diff --git a/doc/Manual.html b/doc/Manual.html index 23b0e384b5..002c5b4853 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -22,7 +22,7 @@

LAMMPS-ICMS Documentation

-

17 Jun 2013 version +

26 Jun 2013 version

Version info:

diff --git a/doc/Manual.txt b/doc/Manual.txt index 40a80b9d58..98c21ae073 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -18,7 +18,7 @@

LAMMPS-ICMS Documentation :c,h3 -17 Jun 2013 version :c,h4 +26 Jun 2013 version :c,h4 Version info: :h4 diff --git a/doc/Section_accelerate.html b/doc/Section_accelerate.html index ff31520e64..d3f6f67d02 100644 --- a/doc/Section_accelerate.html +++ b/doc/Section_accelerate.html @@ -92,6 +92,7 @@ simply trying them out.

+

2-FFT PPPM, also called analytic differentiation or ad PPPM, uses 2 FFTs +instead of the 4 FFTs used by the default ik differentiation PPPM. However, +2-FFT PPPM also requires a slightly larger mesh size to achieve the same accuracy +as 4-FFT PPPM. For problems where the FFT cost is the performance bottleneck (typically +large problems running on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM. +

+

Staggered PPPM performs calculations using two different meshes, one shifted slightly with +respect to the other. This can reduce force aliasing errors and increase the accuracy of the +method, but also doubles the amount of work required. For high relative accuracy, using staggered +PPPM allows one to half the mesh size in each dimension as compared to regular PPPM, +which can give around a 4x speedup in the kspace time. However, for low relative +accuracy, using staggered PPPM gives little benefit and can be up to 2x slower in the +kspace time. For example, the rhodopsin benchmark was run on a single processor, +and results for kspace time vs. relative accuracy for the different methods are shown +in the figure below. For this system, staggered PPPM (using ik differentiation) +becomes useful when using a relative accuracy of slightly greater than 1e-5 and above. +

+
+
+

IMPORTANT NOTE: Using staggered PPPM may not give the same increase in accuracy of energy and pressure +as it does in forces, so some caution must be used if energy and/or pressure are quantities of interest, such +as when using a barostat. +

5.3 Packages with optimized styles diff --git a/doc/Section_accelerate.txt b/doc/Section_accelerate.txt index 557ab159b3..bc35e25faa 100644 --- a/doc/Section_accelerate.txt +++ b/doc/Section_accelerate.txt @@ -88,6 +88,7 @@ simply trying them out. rRESPA 2-FFT PPPM +Staggered PPPM single vs double PPPM partial charge PPPM verlet/split @@ -96,6 +97,29 @@ load-balancing: balance and fix balance processor command for layout OMP when lots of cores :ul +2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses 2 FFTs +instead of the 4 FFTs used by the default {ik differentiation} PPPM. However, +2-FFT PPPM also requires a slightly larger mesh size to achieve the same accuracy +as 4-FFT PPPM. For problems where the FFT cost is the performance bottleneck (typically +large problems running on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM. + +Staggered PPPM performs calculations using two different meshes, one shifted slightly with +respect to the other. This can reduce force aliasing errors and increase the accuracy of the +method, but also doubles the amount of work required. For high relative accuracy, using staggered +PPPM allows one to half the mesh size in each dimension as compared to regular PPPM, +which can give around a 4x speedup in the kspace time. However, for low relative +accuracy, using staggered PPPM gives little benefit and can be up to 2x slower in the +kspace time. For example, the rhodopsin benchmark was run on a single processor, +and results for kspace time vs. relative accuracy for the different methods are shown +in the figure below. For this system, staggered PPPM (using ik differentiation) +becomes useful when using a relative accuracy of slightly greater than 1e-5 and above. + +:c,image(JPG/rhodo_staggered.jpg) + +IMPORTANT NOTE: Using staggered PPPM may not give the same increase in accuracy of energy and pressure +as it does in forces, so some caution must be used if energy and/or pressure are quantities of interest, such +as when using a barostat. + :line 5.3 Packages with optimized styles :h4,link(acc_3) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 3545904929..12b78f3b4f 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -364,6 +364,13 @@ in the command's documentation. velocitywrite_datawrite_restart +

These are commands contributed by users, which can be used if LAMMPS +is built with the appropriate package. +

+
+
group2ndx +
+

Fix styles diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 1f1c8d7eab..f25f43cf96 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -431,6 +431,11 @@ in the command's documentation. "write_data"_write_data.html, "write_restart"_write_restart.html :tb(c=6,ea=c) +These are commands contributed by users, which can be used if "LAMMPS +is built with the appropriate package"_Section_start.html#start_3. + +"group2ndx"_group2ndx.html :tb(c=1,ea=c) + :line Fix styles :h4 diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 7d8677f8e2..3b63c4fa43 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -1359,6 +1359,17 @@ output. In each case, the compute, fix, or variable must generate global values for input to the thermo_style custom command.

