_box.txt +++ b/doc/change_box.txt @@ -25,7 +25,7 @@ change_box triclinic :pre By default LAMMPS runs a simulation in an orthogonal, axis-aligned simulation box. LAMMPS can also run simulations in "non-orthogonal -(triclinic) simulation boxes"_Section_howto.html#4_12. A box is +(triclinic) simulation boxes"_Section_howto.html#howto_12. A box is defined as either orthogonal or non-orthogonal when it is created via the "create_box"_create_box.html, "read_data"_read_data.html, or "read_restart"_read_restart.html commands. @@ -34,8 +34,8 @@ This command allows you to toggle the existing simulation box from orthogonal to non-orthogonal and vice versa. For example, an initial equilibration simulation can be run in an orthogonal box, the box can be toggled to non-orthogonal, and then a "non-equilibrium MD (NEMD) -simulation"_Section_howto.html#4_13 can be run with deformation via -the "fix deform"_fix_deform.html command. +simulation"_Section_howto.html#howto_13 can be run with deformation +via the "fix deform"_fix_deform.html command. Note that if the simulation box is currently non-orthogonal and has non-zero tilt in xy, yz, or xz, then it cannot be converted to an diff --git a/doc/compute.html b/doc/compute.html index 9f5ed1945c..4e3d6ffee0 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -36,7 +36,7 @@ information about a previous state of the system. Defining a compute does not perform a computation. Instead computes are invoked by other LAMMPS commands as needed, e.g. to calculate a temperature needed for a thermostat fix or to generate thermodynamic or dump file output. -See this howto section for a summary of +See this howto section for a summary of various LAMMPS output options, many of which involve computes.

    The ID of a compute can only contain alphanumeric characters and @@ -217,13 +217,13 @@ available in LAMMPS:

    There are also additional compute styles submitted by users which are included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the compute section of this +the individual styles are given in the compute section of this page.

    There are also additional accelerated compute styles included in the LAMMPS distribution for faster performance on CPUs and GPUs. The list of these with links to the individual styles are given in the pair -section of this page. +section of this page.

    Restrictions: none

    diff --git a/doc/compute.txt b/doc/compute.txt index 47a3ed8291..2c53f5f4e6 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -33,7 +33,7 @@ information about a previous state of the system. Defining a compute does not perform a computation. Instead computes are invoked by other LAMMPS commands as needed, e.g. to calculate a temperature needed for a thermostat fix or to generate thermodynamic or dump file output. -See this "howto section"_Section_howto.html#4_15 for a summary of +See this "howto section"_Section_howto.html#howto_15 for a summary of various LAMMPS output options, many of which involve computes. The ID of a compute can only contain alphanumeric characters and @@ -213,12 +213,12 @@ available in LAMMPS: There are also additional compute styles submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the compute section of "this -page"_Section_commands.html#3_5. +page"_Section_commands.html#cmd_5. There are also additional accelerated compute styles included in the LAMMPS distribution for faster performance on CPUs and GPUs. The list of these with links to the individual styles are given in the pair -section of "this page"_Section_commands.html#3_5. +section of "this page"_Section_commands.html#cmd_5. [Restrictions:] none diff --git a/doc/compute_ackland_atom.html b/doc/compute_ackland_atom.html index 8b00859d07..31abcf1f93 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 scalar quantity for each atom, 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. +input. See this section for an overview +of LAMMPS output options.

    Restrictions:

    diff --git a/doc/compute_ackland_atom.txt b/doc/compute_ackland_atom.txt index f8fafcfdac..99991c7988 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 scalar quantity for each atom, 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. +input. See "this section"_Section_howto.html#howto_15 for an overview +of LAMMPS output options. [Restrictions:] diff --git a/doc/compute_angle_local.html b/doc/compute_angle_local.html index 547bc7b862..772388db4c 100644 --- a/doc/compute_angle_local.html +++ b/doc/compute_angle_local.html @@ -67,7 +67,7 @@ array is the number of angles. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See this +uses local values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_angle_local.txt b/doc/compute_angle_local.txt index 91cf1dcdf8..253a78e8fc 100644 --- a/doc/compute_angle_local.txt +++ b/doc/compute_angle_local.txt @@ -60,7 +60,7 @@ local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See "this -section"_Section_howto.html#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The output for {theta} will be in degrees. The output for {eng} will diff --git a/doc/compute_atom_molecule.html b/doc/compute_atom_molecule.html index 322679449d..d185c1e995 100644 --- a/doc/compute_atom_molecule.html +++ b/doc/compute_atom_molecule.html @@ -97,7 +97,7 @@ rows in the array is the number of molecules. If a single input is specified, a global vector is produced. If two or more inputs are specified, a global array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any -command that uses global values from a compute as input. See this +command that uses global values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_atom_molecule.txt b/doc/compute_atom_molecule.txt index d348b82563..53d4d38890 100644 --- a/doc/compute_atom_molecule.txt +++ b/doc/compute_atom_molecule.txt @@ -90,7 +90,7 @@ specified, a global vector is produced. If two or more inputs are specified, a global array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses global values from a compute as input. See "this -section"_Section_howto.html#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. All the vector or array values calculated by this compute are diff --git a/doc/compute_bond_local.html b/doc/compute_bond_local.html index 59e647cf35..67bb43353b 100644 --- a/doc/compute_bond_local.html +++ b/doc/compute_bond_local.html @@ -66,7 +66,7 @@ array is the number of bonds. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See this +uses local values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_bond_local.txt b/doc/compute_bond_local.txt index a7801a66fb..92768b6a5d 100644 --- a/doc/compute_bond_local.txt +++ b/doc/compute_bond_local.txt @@ -59,7 +59,7 @@ local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See "this -section"_Section_howto.html#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The output for {dist} will be in distance "units"_units.html. The diff --git a/doc/compute_centro_atom.html b/doc/compute_centro_atom.html index caac6e53fb..63c0c2b95f 100644 --- a/doc/compute_centro_atom.html +++ b/doc/compute_centro_atom.html @@ -79,7 +79,7 @@ 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 +this section for an overview of LAMMPS output options.

    The per-atom vector values are unitless values >= 0.0. Their diff --git a/doc/compute_centro_atom.txt b/doc/compute_centro_atom.txt index ec9dc2060d..a5a83a0c32 100644 --- a/doc/compute_centro_atom.txt +++ b/doc/compute_centro_atom.txt @@ -75,7 +75,7 @@ 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#4_15 for an overview of LAMMPS +"this section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values are unitless values >= 0.0. Their diff --git a/doc/compute_cluster_atom.html b/doc/compute_cluster_atom.html index 1cb85dad15..b2f7b49fdd 100644 --- a/doc/compute_cluster_atom.html +++ b/doc/compute_cluster_atom.html @@ -46,7 +46,7 @@ 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 +this section 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 497417b4cd..3193331f91 100644 --- a/doc/compute_cluster_atom.txt +++ b/doc/compute_cluster_atom.txt @@ -43,7 +43,7 @@ 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#4_15 for an overview of LAMMPS +"this section"_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 958c039127..7549fa7c6c 100644 --- a/doc/compute_cna_atom.html +++ b/doc/compute_cna_atom.html @@ -77,7 +77,7 @@ 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 +this section for an overview of LAMMPS output options.

    The per-atom vector values will be a number from 0 to 5, as explained diff --git a/doc/compute_cna_atom.txt b/doc/compute_cna_atom.txt index 8184597817..63afcf9a82 100644 --- a/doc/compute_cna_atom.txt +++ b/doc/compute_cna_atom.txt @@ -74,7 +74,7 @@ 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#4_15 for an overview of LAMMPS +"this section"_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 diff --git a/doc/compute_com.html b/doc/compute_com.html index 10b02794fc..b8bdb05531 100644 --- a/doc/compute_com.html +++ b/doc/compute_com.html @@ -52,8 +52,9 @@ file containing coordinates of the atoms in the bodies.

    This compute calculates a global vector of length 3, which can be accessed by indices 1-3 by any command that uses global vector values -from a compute as input. See this section -for an overview of LAMMPS output options. +from a compute as input. See this +section for an overview of LAMMPS output +options.

    The vector values are "intensive". The vector values will be in distance units. diff --git a/doc/compute_com.txt b/doc/compute_com.txt index 4b678ae011..43844dfd25 100644 --- a/doc/compute_com.txt +++ b/doc/compute_com.txt @@ -49,8 +49,9 @@ file"_dump.html containing coordinates of the atoms in the bodies. This compute calculates a global vector of length 3, which can be accessed by indices 1-3 by any command that uses global vector values -from a compute as input. See "this section"_Section_howto.html#4_15 -for an overview of LAMMPS output options. +from a compute as input. See "this +section"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. The vector values are "intensive". The vector values will be in distance "units"_units.html. diff --git a/doc/compute_com_molecule.html b/doc/compute_com_molecule.html index 3f6ac13cb8..957b3feca8 100644 --- a/doc/compute_com_molecule.html +++ b/doc/compute_com_molecule.html @@ -64,7 +64,7 @@ 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 +this section for an overview of LAMMPS output options.