+

Note that thermodynamic output values can be "extensive" or +"intensive". The former scale with the number of atoms in the system +(e.g. total energy), the latter do not (e.g. temperature). The +setting for thermo_modify norm determines whether +extensive quantities are normalized or not. Computes and fixes +produce either extensive or intensive values; see their individual doc +pages for details. Equal-style variables produce only +intensive values; you can include a division by "natoms" in the +formula if desired, to make an extensive calculation produce an +intensive result. +

Dump file output

Dump file output is specified by the dump and diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index f8254f90b9..49ad45fbda 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -1348,6 +1348,17 @@ output. In each case, the compute, fix, or variable must generate global values for input to the "thermo_style custom"_dump.html command. +Note that thermodynamic output values can be "extensive" or +"intensive". The former scale with the number of atoms in the system +(e.g. total energy), the latter do not (e.g. temperature). The +setting for "thermo_modify norm"_thermo_modify.html determines whether +extensive quantities are normalized or not. Computes and fixes +produce either extensive or intensive values; see their individual doc +pages for details. "Equal-style variables"_variable.html produce only +intensive values; you can include a division by "natoms" in the +formula if desired, to make an extensive calculation produce an +intensive result. + Dump file output :h5,link(dump) Dump file output is specified by the "dump"_dump.html and diff --git a/doc/fix_colvars.html b/doc/fix_colvars.html index c622a6ff4f..5aa30bb707 100644 --- a/doc/fix_colvars.html +++ b/doc/fix_colvars.html @@ -44,30 +44,38 @@ module library which allows to calculate potentials of mean force (PMFs) for any set of colvars, using different sampling methods: currently implemented are the Adaptive Biasing Force (ABF) method, metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling -(US) via a flexible harmonic restraint bias. This documentation -describes only the colvars fix itself and LAMMPS specific parts of the -code. The documentation of the colvars implementation itself is -available as part of the NAMD online -documentation +(US) via a flexible harmonic restraint bias. The colvars library is +hosted at http://colvars.github.io/

-

There are example scripts for using this package with LAMMPS in -examples/USER/colvars. +

This documentation describes only the fix colvars command itself and +LAMMPS specific parts of the code. The full documentation of the +colvars library is available as this supplementary PDF document

-

The implementation of the portable collective variable library is also -documented in (Henin) +

A detailed discussion of the implementation of the portable collective +variable library is in (Fiorin). Additional information can +be found in (Henin). +

+

There are some example scripts for using this package with LAMMPS in the +examples/USER/colvars directory.

The only mandatory argument to the fix is the filename to the colvars -input file that contains all input that is independent from the MD +input file that contains the input that is independent from the MD program in which the colvars library has been integrated.

The group-ID entry is ignored. The collective variable module will -always apply to the entire system, i.e. use the group all. +always apply to the entire system and there can only be one instance +of the colvars fix at a time. The colvars fix will only communicate +the minimum information necessary and the colvars library supports +multiple, completely independent collective variables, so there is +no restriction to functionaliry by limiting the number of colvars fixes.

The input keyword allows to specify a state file that would contain -the information required in order to continue a calculation, e.g. -from a restart. Setting it to NULL will start a new colvars run. +the restart information required in order to continue a calculation from +a prerecorded state. Fix colvars records it state in binary restart +files, so when using the read_restart command, +this is usually not needed.

The output keyword allows to specify the output prefix. All output files generated will use this prefix followed by the ".colvars." and @@ -90,8 +98,10 @@ temperature.

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

-

No information about this fix is written to binary restart -files. +

This fix writes the current status of the colvars module into +binary restart files. This is in addition to the text +mode status file that is written by the colvars module itself and the +kind of information in both files is identical.

The fix_modify energy option is supported by this fix to add the energy change from the biasing force added by the fix @@ -109,10 +119,10 @@ calculated by this fix is "extensive". LAMMPS was built with that package. See the Making LAMMPS section for more info.

-

There can only be one colvars fix active at a time. Since the -colvars module itself can handle an arbitrary number of collective -variables and always applies to the entire system, this is not -really a deficit in practice. +

There can only be one colvars fix active at a time. Since the interface +communicates only the minimum amount of information and colvars module +itself can handle an arbitrary number of collective variables, this is +not a limitation of functionality.

Related commands:

@@ -125,9 +135,13 @@ and tstat = NULL.

+ + +

(Fiorin) Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594 +

-

(Henin) Hénin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6, +

(Henin) Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6, 35-47 (2010)

diff --git a/doc/fix_tune_kspace.html b/doc/fix_tune_kspace.html index c38a754031..91fa49b6de 100644 --- a/doc/fix_tune_kspace.html +++ b/doc/fix_tune_kspace.html @@ -38,16 +38,17 @@ to use for maximum simulation speed. The kspace parameters may include the style, cutoff, grid points in each direction, order, Ewald parameter, MSM parallelization cut-point, MPI tasks to use, etc.

-

The rationale for this fix is to provide the user with as-fast-as-possible -simulations that include long-range electrostatics (kspace) while meeting -the user-prescribed accuracy requirement. A simple heuristic could never -capture the optimal combination of parameters for every possible run-time -scenario. But by performing short tests of various kspace parameter sets, -this fix allows parameters to be tailored specifically to the user’s -machine, MPI ranks, use of threading or accelerators, the simulated system, -and the simulation details. In addition, it is possible that parameters -could be evolved with the simulation on-the-fly, which is useful for -systems that are dynamically evolving (e.g. changes in box size/shape or +

The rationale for this fix is to provide the user with +as-fast-as-possible simulations that include long-range electrostatics +(kspace) while meeting the user-prescribed accuracy requirement. A +simple heuristic could never capture the optimal combination of +parameters for every possible run-time scenario. But by performing +short tests of various kspace parameter sets, this fix allows +parameters to be tailored specifically to the user's machine, MPI +ranks, use of threading or accelerators, the simulated system, and the +simulation details. In addition, it is possible that parameters could +be evolved with the simulation on-the-fly, which is useful for systems +that are dynamically evolving (e.g. changes in box size/shape or number of particles).

When this fix is invoked, LAMMPS will perform short timed tests of diff --git a/doc/fix_tune_kspace.txt b/doc/fix_tune_kspace.txt index a679f89e32..61b56d70ce 100644 --- a/doc/fix_tune_kspace.txt +++ b/doc/fix_tune_kspace.txt @@ -32,16 +32,17 @@ to use for maximum simulation speed. The kspace parameters may include the style, cutoff, grid points in each direction, order, Ewald parameter, MSM parallelization cut-point, MPI tasks to use, etc. -The rationale for this fix is to provide the user with as-fast-as-possible -simulations that include long-range electrostatics (kspace) while meeting -the user-prescribed accuracy requirement. A simple heuristic could never -capture the optimal combination of parameters for every possible run-time -scenario. But by performing short tests of various kspace parameter sets, -this fix allows parameters to be tailored specifically to the user's -machine, MPI ranks, use of threading or accelerators, the simulated system, -and the simulation details. In addition, it is possible that parameters -could be evolved with the simulation on-the-fly, which is useful for -systems that are dynamically evolving (e.g. changes in box size/shape or +The rationale for this fix is to provide the user with +as-fast-as-possible simulations that include long-range electrostatics +(kspace) while meeting the user-prescribed accuracy requirement. A +simple heuristic could never capture the optimal combination of +parameters for every possible run-time scenario. But by performing +short tests of various kspace parameter sets, this fix allows +parameters to be tailored specifically to the user's machine, MPI +ranks, use of threading or accelerators, the simulated system, and the +simulation details. In addition, it is possible that parameters could +be evolved with the simulation on-the-fly, which is useful for systems +that are dynamically evolving (e.g. changes in box size/shape or number of particles). When this fix is invoked, LAMMPS will perform short timed tests of diff --git a/doc/group2ndx.html b/doc/group2ndx.html new file mode 100644 index 0000000000..3fb0670fcd --- /dev/null +++ b/doc/group2ndx.html @@ -0,0 +1,58 @@ + +

LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
+ + + + + + +
+ +

group2ndx command +

+

Syntax: +

+
group2ndx file group-ID ... 
+
+ +

Examples: +

+
group2ndx allindex.ndx
+group2ndx someindex.ndx upper lower mobile 
+
+

Description: +

+

Write a Gromacs style index file in text format that associates atom IDs +with the corresponding group definitions. This index file can be used +with in combination with Gromacs analysis tools or to import group +definitions into the fix colvars input file. +

+

Without specifying any group IDs, all groups will be written to the index +file. When specifying group IDs, only those groups will be written to the +index file. In order to follow the Gromacs conventions, the group all +will be renamed to System in the index file. +

+
+ +

Restrictions: +

+

This command requires that atoms have atom IDs, since this is the +information that is written to the index file. +

+

This fix is part of the USER-COLVARS package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info. +

+

Related commands: +

+

group, dump, fix colvars +

+

Default: none +

+ diff --git a/doc/group2ndx.txt b/doc/group2ndx.txt index 27c0d652b4..d40d4399f9 100644 --- a/doc/group2ndx.txt +++ b/doc/group2ndx.txt @@ -48,6 +48,4 @@ LAMMPS"_Section_start.html#start_3 section for more info. "group"_group.html, "dump"_dump.html, "fix colvars"_fix_colvars.html -[Default:] - -none +[Default:] none diff --git a/doc/kspace_style.html b/doc/kspace_style.html index 2f875ebc2f..d7f7874b0f 100644 --- a/doc/kspace_style.html +++ b/doc/kspace_style.html @@ -15,7 +15,7 @@ 

kspace_style style value
-