    The array values are "intensive". The array values will be in diff --git a/doc/compute_com_molecule.txt b/doc/compute_com_molecule.txt index 670c9117a8..accfd389cf 100644 --- a/doc/compute_com_molecule.txt +++ b/doc/compute_com_molecule.txt @@ -61,7 +61,7 @@ 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#4_15 for an overview of LAMMPS +"this section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/compute_coord_atom.html b/doc/compute_coord_atom.html index 6ab22c03b3..57738b4f3d 100644 --- a/doc/compute_coord_atom.html +++ b/doc/compute_coord_atom.html @@ -46,7 +46,7 @@ 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 +this section for an overview of LAMMPS output options.

    The per-atom vector values will be a number >= 0.0, as explained diff --git a/doc/compute_coord_atom.txt b/doc/compute_coord_atom.txt index bd9c471a78..fc5f2c9000 100644 --- a/doc/compute_coord_atom.txt +++ b/doc/compute_coord_atom.txt @@ -43,7 +43,7 @@ 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#4_15 for an overview of LAMMPS +"this section"_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 diff --git a/doc/compute_damage_atom.html b/doc/compute_damage_atom.html index 4de3dc8956..b15291a14d 100644 --- a/doc/compute_damage_atom.html +++ b/doc/compute_damage_atom.html @@ -37,7 +37,7 @@ 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 +this section for an overview of LAMMPS output options.

    The per-atom vector values will be a number >= 0.0, as explained diff --git a/doc/compute_damage_atom.txt b/doc/compute_damage_atom.txt index 31a1e25bfc..830caa9334 100644 --- a/doc/compute_damage_atom.txt +++ b/doc/compute_damage_atom.txt @@ -34,7 +34,7 @@ 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 +"this section"_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 diff --git a/doc/compute_dihedral_local.html b/doc/compute_dihedral_local.html index a5a122cb7f..e1f9cf13b7 100644 --- a/doc/compute_dihedral_local.html +++ b/doc/compute_dihedral_local.html @@ -60,7 +60,7 @@ array is the number of dihedrals. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See this +uses local values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_dihedral_local.txt b/doc/compute_dihedral_local.txt index 405465a0e3..0bc32936f9 100644 --- a/doc/compute_dihedral_local.txt +++ b/doc/compute_dihedral_local.txt @@ -53,7 +53,7 @@ local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See "this -section"_Section_howto.html#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The output for {phi} will be in degrees. diff --git a/doc/compute_displace_atom.html b/doc/compute_displace_atom.html index e21919b5ee..79dae15622 100644 --- a/doc/compute_displace_atom.html +++ b/doc/compute_displace_atom.html @@ -76,8 +76,8 @@ 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 this section +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 9cd35c4a23..ecbdf22b38 100644 --- a/doc/compute_displace_atom.txt +++ b/doc/compute_displace_atom.txt @@ -73,8 +73,8 @@ 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#4_15 for an -overview of LAMMPS output options. +a compute as input. See "this section"_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 60317c200a..642fb57767 100644 --- a/doc/compute_erotate_asphere.html +++ b/doc/compute_erotate_asphere.html @@ -39,8 +39,8 @@ 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 this section 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 c71bee3f0d..607d9d4425 100644 --- a/doc/compute_erotate_asphere.txt +++ b/doc/compute_erotate_asphere.txt @@ -36,8 +36,8 @@ 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#4_15 for an overview of -LAMMPS output options. +input. See "this section"_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 9a1468eb34..d9e328364c 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 this section 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 21c016b70b..7e480a2812 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#4_15 for an overview of -LAMMPS output options. +input. See "this section"_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 81acdaf3ed..66a3d841c9 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 this section 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 99dfe148cb..2b84eafab2 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#4_15 for an overview of -LAMMPS output options. +input. See "this section"_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_group_group.html b/doc/compute_group_group.html index bb665ca6f7..bd1aacc412 100644 --- a/doc/compute_group_group.html +++ b/doc/compute_group_group.html @@ -44,7 +44,7 @@ quantity too frequently.

    This compute calculates a global scalar (the energy) and a global vector of length 3 (force), which can be accessed by indices 1-3. These values can be used by any command that uses global scalar or -vector values from a compute as input. See this +vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_group_group.txt b/doc/compute_group_group.txt index 5a77bcd561..cb49e7558b 100644 --- a/doc/compute_group_group.txt +++ b/doc/compute_group_group.txt @@ -42,7 +42,7 @@ This compute calculates a global scalar (the energy) and a global vector of length 3 (force), which can be accessed by indices 1-3. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. Both the scalar and vector values calculated by this compute are diff --git a/doc/compute_gyration.html b/doc/compute_gyration.html index 65fb731169..1d8b8389cd 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 this section 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 c3390ba5ac..867669d0a7 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#4_15 for an overview of -LAMMPS output options. +input. See "this section"_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_gyration_molecule.html b/doc/compute_gyration_molecule.html index b8ad07e64c..f74218009f 100644 --- a/doc/compute_gyration_molecule.html +++ b/doc/compute_gyration_molecule.html @@ -62,7 +62,7 @@ image command.

    This compute calculates a global vector of Rg values where the length of the vector = Nmolecules. These values can be used by any command -that uses global vector values from a compute as input. See this +that uses global vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_gyration_molecule.txt b/doc/compute_gyration_molecule.txt index 52abb883c5..375e109326 100644 --- a/doc/compute_gyration_molecule.txt +++ b/doc/compute_gyration_molecule.txt @@ -60,7 +60,7 @@ image"_set.html command. This compute calculates a global vector of Rg values where the length of the vector = Nmolecules. These values can be used by any command that uses global vector values from a compute as input. See "this -section"_Section_howto.html#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The vector values calculated by this compute are "intensive". The diff --git a/doc/compute_heat_flux.html b/doc/compute_heat_flux.html index 84f8b28351..b56ce96f33 100644 --- a/doc/compute_heat_flux.html +++ b/doc/compute_heat_flux.html @@ -99,7 +99,7 @@ result should be: average conductivity ~0.29 in W/mK.

    This compute calculates a global vector of length 6 (total heat flux vector, followed by conductive heat flux vector), which can be accessed by indices 1-6. These values can be used by any command that -uses global vector values from a compute as input. See this +uses global vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_heat_flux.txt b/doc/compute_heat_flux.txt index ef4907cdd3..2d9816a066 100644 --- a/doc/compute_heat_flux.txt +++ b/doc/compute_heat_flux.txt @@ -97,7 +97,7 @@ This compute calculates a global vector of length 6 (total heat flux vector, followed by conductive heat flux vector), which can be accessed by indices 1-6. These values can be used by any command that uses global vector values from a compute as input. See "this -section"_Section_howto.html#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The vector values calculated by this compute are "extensive", meaning diff --git a/doc/compute_improper_local.html b/doc/compute_improper_local.html index ceb67530a4..cf529f222d 100644 --- a/doc/compute_improper_local.html +++ b/doc/compute_improper_local.html @@ -60,7 +60,7 @@ array is the number of impropers. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See this +uses local values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_improper_local.txt b/doc/compute_improper_local.txt index 401e3b509d..c227cb2b85 100644 --- a/doc/compute_improper_local.txt +++ b/doc/compute_improper_local.txt @@ -53,7 +53,7 @@ local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See "this -section"_Section_howto.html#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The output for {chi} will be in degrees. diff --git a/doc/compute_ke.html b/doc/compute_ke.html index c974ab79bb..12769e0f55 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 this section 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 d9847cb506..003332c073 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#4_15 for an overview of -LAMMPS output options. +input. See "this section"_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 6ad15d64da..434718e6a6 100644 --- a/doc/compute_ke_atom.html +++ b/doc/compute_ke_atom.html @@ -37,7 +37,7 @@ 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 +this section 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 590ee3fae6..fd42651300 100644 --- a/doc/compute_ke_atom.txt +++ b/doc/compute_ke_atom.txt @@ -34,7 +34,7 @@ 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 +"this section"_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 6d4240ed3a..4bd6b6f957 100644 --- a/doc/compute_ke_atom_eff.html +++ b/doc/compute_ke_atom_eff.html @@ -62,7 +62,7 @@ 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 +this section 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 07019fe944..cb69fc5a86 100644 --- a/doc/compute_ke_atom_eff.txt +++ b/doc/compute_ke_atom_eff.txt @@ -59,7 +59,7 @@ 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#4_15 for an overview of LAMMPS +"this section"_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 f9c0831f9d..3b0d55b2df 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 this section 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 01bfb3f323..e5c0216db3 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#4_15 for an overview of -LAMMPS output options. +input. See "this section"_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_msd.html b/doc/compute_msd.html index fde408b9e4..7814701ffd 100644 --- a/doc/compute_msd.html +++ b/doc/compute_msd.html @@ -92,8 +92,9 @@ file.

    This compute calculates a global vector of length 4, which can be accessed by indices 1-4 by any command that uses global vector values -from a compute as input. See this section -for an overview of LAMMPS output options. +from a compute as input. See this +section for an overview of LAMMPS output +options.

    The vector values are "intensive". The vector values will be in distance^2 units. diff --git a/doc/compute_msd.txt b/doc/compute_msd.txt index 10bd9fecdc..e40a18b22f 100644 --- a/doc/compute_msd.txt +++ b/doc/compute_msd.txt @@ -84,8 +84,9 @@ file. This compute calculates a global vector of length 4, which can be accessed by indices 1-4 by any command that uses global vector values -from a compute as input. See "this section"_Section_howto.html#4_15 -for an overview of LAMMPS output options. +from a compute as input. See "this +section"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. The vector values are "intensive". The vector values will be in distance^2 "units"_units.html. diff --git a/doc/compute_msd_molecule.html b/doc/compute_msd_molecule.html index f00536e0d1..2f30e14385 100644 --- a/doc/compute_msd_molecule.html +++ b/doc/compute_msd_molecule.html @@ -81,7 +81,7 @@ file.

    This compute calculates a global array where the number of rows = Nmolecules and the number of columns = 4 for dx,dy,dz and the total displacement. These values can be accessed by any command that uses -global array values from a compute as input. See this +global array values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_msd_molecule.txt b/doc/compute_msd_molecule.txt index d411a49d06..2b8bd93cf2 100644 --- a/doc/compute_msd_molecule.txt +++ b/doc/compute_msd_molecule.txt @@ -79,7 +79,7 @@ This compute calculates a global array where the number of rows = Nmolecules and the number of columns = 4 for dx,dy,dz and the total displacement. These values can be accessed by any command that uses global array values from a compute as input. See "this -section"_Section_howto.html#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/compute_pair.html b/doc/compute_pair.html index b59204428f..b456d96ba6 100644 --- a/doc/compute_pair.html +++ b/doc/compute_pair.html @@ -62,8 +62,9 @@ are stored as a global vector by this compute. See the doc page for ecoul. If the pair style supports it, it also calculates a global vector of length >= 1, as determined by the pair style. 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. +from a compute as input. See this +section for an overview of LAMMPS output +options.

    The scalar and vector values calculated by this compute are "extensive". diff --git a/doc/compute_pair.txt b/doc/compute_pair.txt index c1144013da..d1662acfa5 100644 --- a/doc/compute_pair.txt +++ b/doc/compute_pair.txt @@ -59,8 +59,9 @@ This compute calculates a global scalar which is {epair} or {evdwl} or {ecoul}. If the pair style supports it, it also calculates a global vector of length >= 1, as determined by the pair style. 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#4_15 -for an overview of LAMMPS output options. +from a compute as input. See "this +section"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. The scalar and vector values calculated by this compute are "extensive". diff --git a/doc/compute_pair_local.html b/doc/compute_pair_local.html index f6bea11cea..49a9d3780d 100644 --- a/doc/compute_pair_local.html +++ b/doc/compute_pair_local.html @@ -80,7 +80,7 @@ array is the number of pairs. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See this +uses local values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_pair_local.txt b/doc/compute_pair_local.txt index 0659e80821..7f9f0cb4e9 100644 --- a/doc/compute_pair_local.txt +++ b/doc/compute_pair_local.txt @@ -73,7 +73,7 @@ local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See "this -section"_Section_howto.html#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The output for {dist} will be in distance "units"_units.html. The diff --git a/doc/compute_pe.html b/doc/compute_pe.html index 743c5690a4..f86c8d8bd7 100644 --- a/doc/compute_pe.html +++ b/doc/compute_pe.html @@ -83,8 +83,8 @@ 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 this section +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 d1b91c6249..17d0cc0e23 100644 --- a/doc/compute_pe.txt +++ b/doc/compute_pe.txt @@ -79,8 +79,8 @@ 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#4_15 for an -overview of LAMMPS output options. +a compute as input. See "this section"_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 31d0eef2d5..af5f158fc7 100644 --- a/doc/compute_pe_atom.html +++ b/doc/compute_pe_atom.html @@ -70,7 +70,7 @@ 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 +this section 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 e9d879aa1a..c71dceec48 100644 --- a/doc/compute_pe_atom.txt +++ b/doc/compute_pe_atom.txt @@ -67,7 +67,7 @@ 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#4_15 for an overview of LAMMPS +"this section"_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_pressure.html b/doc/compute_pressure.html index b0c24b74ef..95f7eeebc4 100644 --- a/doc/compute_pressure.html +++ b/doc/compute_pressure.html @@ -114,7 +114,7 @@ instructions on how to use the accelerated styles effectively.

    This compute calculates a global scalar (the pressure) and a global vector of length 6 (pressure tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar -or vector values from a compute as input. See this +or vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_pressure.txt b/doc/compute_pressure.txt index 23c616d6d0..c8dafd229f 100644 --- a/doc/compute_pressure.txt +++ b/doc/compute_pressure.txt @@ -111,7 +111,7 @@ This compute calculates a global scalar (the pressure) and a global vector of length 6 (pressure tensor), which can be accessed by indices 1-6. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar and vector values calculated by this compute are diff --git a/doc/compute_property_atom.html b/doc/compute_property_atom.html index b90cfafb02..6390d3e029 100644 --- a/doc/compute_property_atom.html +++ b/doc/compute_property_atom.html @@ -67,7 +67,7 @@ compute 1 all property/atom ix iy iz

    Define a computation that simply stores atom attributes for each atom in the group. This is useful so that the values can be used by other -output commands that take computes as +output commands that take computes as inputs. See for example, the compute reduce, fix ave/atom, fix ave/histo, fix ave/spatial, and atom-style @@ -100,7 +100,7 @@ on the number of input values. If a single input is specified, a per-atom vector is produced. If two or more inputs are specified, a per-atom array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses -per-atom values from a compute as input. See this +per-atom values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_property_atom.txt b/doc/compute_property_atom.txt index 60972bce46..bae2846f4e 100644 --- a/doc/compute_property_atom.txt +++ b/doc/compute_property_atom.txt @@ -60,7 +60,7 @@ compute 1 all property/atom ix iy iz :pre Define a computation that simply stores atom attributes for each atom in the group. This is useful so that the values can be used by other -"output commands"_Section_howto.html#4_15 that take computes as +"output commands"_Section_howto.html#howto_15 that take computes as inputs. See for example, the "compute reduce"_compute_reduce.html, "fix ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html, "fix ave/spatial"_fix_ave_spatial.html, and "atom-style @@ -94,7 +94,7 @@ per-atom vector is produced. If two or more inputs are specified, a per-atom array is produced where the number of columns = the number of inputs. The vector or array 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 +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The vector or array values will be in whatever "units"_units.html the diff --git a/doc/compute_property_local.html b/doc/compute_property_local.html index 546ff6ff54..f7c1a32b1c 100644 --- a/doc/compute_property_local.html +++ b/doc/compute_property_local.html @@ -49,9 +49,9 @@ compute 1 all property/local atype aatom2

    Description:

    Define a computation that stores the specified attributes as local -data so it can be accessed by other output -commands. If the input attributes refer to -bond information, then the number of datums generated, aggregated +data so it can be accessed by other output +commands. If the input attributes refer +to bond information, then the number of datums generated, aggregated across all processors, equals the number of bonds in the system. Ditto for pairs, angles, etc.

    @@ -119,7 +119,7 @@ the array is the number of bonds, angles, etc. If a single input is specified, a local vector is produced. If two or more inputs are specified, a local array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command -that uses local values from a compute as input. See this +that uses local values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_property_local.txt b/doc/compute_property_local.txt index 1f3726b43b..33da51c08e 100644 --- a/doc/compute_property_local.txt +++ b/doc/compute_property_local.txt @@ -43,8 +43,8 @@ compute 1 all property/local atype aatom2 :pre Define a computation that stores the specified attributes as local data so it can be accessed by other "output -commands"_Section_howto.html#4_15. If the input attributes refer to -bond information, then the number of datums generated, aggregated +commands"_Section_howto.html#howto_15. If the input attributes refer +to bond information, then the number of datums generated, aggregated across all processors, equals the number of bonds in the system. Ditto for pairs, angles, etc. @@ -113,7 +113,7 @@ specified, a local vector is produced. If two or more inputs are specified, a local array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses local values from a compute as input. See "this -section"_Section_howto.html#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The vector or array values will be integers that correspond to the diff --git a/doc/compute_property_molecule.html b/doc/compute_property_molecule.html index fdb07af960..55cc4955a3 100644 --- a/doc/compute_property_molecule.html +++ b/doc/compute_property_molecule.html @@ -34,9 +34,9 @@

    Description:

    Define a computation that stores the specified attributes as global -data so it can be accessed by other output -commands and used in conjunction with other -commands that generate per-molecule data, such as compute +data so it can be accessed by other output +commands and used in conjunction with +other commands that generate per-molecule data, such as compute com/molecule and compute msd/molecule.

    @@ -61,7 +61,7 @@ rows in the array is the number of molecules. If a single input is specified, a global vector is produced. If two or more inputs are specified, a global array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any -command that uses global values from a compute as input. See this +command that uses global values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_property_molecule.txt b/doc/compute_property_molecule.txt index 540dab079c..c2a4cb0d8e 100644 --- a/doc/compute_property_molecule.txt +++ b/doc/compute_property_molecule.txt @@ -28,8 +28,8 @@ compute 1 all property/molecule mol :pre Define a computation that stores the specified attributes as global data so it can be accessed by other "output -commands"_Section_howto.html#4_15 and used in conjunction with other -commands that generate per-molecule data, such as "compute +commands"_Section_howto.html#howto_15 and used in conjunction with +other commands that generate per-molecule data, such as "compute com/molecule"_compute_com_molecule.html and "compute msd/molecule"_compute_msd_molecule.html. @@ -55,7 +55,7 @@ specified, a global vector is produced. If two or more inputs are specified, a global array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses global values from a compute as input. See "this -section"_Section_howto.html#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The vector or array values will be integers that correspond to the diff --git a/doc/compute_rdf.html b/doc/compute_rdf.html index dd93bfd8f2..ae66e375bc 100644 --- a/doc/compute_rdf.html +++ b/doc/compute_rdf.html @@ -104,7 +104,7 @@ 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 +this section 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 a4ddf137d7..83e835ff3c 100644 --- a/doc/compute_rdf.txt +++ b/doc/compute_rdf.txt @@ -101,7 +101,7 @@ 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#4_15 for an overview of LAMMPS +"this section"_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 d0f6b2505b..f5533307e5 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 this section 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 043e79fd59..135f83eefe 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#4_15 for an -overview of LAMMPS output options. +compute as input. See "this section"_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_slice.html b/doc/compute_slice.html index 0519c5be15..a48710c249 100644 --- a/doc/compute_slice.html +++ b/doc/compute_slice.html @@ -94,7 +94,7 @@ specified or a global array with N columns where N is the number of inputs. The length of the vector or the number of rows in the array is equal to the number of values extracted from each input vector. These values can be used by any command that uses global vector or -array values from a compute as input. See this +array values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_slice.txt b/doc/compute_slice.txt index 14e5e42f8a..fea181dd2d 100644 --- a/doc/compute_slice.txt +++ b/doc/compute_slice.txt @@ -85,7 +85,7 @@ inputs. The length of the vector or the number of rows in the array is equal to the number of values extracted from each input vector. These values can be used by any command that uses global vector or array values from a compute as input. See "this -section"_Section_howto.html#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The vector or array values calculated by this compute are simply diff --git a/doc/compute_stress_atom.html b/doc/compute_stress_atom.html index c85d572fce..f39d75300f 100644 --- a/doc/compute_stress_atom.html +++ b/doc/compute_stress_atom.html @@ -102,8 +102,8 @@ 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 this section +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 d055334842..f8d073397f 100644 --- a/doc/compute_stress_atom.txt +++ b/doc/compute_stress_atom.txt @@ -99,8 +99,8 @@ 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#4_15 for an -overview of LAMMPS output options. +a compute as input. See "this section"_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_temp.html b/doc/compute_temp.html index 93a62101c3..d93a945e14 100644 --- a/doc/compute_temp.html +++ b/doc/compute_temp.html @@ -62,8 +62,8 @@ LAMMPS starts up, as if this command were in the input script:

    See the "thermo_style" command for more details.

    -

    See this howto section of the manual for a -discussion of different ways to compute temperature and perform +

    See this howto section of the manual for +a discussion of different ways to compute temperature and perform thermostatting.

    @@ -94,7 +94,7 @@ instructions on how to use the accelerated styles effectively.

    This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See this +vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_temp.txt b/doc/compute_temp.txt index b651824ff0..3ead16acaa 100644 --- a/doc/compute_temp.txt +++ b/doc/compute_temp.txt @@ -58,8 +58,8 @@ compute thermo_temp all temp :pre See the "thermo_style" command for more details. -See "this howto section"_Section_howto.html#4_16 of the manual for a -discussion of different ways to compute temperature and perform +See "this howto section"_Section_howto.html#howto_16 of the manual for +a discussion of different ways to compute temperature and perform thermostatting. :line @@ -91,7 +91,7 @@ This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/compute_temp_asphere.html b/doc/compute_temp_asphere.html index 52de510468..64815209b2 100644 --- a/doc/compute_temp_asphere.html +++ b/doc/compute_temp_asphere.html @@ -96,8 +96,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the extra option of the compute_modify command.

    -

    See this howto section of the manual for a -discussion of different ways to compute temperature and perform +

    See this howto section of the manual for +a discussion of different ways to compute temperature and perform thermostatting.

    @@ -125,7 +125,7 @@ rotational degrees of freedom.

    This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See this +vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_temp_asphere.txt b/doc/compute_temp_asphere.txt index d4de986da5..3be406ffb0 100755 --- a/doc/compute_temp_asphere.txt +++ b/doc/compute_temp_asphere.txt @@ -88,8 +88,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#4_16 of the manual for a -discussion of different ways to compute temperature and perform +See "this howto section"_Section_howto.html#howto_16 of the manual for +a discussion of different ways to compute temperature and perform thermostatting. :line @@ -118,7 +118,7 @@ This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/compute_temp_com.html b/doc/compute_temp_com.html index d55c85a074..5635c606d3 100644 --- a/doc/compute_temp_com.html +++ b/doc/compute_temp_com.html @@ -68,8 +68,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the extra option of the compute_modify command.

    -

    See this howto section of the manual for a -discussion of different ways to compute temperature and perform +

    See this howto section of the manual for +a discussion of different ways to compute temperature and perform thermostatting.

    Output info: @@ -77,7 +77,7 @@ thermostatting.

    This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See this +vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_temp_com.txt b/doc/compute_temp_com.txt index 80cc4ea737..c7cc5ec4e2 100644 --- a/doc/compute_temp_com.txt +++ b/doc/compute_temp_com.txt @@ -65,8 +65,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#4_16 of the manual for a -discussion of different ways to compute temperature and perform +See "this howto section"_Section_howto.html#howto_16 of the manual for +a discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -75,7 +75,7 @@ This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/compute_temp_deform.html b/doc/compute_temp_deform.html index 31ba8d6776..def9a12187 100644 --- a/doc/compute_temp_deform.html +++ b/doc/compute_temp_deform.html @@ -92,8 +92,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the extra option of the compute_modify command.

    -

    See this howto section of the manual for a -discussion of different ways to compute temperature and perform +

    See this howto section of the manual for +a discussion of different ways to compute temperature and perform thermostatting.

    Output info: @@ -101,7 +101,7 @@ thermostatting.

    This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See this +vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_temp_deform.txt b/doc/compute_temp_deform.txt index 26703f1d02..02b7ca3c22 100644 --- a/doc/compute_temp_deform.txt +++ b/doc/compute_temp_deform.txt @@ -89,8 +89,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#4_16 of the manual for a -discussion of different ways to compute temperature and perform +See "this howto section"_Section_howto.html#howto_16 of the manual for +a discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -99,7 +99,7 @@ This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/compute_temp_deform_eff.html b/doc/compute_temp_deform_eff.html index 7e2b362c48..d366492193 100644 --- a/doc/compute_temp_deform_eff.html +++ b/doc/compute_temp_deform_eff.html @@ -51,7 +51,7 @@ component of the electrons is not affected.

    This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See this +vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_temp_deform_eff.txt b/doc/compute_temp_deform_eff.txt index 9d6b2d5b6b..3a0497e5bf 100644 --- a/doc/compute_temp_deform_eff.txt +++ b/doc/compute_temp_deform_eff.txt @@ -49,7 +49,7 @@ This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/compute_temp_eff.html b/doc/compute_temp_eff.html index 4cdc555753..bdb8a4ee77 100644 --- a/doc/compute_temp_eff.html +++ b/doc/compute_temp_eff.html @@ -72,8 +72,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the extra option of the compute_modify command.

    -

    See this howto section of the manual for a -discussion of different ways to compute temperature and perform +

    See this howto section of the manual for +a discussion of different ways to compute temperature and perform thermostatting.

    Output info: diff --git a/doc/compute_temp_eff.txt b/doc/compute_temp_eff.txt index dbccaa9424..a83ee8b61c 100644 --- a/doc/compute_temp_eff.txt +++ b/doc/compute_temp_eff.txt @@ -69,8 +69,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#4_16 of the manual for a -discussion of different ways to compute temperature and perform +See "this howto section"_Section_howto.html#howto_16 of the manual for +a discussion of different ways to compute temperature and perform thermostatting. [Output info:] diff --git a/doc/compute_temp_partial.html b/doc/compute_temp_partial.html index 2a2bed5d4a..62529fcfb1 100644 --- a/doc/compute_temp_partial.html +++ b/doc/compute_temp_partial.html @@ -70,8 +70,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the extra option of the compute_modify command.

    -

    See this howto section of the manual for a -discussion of different ways to compute temperature and perform +

    See this howto section of the manual for +a discussion of different ways to compute temperature and perform thermostatting.

    @@ -102,7 +102,7 @@ instructions on how to use the accelerated styles effectively.

    This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See this +vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_temp_partial.txt b/doc/compute_temp_partial.txt index b734593e41..1d81bd29c4 100644 --- a/doc/compute_temp_partial.txt +++ b/doc/compute_temp_partial.txt @@ -66,8 +66,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#4_16 of the manual for a -discussion of different ways to compute temperature and perform +See "this howto section"_Section_howto.html#howto_16 of the manual for +a discussion of different ways to compute temperature and perform thermostatting. :line @@ -99,7 +99,7 @@ This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/compute_temp_profile.html b/doc/compute_temp_profile.html index 242674a005..52a9f67dfd 100644 --- a/doc/compute_temp_profile.html +++ b/doc/compute_temp_profile.html @@ -106,8 +106,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the extra option of the compute_modify command.

    -

    See this howto section of the manual for a -discussion of different ways to compute temperature and perform +

    See this howto section of the manual for +a discussion of different ways to compute temperature and perform thermostatting. Using this compute in conjunction with a thermostatting fix, as explained there, will effectively implement a profile-unbiased thermostat (PUT), as described in (Evans). @@ -117,7 +117,7 @@ profile-unbiased thermostat (PUT), as described in (Evans)This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See this +vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_temp_profile.txt b/doc/compute_temp_profile.txt index bf2d921287..8eaae69483 100644 --- a/doc/compute_temp_profile.txt +++ b/doc/compute_temp_profile.txt @@ -98,8 +98,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#4_16 of the manual for a -discussion of different ways to compute temperature and perform +See "this howto section"_Section_howto.html#howto_16 of the manual for +a discussion of different ways to compute temperature and perform thermostatting. Using this compute in conjunction with a thermostatting fix, as explained there, will effectively implement a profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans. @@ -110,7 +110,7 @@ This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/compute_temp_ramp.html b/doc/compute_temp_ramp.html index fa8b6b0ecf..686ad9cd61 100644 --- a/doc/compute_temp_ramp.html +++ b/doc/compute_temp_ramp.html @@ -87,8 +87,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the extra option of the compute_modify command.

    -

    See this howto section of the manual for a -discussion of different ways to compute temperature and perform +

    See this howto section of the manual for +a discussion of different ways to compute temperature and perform thermostatting.

    Output info: @@ -96,7 +96,7 @@ thermostatting.

    This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See this +vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_temp_ramp.txt b/doc/compute_temp_ramp.txt index 4f1ccc5963..bc9283469c 100644 --- a/doc/compute_temp_ramp.txt +++ b/doc/compute_temp_ramp.txt @@ -83,8 +83,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#4_16 of the manual for a -discussion of different ways to compute temperature and perform +See "this howto section"_Section_howto.html#howto_16 of the manual for +a discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -93,7 +93,7 @@ This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/compute_temp_region.html b/doc/compute_temp_region.html index 260dd408b4..62f57cacac 100644 --- a/doc/compute_temp_region.html +++ b/doc/compute_temp_region.html @@ -79,8 +79,8 @@ constrain molecular motion, such as fix shake and degrees-of-freedom can be altered using the extra option of the compute_modify command.

    -

    See this howto section of the manual for a -discussion of different ways to compute temperature and perform +

    See this howto section of the manual for +a discussion of different ways to compute temperature and perform thermostatting.

    Output info: @@ -88,7 +88,7 @@ thermostatting.

    This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See this +vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_temp_region.txt b/doc/compute_temp_region.txt index 0733eb7a41..c617eeb7a6 100644 --- a/doc/compute_temp_region.txt +++ b/doc/compute_temp_region.txt @@ -76,8 +76,8 @@ constrain molecular motion, such as "fix shake"_fix_shake.html and degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#4_16 of the manual for a -discussion of different ways to compute temperature and perform +See "this howto section"_Section_howto.html#howto_16 of the manual for +a discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -86,7 +86,7 @@ This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/compute_temp_region_eff.html b/doc/compute_temp_region_eff.html index e88f15d668..6bb12a428b 100644 --- a/doc/compute_temp_region_eff.html +++ b/doc/compute_temp_region_eff.html @@ -42,7 +42,7 @@ temp/eff command.

    This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See this +vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_temp_region_eff.txt b/doc/compute_temp_region_eff.txt index 5194077685..7231f98622 100644 --- a/doc/compute_temp_region_eff.txt +++ b/doc/compute_temp_region_eff.txt @@ -40,7 +40,7 @@ This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/compute_temp_rotate.html b/doc/compute_temp_rotate.html index 2bb40f52b1..389fa20ce2 100644 --- a/doc/compute_temp_rotate.html +++ b/doc/compute_temp_rotate.html @@ -67,8 +67,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the extra option of the compute_modify command.

    -

    See this howto section of the manual for a -discussion of different ways to compute temperature and perform +

    See this howto section of the manual for +a discussion of different ways to compute temperature and perform thermostatting.

    Output info: @@ -76,7 +76,7 @@ thermostatting.

    This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See this +vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_temp_rotate.txt b/doc/compute_temp_rotate.txt index e7b2d49313..13acc2a976 100644 --- a/doc/compute_temp_rotate.txt +++ b/doc/compute_temp_rotate.txt @@ -64,8 +64,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#4_16 of the manual for a -discussion of different ways to compute temperature and perform +See "this howto section"_Section_howto.html#howto_16 of the manual for +a discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -74,7 +74,7 @@ This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/compute_temp_sphere.html b/doc/compute_temp_sphere.html index 23e18d16b5..923dab5045 100644 --- a/doc/compute_temp_sphere.html +++ b/doc/compute_temp_sphere.html @@ -87,8 +87,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the extra option of the compute_modify command.

    -

    See this howto section of the manual for a -discussion of different ways to compute temperature and perform +

    See this howto section of the manual for +a discussion of different ways to compute temperature and perform thermostatting.

    @@ -116,7 +116,7 @@ rotational degrees of freedom.

    This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See this +vector values from a compute as input. See this section for an overview of LAMMPS output options.

    diff --git a/doc/compute_temp_sphere.txt b/doc/compute_temp_sphere.txt index 16d1fcc761..24885e2378 100755 --- a/doc/compute_temp_sphere.txt +++ b/doc/compute_temp_sphere.txt @@ -79,8 +79,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#4_16 of the manual for a -discussion of different ways to compute temperature and perform +See "this howto section"_Section_howto.html#howto_16 of the manual for +a discussion of different ways to compute temperature and perform thermostatting. :line @@ -109,7 +109,7 @@ This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. 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#4_15 for an overview of LAMMPS output +section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/compute_ti.html b/doc/compute_ti.html index 404f33e821..4e997fb1c5 100644 --- a/doc/compute_ti.html +++ b/doc/compute_ti.html @@ -102,8 +102,8 @@ 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 this section +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 39078cbd28..1d8041ae97 100644 --- a/doc/compute_ti.txt +++ b/doc/compute_ti.txt @@ -94,8 +94,8 @@ 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#4_15 for an -overview of LAMMPS output options. +a compute as input. See "this section"_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 a4c2a918b0..974af9ee35 100644 --- a/doc/create_box.html +++ b/doc/create_box.html @@ -55,7 +55,7 @@ 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 +

    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 triclinic representations. diff --git a/doc/create_box.txt b/doc/create_box.txt index 3576b815fc..247486503a 100644 --- a/doc/create_box.txt +++ b/doc/create_box.txt @@ -52,7 +52,7 @@ 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#4_12 of the doc pages for a +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 triclinic representations. diff --git a/doc/dihedral_coeff.html b/doc/dihedral_coeff.html index 26021e3a64..9159ee5b21 100644 --- a/doc/dihedral_coeff.html +++ b/doc/dihedral_coeff.html @@ -81,7 +81,7 @@ specified by the associated dihedral_coeff c

    There are also additional dihedral styles submitted by users which are included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the dihedral section of this +the individual styles are given in the dihedral section of this page.

    diff --git a/doc/dihedral_coeff.txt b/doc/dihedral_coeff.txt index e66ac90b75..21228218f2 100644 --- a/doc/dihedral_coeff.txt +++ b/doc/dihedral_coeff.txt @@ -79,7 +79,7 @@ specified by the associated "dihedral_coeff"_dihedral_coeff.html command: There are also additional dihedral styles submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the dihedral section of "this -page"_Section_commands.html#3_5. +page"_Section_commands.html#cmd_5. :line diff --git a/doc/dihedral_style.html b/doc/dihedral_style.html index 494bf400d4..654f0f81e4 100644 --- a/doc/dihedral_style.html +++ b/doc/dihedral_style.html @@ -88,7 +88,7 @@ specified by the associated dihedral_coeff c

    There are also additional dihedral styles submitted by users which are included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the dihedral section of this +the individual styles are given in the dihedral section of this page.

    diff --git a/doc/dihedral_style.txt b/doc/dihedral_style.txt index 12e83876c3..82c2123de7 100644 --- a/doc/dihedral_style.txt +++ b/doc/dihedral_style.txt @@ -87,7 +87,7 @@ specified by the associated "dihedral_coeff"_dihedral_coeff.html command: There are also additional dihedral styles submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the dihedral section of "this -page"_Section_commands.html#3_5. +page"_Section_commands.html#cmd_5. :line diff --git a/doc/dump.html b/doc/dump.html index 98429d1baf..7e599ea3cb 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -183,7 +183,7 @@ This bounding box is convenient for many visualization programs. The meaning of the 6 character flags for "xx yy zz" is the same as above.

    Note that the first two numbers on each line are now xlo_bound instead -of xlo, etc, since they repesent a bounding box. See this +of xlo, etc, since they repesent a bounding box. See this section of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, simple formulas for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are diff --git a/doc/dump.txt b/doc/dump.txt index a5e32b4fdb..96b3126b4a 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -173,7 +173,7 @@ meaning of the 6 character flags for "xx yy zz" is the same as above. Note that the first two numbers on each line are now xlo_bound instead of xlo, etc, since they repesent a bounding box. See "this -section"_Section_howto.html#4_12 of the doc pages for a geometric +section"_Section_howto.html#howto_12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, simple formulas for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are calculated from the triclinic parameters, and how to transform those diff --git a/doc/fix.html b/doc/fix.html index 94e558e8b5..239e0ae195 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -138,7 +138,7 @@ variable. reduce command, or histogrammed by the fix ave/histo command. -

    See this howto section for a summary of +

    See this howto section for a summary of various LAMMPS output options, many of which involve fixes.

    The results of fixes that calculate global quantities can be either @@ -242,13 +242,13 @@ list of fix styles available in LAMMPS:

    There are also additional fix styles submitted by users which are included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the fix section of this +the individual styles are given in the fix section of this page.

    There are also additional accelerated fix styles included in the LAMMPS distribution for faster performance on CPUs and GPUs. The list of these with links to the individual styles are given in the pair -section of this page. +section of this page.

    Restrictions:

    diff --git a/doc/fix.txt b/doc/fix.txt index 07ca6cddf4..23a478c496 100644 --- a/doc/fix.txt +++ b/doc/fix.txt @@ -133,7 +133,7 @@ Local values can be reduced by the "compute reduce"_compute_reduce.html command, or histogrammed by the "fix ave/histo"_fix_ave_histo.html command. :l,ule -See this "howto section"_Section_howto.html#4_15 for a summary of +See this "howto section"_Section_howto.html#howto_15 for a summary of various LAMMPS output options, many of which involve fixes. The results of fixes that calculate global quantities can be either @@ -250,12 +250,12 @@ list of fix styles available in LAMMPS: There are also additional fix styles submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the fix section of "this -page"_Section_commands.html#3_5. +page"_Section_commands.html#cmd_5. There are also additional accelerated fix styles included in the LAMMPS distribution for faster performance on CPUs and GPUs. The list of these with links to the individual styles are given in the pair -section of "this page"_Section_commands.html#3_5. +section of "this page"_Section_commands.html#cmd_5. [Restrictions:] diff --git a/doc/fix_adapt.html b/doc/fix_adapt.html index 810a1c26d2..3d6c1a3430 100644 --- a/doc/fix_adapt.html +++ b/doc/fix_adapt.html @@ -233,9 +233,9 @@ fix 1 center adapt 10 atom diameter v_size

    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: none diff --git a/doc/fix_adapt.txt b/doc/fix_adapt.txt index c9f625d054..04e383f2cf 100644 --- a/doc/fix_adapt.txt +++ b/doc/fix_adapt.txt @@ -219,8 +219,8 @@ 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:] none diff --git a/doc/fix_addforce.html b/doc/fix_addforce.html index 7e77ed82bc..2e54554184 100644 --- a/doc/fix_addforce.html +++ b/doc/fix_addforce.html @@ -145,11 +145,11 @@ decrease in potential energy when atoms move in the direction of the added force.

    This fix computes a global scalar and a global 3-vector of forces, -which can be accessed by various output -commands. The scalar is the potential energy -discussed above. The vector is the total force on the group of atoms -before the forces on individual atoms are changed by the fix. The -scalar and vector values calculated by this fix are "extensive". +which can be accessed by various output +commands. The scalar is the potential +energy discussed above. The vector is the total force on the group of +atoms before the forces on individual atoms are changed by the fix. +The scalar and vector values calculated by this fix are "extensive".

    No parameter of this fix can be used with the start/stop keywords of the run command. diff --git a/doc/fix_addforce.txt b/doc/fix_addforce.txt index 9a75134d67..3dc0b740bb 100644 --- a/doc/fix_addforce.txt +++ b/doc/fix_addforce.txt @@ -135,10 +135,10 @@ added force. This fix computes a global scalar and a global 3-vector of forces, which can be accessed by various "output -commands"_Section_howto.html#4_15. The scalar is the potential energy -discussed above. The vector is the total force on the group of atoms -before the forces on individual atoms are changed by the fix. The -scalar and vector values calculated by this fix are "extensive". +commands"_Section_howto.html#howto_15. The scalar is the potential +energy discussed above. The vector is the total force on the group of +atoms before the forces on individual atoms are changed by the fix. +The scalar and vector values calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/fix_addtorque.html b/doc/fix_addtorque.html index c4c712817a..5db501ff5f 100644 --- a/doc/fix_addtorque.html +++ b/doc/fix_addtorque.html @@ -71,12 +71,12 @@ forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added forces.

    -

    This fix computes a global scalar and a global 3-vector, -which can be accessed by various output -commands. The scalar is the potential energy -discussed above. The vector is the total torque on the group of atoms -before the forces on individual atoms are changed by the fix. The -scalar and vector values calculated by this fix are "extensive". +

    This fix computes a global scalar and a global 3-vector, which can be +accessed by various output commands. +The scalar is the potential energy discussed above. The vector is the +total torque on the group of atoms before the forces on individual +atoms are changed by the fix. The scalar and vector values calculated +by this fix are "extensive".

    No parameter of this fix can be used with the start/stop keywords of the run command. diff --git a/doc/fix_addtorque.txt b/doc/fix_addtorque.txt index ecf25242a7..9e8b82f732 100644 --- a/doc/fix_addtorque.txt +++ b/doc/fix_addtorque.txt @@ -64,12 +64,12 @@ forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added forces. -This fix computes a global scalar and a global 3-vector, -which can be accessed by various "output -commands"_Section_howto.html#4_15. The scalar is the potential energy -discussed above. The vector is the total torque on the group of atoms -before the forces on individual atoms are changed by the fix. The -scalar and vector values calculated by this fix are "extensive". +This fix computes a global scalar and a global 3-vector, which can be +accessed by various "output commands"_Section_howto.html#howto_15. +The scalar is the potential energy discussed above. The vector is the +total torque on the group of atoms before the forces on individual +atoms are changed by the fix. The scalar and vector values calculated +by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/fix_atc.html b/doc/fix_atc.html index d2f5da1ad6..7e37dd1988 100644 --- a/doc/fix_atc.html +++ b/doc/fix_atc.html @@ -144,8 +144,8 @@ distribution. Individual doc pages are listed and linked to below. files. The fix_modify options relevant to this fix are listed below. No global scalar or vector 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 +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.

    diff --git a/doc/fix_atc.txt b/doc/fix_atc.txt index 203687fe83..d7ad329dde 100644 --- a/doc/fix_atc.txt +++ b/doc/fix_atc.txt @@ -137,8 +137,8 @@ No information about this fix is written to "binary restart files"_restart.html. The "fix_modify"_fix_modify.html options relevant to this fix are listed below. 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. No parameter of this fix -can be used with the {start/stop} keywords of the "run"_run.html +"output 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/fix_ave_atom.html b/doc/fix_ave_atom.html index d8a0cbc748..ea961b1fd1 100644 --- a/doc/fix_ave_atom.html +++ b/doc/fix_ave_atom.html @@ -46,7 +46,7 @@ fix 1 all ave/atom 10 20 1000 c_my_stress1

    Use one or more per-atom vectors as inputs every few timesteps, and average them atom by atom over longer timescales. The resulting -per-atom averages can be used by other output +per-atom averages can be used by other output commands such as the fix ave/spatial or dump custom commands.

    @@ -129,11 +129,11 @@ per-atom quantities to time average.

    No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global scalar or vector quantities are -stored by this fix for access by various output +stored by this fix for access by various output commands.

    This fix produces a per-atom vector or array which can be accessed by -various output commands. A vector is +various output commands. A vector is produced if only a single quantity is averaged by this fix. If two or more quantities are averaged, then an array of values is produced. The per-atom values can only be accessed on timesteps that are diff --git a/doc/fix_ave_atom.txt b/doc/fix_ave_atom.txt index 095a8b4c19..67810b4b18 100644 --- a/doc/fix_ave_atom.txt +++ b/doc/fix_ave_atom.txt @@ -37,7 +37,7 @@ fix 1 all ave/atom 10 20 1000 c_my_stress[1] :pre Use one or more per-atom vectors as inputs every few timesteps, and average them atom by atom over longer timescales. The resulting per-atom averages can be used by other "output -commands"_Section_howto.html#4_15 such as the "fix +commands"_Section_howto.html#howto_15 such as the "fix ave/spatial"_fix_ave_spatial.html or "dump custom"_dump.html commands. The group specified with the command means only atoms within the group @@ -120,10 +120,10 @@ 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 scalar or vector quantities are stored by this fix for access by various "output -commands"_Section_howto.html#4_15. +commands"_Section_howto.html#howto_15. This fix produces a per-atom vector or array which can be accessed by -various "output commands"_Section_howto.html#4_15. A vector is +various "output commands"_Section_howto.html#howto_15. A vector is produced if only a single quantity is averaged by this fix. If two or more quantities are averaged, then an array of values is produced. The per-atom values can only be accessed on timesteps that are diff --git a/doc/fix_ave_correlate.html b/doc/fix_ave_correlate.html index 40e2fb8916..76e1c2edde 100644 --- a/doc/fix_ave_correlate.html +++ b/doc/fix_ave_correlate.html @@ -77,7 +77,7 @@ fix 1 all ave/correlate 1 50 10000 & calculate time correlations bewteen them at varying time intervals, and average the correlation data over longer timescales. The resulting correlation values can be time integrated by -variables or used by other output +variables or used by other output commands such as thermo_style custom, and can also be written to a file.

    @@ -287,7 +287,7 @@ files. None of the fix_modify options are relevant to this fix.

    This fix computes a global array of values which can be accessed by -various output commands. The values can +various output commands. The values can only be accessed on timesteps that are multiples of Nfreq since that is when averaging is performed. The global array has # of rows = Nrepeat and # of columns = Npair+2. The first column has the time diff --git a/doc/fix_ave_correlate.txt b/doc/fix_ave_correlate.txt index ce20deead6..cf792ee112 100644 --- a/doc/fix_ave_correlate.txt +++ b/doc/fix_ave_correlate.txt @@ -65,7 +65,7 @@ calculate time correlations bewteen them at varying time intervals, and average the correlation data over longer timescales. The resulting correlation values can be time integrated by "variables"_variable.html or used by other "output -commands"_Section_howto.html#4_15 such as "thermo_style +commands"_Section_howto.html#howto_15 such as "thermo_style custom"_thermo_style.html, and can also be written to a file. The group specified with this command is ignored. However, note that @@ -274,7 +274,7 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global array of values which can be accessed by -various "output commands"_Section_howto.html#4_15. The values can +various "output commands"_Section_howto.html#howto_15. The values can only be accessed on timesteps that are multiples of {Nfreq} since that is when averaging is performed. The global array has # of rows = {Nrepeat} and # of columns = Npair+2. The first column has the time diff --git a/doc/fix_ave_histo.html b/doc/fix_ave_histo.html index 6330a34e66..ee99ee5236 100644 --- a/doc/fix_ave_histo.html +++ b/doc/fix_ave_histo.html @@ -78,8 +78,9 @@ fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyo

    Use one or more values as inputs every few timesteps, histogram them, and average the histogram over longer timescales. The resulting -histogram can be used by other output -commands, and can also be written to a file. +histogram can be used by other output +commands, and can also be written to a +file.

    The group specified with this command is ignored for global and local input values. For per-atom input values, only atoms in the group @@ -290,10 +291,10 @@ files. None of the fix_modify options are relevant to this fix.

    This fix produces a global vector and global array which can be -accessed by various output commands. The -values can only be accessed on timesteps that are multiples of Nfreq -since that is when a histogram is generated. -The global vector has 4 values: +accessed by various output commands. +The values can only be accessed on timesteps that are multiples of +Nfreq since that is when a histogram is generated. The global +vector has 4 values:

    There are also additional improper styles submitted by users which are included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the improper section of this +the individual styles are given in the improper section of this page.

    diff --git a/doc/improper_style.txt b/doc/improper_style.txt index 9da54b0ed5..da255312e4 100644 --- a/doc/improper_style.txt +++ b/doc/improper_style.txt @@ -69,7 +69,7 @@ specified by the associated "improper_coeff"_improper_coeff.html command: There are also additional improper styles submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the improper section of "this -page"_Section_commands.html#3_5. +page"_Section_commands.html#cmd_5. :line diff --git a/doc/improper_umbrella.html b/doc/improper_umbrella.html index fc86a9caca..3ccfd10f18 100644 --- a/doc/improper_umbrella.html +++ b/doc/improper_umbrella.html @@ -24,7 +24,7 @@ improper_coeff 1 100.0 180.0

    The umbrella improper style uses the following potential, which is commonly referred to as a classic inversion and used in the -DREIDING force field: +DREIDING force field:

    diff --git a/doc/improper_umbrella.txt b/doc/improper_umbrella.txt index f4905ab392..232c46f68f 100644 --- a/doc/improper_umbrella.txt +++ b/doc/improper_umbrella.txt @@ -21,7 +21,7 @@ improper_coeff 1 100.0 180.0 :pre The {umbrella} improper style uses the following potential, which is commonly referred to as a classic inversion and used in the -"DREIDING"_Section_howto.html#4_4 force field: +"DREIDING"_Section_howto.html#howto_4 force field: :c,image(Eqs/improper_umbrella.jpg) diff --git a/doc/neb.html b/doc/neb.html index a165e82119..75f02c4b47 100644 --- a/doc/neb.html +++ b/doc/neb.html @@ -47,8 +47,9 @@ 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. +would see with one or more physical processors per replica. See this +section of the manual for further +discussion.

    NOTE: The current NEB implementation in LAMMPS restricts you to having exactly one processor per replica. diff --git a/doc/neb.txt b/doc/neb.txt index 3caba8cf0f..993ecd0b0d 100644 --- a/doc/neb.txt +++ b/doc/neb.txt @@ -45,7 +45,8 @@ 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#4_5 of the manual for further discussion. +section"_Section_howto.html#howto_5 of the manual for further +discussion. NOTE: The current NEB implementation in LAMMPS restricts you to having exactly one processor per replica. diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html index 7debbbd72e..fb5ffd893a 100644 --- a/doc/pair_coeff.html +++ b/doc/pair_coeff.html @@ -147,13 +147,13 @@ the pair_style command, and coefficients specified by the associated

    There are also additional pair styles submitted by users which are included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the pair section of this +the individual styles are given in the pair section of this page.

    There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs and GPUs. The list of these with links to the individual styles are given in the pair -section of this page. +section of this page.

    diff --git a/doc/pair_coeff.txt b/doc/pair_coeff.txt index 887ef456d5..5a6c00a247 100644 --- a/doc/pair_coeff.txt +++ b/doc/pair_coeff.txt @@ -145,12 +145,12 @@ the pair_style command, and coefficients specified by the associated There are also additional pair styles submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the pair section of "this -page"_Section_commands.html#3_5. +page"_Section_commands.html#cmd_5. There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs and GPUs. The list of these with links to the individual styles are given in the pair -section of "this page"_Section_commands.html#3_5. +section of "this page"_Section_commands.html#cmd_5. :line diff --git a/doc/pair_hbond_dreiding.html b/doc/pair_hbond_dreiding.html index 8c6358faa7..624b0c22b8 100644 --- a/doc/pair_hbond_dreiding.html +++ b/doc/pair_hbond_dreiding.html @@ -38,7 +38,7 @@ pair_coeff * * 2*5 j 100.0 1.0 2.0 4.0 6.0

    The hbond/dreiding styles compute the Acceptor-Hydrogen-Donor (AHD) 3-body hydrogen bond interaction for the -DREIDING force field, given by: +DREIDING force field, given by:

    @@ -69,8 +69,8 @@ potential for the Donor-Acceptor interactions. (Liu) showed that the Morse form gives improved results for Dendrimer simulations, when n = 2.

    -

    See this howto section of the manual for more -information on the DREIDING forcefield. +

    See this howto section of the manual for +more information on the DREIDING forcefield.

    Because the Dreiding hydrogen bond potential is only one portion of an overall force field which typically includes other pairwise diff --git a/doc/pair_hbond_dreiding.txt b/doc/pair_hbond_dreiding.txt index bcd3c15add..8f7c09f1f0 100644 --- a/doc/pair_hbond_dreiding.txt +++ b/doc/pair_hbond_dreiding.txt @@ -34,7 +34,7 @@ pair_coeff * * 2*5 j 100.0 1.0 2.0 4.0 6.0 :pre The {hbond/dreiding} styles compute the Acceptor-Hydrogen-Donor (AHD) 3-body hydrogen bond interaction for the -"DREIDING"_Section_howto.html#4_4 force field, given by: +"DREIDING"_Section_howto.html#howto_4 force field, given by: :c,image(Eqs/pair_hbond_dreiding.jpg) @@ -65,8 +65,8 @@ potential for the Donor-Acceptor interactions. "(Liu)"_#Liu showed that the Morse form gives improved results for Dendrimer simulations, when n = 2. -See this "howto section"_Section_howto.html#4_4 of the manual for more -information on the DREIDING forcefield. +See this "howto section"_Section_howto.html#howto_4 of the manual for +more information on the DREIDING forcefield. Because the Dreiding hydrogen bond potential is only one portion of an overall force field which typically includes other pairwise diff --git a/doc/pair_lj.html b/doc/pair_lj.html index cb8f790672..a15688735a 100644 --- a/doc/pair_lj.html +++ b/doc/pair_lj.html @@ -140,8 +140,8 @@ first. This is to enable LAMMPS to "find" the 2 H atoms associated with each O atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502.

    -

    See the howto section for more information on -how to use the TIP4P pair style. +

    See the howto section for more +information on how to use the TIP4P pair style.

    The following coefficients must be defined for each pair of atoms types via the pair_coeff command as in the examples diff --git a/doc/pair_lj.txt b/doc/pair_lj.txt index 2cc5931563..93f371cbab 100644 --- a/doc/pair_lj.txt +++ b/doc/pair_lj.txt @@ -123,8 +123,8 @@ first. This is to enable LAMMPS to "find" the 2 H atoms associated with each O atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the "howto section"_Section_howto.html#4_8 for more information on -how to use the TIP4P pair style. +See the "howto section"_Section_howto.html#howto_8 for more +information on how to use the TIP4P pair style. The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples diff --git a/doc/pair_style.html b/doc/pair_style.html index 82f2bb4e3a..0fd6871819 100644 --- a/doc/pair_style.html +++ b/doc/pair_style.html @@ -149,13 +149,13 @@ the pair_style command, and coefficients specified by the associated

    There are also additional pair styles submitted by users which are included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the pair section of this +the individual styles are given in the pair section of this page.

    There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs and GPUs. The list of these with links to the individual styles are given in the pair -section of this page. +section of this page.

    diff --git a/doc/pair_style.txt b/doc/pair_style.txt index b9c8b450ff..d7ae16d690 100644 --- a/doc/pair_style.txt +++ b/doc/pair_style.txt @@ -147,12 +147,12 @@ the pair_style command, and coefficients specified by the associated There are also additional pair styles submitted by users which are included in the LAMMPS distribution. The list of these with links to the individual styles are given in the pair section of "this -page"_Section_commands.html#3_5. +page"_Section_commands.html#cmd_5. There are also additional accelerated pair styles included in the LAMMPS distribution for faster performance on CPUs and GPUs. The list of these with links to the individual styles are given in the pair -section of "this page"_Section_commands.html#3_5. +section of "this page"_Section_commands.html#cmd_5. :line diff --git a/doc/prd.html b/doc/prd.html index 0baa6e241a..ae9cbcda4a 100644 --- a/doc/prd.html +++ b/doc/prd.html @@ -77,7 +77,7 @@ 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 +this section 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 eae8b6ef68..52f6820d83 100644 --- a/doc/prd.txt +++ b/doc/prd.txt @@ -64,7 +64,7 @@ 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#4_5 of the manual for further +"this section"_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 663ebfc239..1bfc95bbb6 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -109,7 +109,7 @@ 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 +

    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 triclinic representations. diff --git a/doc/read_data.txt b/doc/read_data.txt index d07714a077..593b93e571 100644 --- a/doc/read_data.txt +++ b/doc/read_data.txt @@ -106,7 +106,7 @@ 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#4_12 of the doc pages for a +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 triclinic representations. diff --git a/doc/read_restart.html b/doc/read_restart.html index 25ccf115eb..073b9d4dfe 100644 --- a/doc/read_restart.html +++ b/doc/read_restart.html @@ -43,7 +43,7 @@ these cases. Certain fixes will also not restart exactly, though they should provide statistically similar results. These include fix shake and fix langevin. If a restarted run is immediately different than the run which produced the -restart file, it could be a LAMMPS bug, so consider reporting +restart file, it could be a LAMMPS bug, so consider reporting it if you think the behavior is wrong.

    Because restart files are binary, they may not be portable to other diff --git a/doc/read_restart.txt b/doc/read_restart.txt index 854a27bd22..c4afb2a57a 100644 --- a/doc/read_restart.txt +++ b/doc/read_restart.txt @@ -41,7 +41,7 @@ should provide statistically similar results. These include "fix shake"_fix_shake.html and "fix langevin"_fix_langevin.html. If a restarted run is immediately different than the run which produced the restart file, it could be a LAMMPS bug, so consider "reporting -it"_Section_errors.html#10_2 if you think the behavior is wrong. +it"_Section_errors.html#err_2 if you think the behavior is wrong. Because restart files are binary, they may not be portable to other machines. They can be converted to ASCII data files using the diff --git a/doc/region.html b/doc/region.html index df278065f4..a9b089de7c 100644 --- a/doc/region.html +++ b/doc/region.html @@ -175,7 +175,7 @@ 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 +

    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 triclinic representations. diff --git a/doc/region.txt b/doc/region.txt index 0f72de9d5d..c8da7594f3 100644 --- a/doc/region.txt +++ b/doc/region.txt @@ -166,7 +166,7 @@ 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#4_12 of the doc pages for a +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 triclinic representations. diff --git a/doc/run.html b/doc/run.html index da99cd1fb3..f190d487ae 100644 --- a/doc/run.html +++ b/doc/run.html @@ -133,9 +133,9 @@ be useful for invoking a command you have added to LAMMPS that wraps some other code (e.g. as a library) to perform a computation periodically during a long LAMMPS run. See this section of the documentation for info about how -to add new commands to LAMMPS. See this -section of the documentation for ideas about -how to couple LAMMPS to other codes. +to add new commands to LAMMPS. See this +section of the documentation for ideas +about how to couple LAMMPS to other codes.

    With the every option, N total steps are simulated, in shorter runs of M steps each. After each M-length run, the specified commands are diff --git a/doc/run.txt b/doc/run.txt index febf22777a..c3d50ed7ff 100644 --- a/doc/run.txt +++ b/doc/run.txt @@ -127,8 +127,8 @@ some other code (e.g. as a library) to perform a computation periodically during a long LAMMPS run. See "this section"_Section_modify.html of the documentation for info about how to add new commands to LAMMPS. See "this -section"_Section_howto.html#4_10 of the documentation for ideas about -how to couple LAMMPS to other codes. +section"_Section_howto.html#howto_10 of the documentation for ideas +about how to couple LAMMPS to other codes. With the {every} option, N total steps are simulated, in shorter runs of M steps each. After each M-length run, the specified commands are diff --git a/doc/tad.html b/doc/tad.html index 4a90099f1b..ff74027e28 100644 --- a/doc/tad.html +++ b/doc/tad.html @@ -102,9 +102,8 @@ 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 this section +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 97fa64f7f2..85115cfa25 100644 --- a/doc/tad.txt +++ b/doc/tad.txt @@ -91,9 +91,8 @@ 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#4_5 of the manual for further discussion -of multi-replica simulations. +partitions remain idle. See "this section"_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 7affc1bcde..ce9f7e8b46 100644 --- a/doc/temper.html +++ b/doc/temper.html @@ -40,8 +40,9 @@ 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. +would see with one or more physical processors per replica. See this +section of the manual for further +discussion.

    Each replica's temperature is controlled at a different value by a fix with fix-ID that controls temperature. Possible fix styles are diff --git a/doc/temper.txt b/doc/temper.txt index 0f1f16b531..ac79b6e5d9 100644 --- a/doc/temper.txt +++ b/doc/temper.txt @@ -38,7 +38,8 @@ 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#4_5 of the manual for further discussion. +section"_Section_howto.html#howto_5 of the manual for further +discussion. Each replica's temperature is controlled at a different value by a fix with {fix-ID} that controls temperature. Possible fix styles are diff --git a/doc/thermo_style.html b/doc/thermo_style.html index 11d4e7a8be..3c58443544 100644 --- a/doc/thermo_style.html +++ b/doc/thermo_style.html @@ -233,13 +233,13 @@ calculates the maximum force in any dimension on any atom in the system, or the infinity-norm of the force vector for the system. The fnorm keyword calculates the 2-norm or length of the force vector.

    -

    The keywords cella, cellb, cellc, cellalpha, cellbeta, cellgamma, -correspond to the usual crystallographic quantities that define -the periodic unit cell of a crystal. -See this section of the doc pages for a -geometric description of triclinic periodic cells, including -a precise defintion of these quantities in terms of the internal -LAMMPS cell dimensions lx, ly, lz, yz, xz, xy, +

    The keywords cella, cellb, cellc, cellalpha, cellbeta, +cellgamma, correspond to the usual crystallographic quantities that +define the periodic unit cell of a crystal. See this +section of the doc pages for a geometric +description of triclinic periodic cells, including a precise defintion +of these quantities in terms of the internal LAMMPS cell dimensions +lx, ly, lz, yz, xz, xy,

    diff --git a/doc/thermo_style.txt b/doc/thermo_style.txt index 03ad2c917b..8f4a64148d 100644 --- a/doc/thermo_style.txt +++ b/doc/thermo_style.txt @@ -227,13 +227,13 @@ calculates the maximum force in any dimension on any atom in the system, or the infinity-norm of the force vector for the system. The {fnorm} keyword calculates the 2-norm or length of the force vector. -The keywords {cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma}, -correspond to the usual crystallographic quantities that define -the periodic unit cell of a crystal. -See "this section"_Section_howto.html#4_12 of the doc pages for a -geometric description of triclinic periodic cells, including -a precise defintion of these quantities in terms of the internal -LAMMPS cell dimensions {lx}, {ly}, {lz}, {yz}, {xz}, {xy}, +The keywords {cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, +{cellgamma}, correspond to the usual crystallographic quantities that +define the periodic unit cell of a crystal. See "this +section"_Section_howto.html#howto_12 of the doc pages for a geometric +description of triclinic periodic cells, including a precise defintion +of these quantities in terms of the internal LAMMPS cell dimensions +{lx}, {ly}, {lz}, {yz}, {xz}, {xy}, :line diff --git a/doc/variable.html b/doc/variable.html index 49f437ee0f..31dae2e600 100644 --- a/doc/variable.html +++ b/doc/variable.html @@ -148,7 +148,7 @@ the same thing.

    -

    This section of the manual explains how +

    This section of the manual explains how occurrences of a variable name in an input script line are replaced by the variable's string. The variable name can be referenced as $x if the name "x" is a single character, or as ${LoopVar} if the name @@ -715,10 +715,10 @@ quotes if it contains variables preceeded by $ signs. For example, 

    variable vratio equal "${vfinal}/${v0}"
    -

    This is because the quotes prevent variable substitution (see this -section on parsing input script commands), -and thus an error will occur when the formula for "vratio" is -evaluated later. +

    This is because the quotes prevent variable substitution (see this +section on parsing input script +commands), and thus an error will occur when the formula for "vratio" +is evaluated later.

    diff --git a/doc/variable.txt b/doc/variable.txt index a37a5538c8..987e806fc3 100644 --- a/doc/variable.txt +++ b/doc/variable.txt @@ -142,7 +142,7 @@ the same thing. :line -"This section"_Section_commands.html#3_2 of the manual explains how +"This section"_Section_commands.html#cmd_2 of the manual explains how occurrences of a variable name in an input script line are replaced by the variable's string. The variable name can be referenced as $x if the name "x" is a single character, or as $\{LoopVar\} if the name @@ -710,9 +710,9 @@ quotes if it contains variables preceeded by $ signs. For example, variable vratio equal "$\{vfinal\}/$\{v0\}" :pre This is because the quotes prevent variable substitution (see "this -section"_Section_commands.html#3_2 on parsing input script commands), -and thus an error will occur when the formula for "vratio" is -evaluated later. +section"_Section_commands.html#cmd_2 on parsing input script +commands), and thus an error will occur when the formula for "vratio" +is evaluated later. :line